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Sample records for chemical shifts torsion

  1. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2013-07-15

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

  2. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2007-01-01

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ 1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ 1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C', respectively, including outliers

  3. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Delaglio, Frank [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Cornilescu, Gabriel [National Magnetic Resonance Facility (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

    2009-08-15

    NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between {sup 13}C, {sup 15}N and {sup 1}H chemical shifts and backbone torsion angles {phi} and {psi} (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted {phi} and {psi} angles, equals {+-}13{sup o}. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

  4. Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

    International Nuclear Information System (INIS)

    Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

    2004-01-01

    A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

  5. Chemical shift imaging: a review

    International Nuclear Information System (INIS)

    Brateman, L.

    1986-01-01

    Chemical shift is the phenomenon that is seen when an isotope possessing a nuclear magnetic dipole moment resonates at a spectrum of resonance frequencies in a given magnetic field. These resonance frequencies, or chemical shifts, depend on the chemical environments of particular nuclei. Mapping the spatial distribution of nuclei associated with a particular chemical shift (e.g., hydrogen nuclei associated with water molecules or with lipid groups) is called chemical shift imaging. Several techniques of proton chemical shift imaging that have been applied in vivo are presented, and their clinical findings are reported and summarized. Acquiring high-resolution spectra for large numbers of volume elements in two or three dimensions may be prohibitive because of time constraints, but other methods of imaging lipid of water distributions (i.e., selective excitation, selective saturation, or variations in conventional magnetic resonance imaging pulse sequences) can provide chemical shift information. These techniques require less time, but they lack spectral information. Since fat deposition seen by chemical shift imaging may not be demonstrated by conventional magnetic resonance imaging, certain applications of chemical shift imaging, such as in the determination of fatty liver disease, have greater diagnostic utility than conventional magnetic resonance imaging. Furthermore, edge artifacts caused by chemical shift effects can be eliminated by certain selective methods of data acquisition employed in chemical shift imaging

  6. Chemical shift homology in proteins

    International Nuclear Information System (INIS)

    Potts, Barbara C.M.; Chazin, Walter J.

    1998-01-01

    The degree of chemical shift similarity for homologous proteins has been determined from a chemical shift database of over 50 proteins representing a variety of families and folds, and spanning a wide range of sequence homologies. After sequence alignment, the similarity of the secondary chemical shifts of C α protons was examined as a function of amino acid sequence identity for 37 pairs of structurally homologous proteins. A correlation between sequence identity and secondary chemical shift rmsd was observed. Important insights are provided by examining the sequence identity of homologous proteins versus percentage of secondary chemical shifts that fall within 0.1 and 0.3 ppm thresholds. These results begin to establish practical guidelines for the extent of chemical shift similarity to expect among structurally homologous proteins

  7. chemical shift tensors in helical peptides by dipolar-modulated chemical shift recoupling NMR

    International Nuclear Information System (INIS)

    Yao Xiaolan; Yamaguchi, Satoru; Hong Mei

    2002-01-01

    The Cα chemical shift tensors of proteins contain information on the backbone conformation. We have determined the magnitude and orientation of the Cα chemical shift tensors of two peptides with α-helical torsion angles: the Ala residue in G*AL (φ=-65.7 deg., ψ=-40 deg.), and the Val residue in GG*V (φ=-81.5 deg., ψ=-50.7 deg.). The magnitude of the tensors was determined from quasi-static powder patterns recoupled under magic-angle spinning, while the orientation of the tensors was extracted from Cα-Hα and Cα-N dipolar modulated powder patterns. The helical Ala Cα chemical shift tensor has a span of 36 ppm and an asymmetry parameter of 0.89. Its σ 11 axis is 116 deg. ± 5 deg. from the Cα-Hα bond while the σ 22 axis is 40 deg. ± 5 deg. from the Cα-N bond. The Val tensor has an anisotropic span of 25 ppm and an asymmetry parameter of 0.33, both much smaller than the values for β-sheet Val found recently (Yao and Hong, 2002). The Val σ 33 axis is tilted by 115 deg. ± 5 deg. from the Cα-Hα bond and 98 deg. ± 5 deg. from the Cα-N bond. These represent the first completely experimentally determined Cα chemical shift tensors of helical peptides. Using an icosahedral representation, we compared the experimental chemical shift tensors with quantum chemical calculations and found overall good agreement. These solid-state chemical shift tensors confirm the observation from cross-correlated relaxation experiments that the projection of the Cα chemical shift tensor onto the Cα-Hα bond is much smaller in α-helices than in β-sheets

  8. Unraveling the meaning of chemical shifts in protein NMR.

    Science.gov (United States)

    Berjanskii, Mark V; Wishart, David S

    2017-11-01

    Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Stereoelectronic effects on 1H nuclear magnetic resonance chemical shifts in methoxybenzenes

    DEFF Research Database (Denmark)

    Lambert, Maja; Olsen, Lars; Jaroszewski, Jerzy W

    2006-01-01

    the Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent...

  10. Electrically, Chemically, and Photonically Powered Torsional and Tensile Actuation of Hybrid Carbon Nanotube Yarn Muscles

    Science.gov (United States)

    Lima, Márcio D.; Li, Na; Jung de Andrade, Mônica; Fang, Shaoli; Oh, Jiyoung; Spinks, Geoffrey M.; Kozlov, Mikhail E.; Haines, Carter S.; Suh, Dongseok; Foroughi, Javad; Kim, Seon Jeong; Chen, Yongsheng; Ware, Taylor; Shin, Min Kyoon; Machado, Leonardo D.; Fonseca, Alexandre F.; Madden, John D. W.; Voit, Walter E.; Galvão, Douglas S.; Baughman, Ray H.

    2012-11-01

    Artificial muscles are of practical interest, but few types have been commercially exploited. Typical problems include slow response, low strain and force generation, short cycle life, use of electrolytes, and low energy efficiency. We have designed guest-filled, twist-spun carbon nanotube yarns as electrolyte-free muscles that provide fast, high-force, large-stroke torsional and tensile actuation. More than a million torsional and tensile actuation cycles are demonstrated, wherein a muscle spins a rotor at an average 11,500 revolutions/minute or delivers 3% tensile contraction at 1200 cycles/minute. Electrical, chemical, or photonic excitation of hybrid yarns changes guest dimensions and generates torsional rotation and contraction of the yarn host. Demonstrations include torsional motors, contractile muscles, and sensors that capture the energy of the sensing process to mechanically actuate.

  11. Empirical isotropic chemical shift surfaces

    International Nuclear Information System (INIS)

    Czinki, Eszter; Csaszar, Attila G.

    2007-01-01

    A list of proteins is given for which spatial structures, with a resolution better than 2.5 A, are known from entries in the Protein Data Bank (PDB) and isotropic chemical shift (ICS) values are known from the RefDB database related to the Biological Magnetic Resonance Bank (BMRB) database. The structures chosen provide, with unknown uncertainties, dihedral angles φ and ψ characterizing the backbone structure of the residues. The joint use of experimental ICSs of the same residues within the proteins, again with mostly unknown uncertainties, and ab initio ICS(φ,ψ) surfaces obtained for the model peptides For-(l-Ala) n -NH 2 , with n = 1, 3, and 5, resulted in so-called empirical ICS(φ,ψ) surfaces for all major nuclei of the 20 naturally occurring α-amino acids. Out of the many empirical surfaces determined, it is the 13C α ICS(φ,ψ) surface which seems to be most promising for identifying major secondary structure types, α-helix, β-strand, left-handed helix (α D ), and polyproline-II. Detailed tests suggest that Ala is a good model for many naturally occurring α-amino acids. Two-dimensional empirical 13C α - 1 H α ICS(φ,ψ) correlation plots, obtained so far only from computations on small peptide models, suggest the utility of the experimental information contained therein and thus they should provide useful constraints for structure determinations of proteins

  12. MR chemical shift imaging of human atheroma

    International Nuclear Information System (INIS)

    Mohiaddin, R.H.; Underwood, R.; Firmin, D.; Abdulla, A.K.; Rees, S.; Longmore, D.

    1988-01-01

    The lipid content of atheromatous plaques has been measured with chemical shift MR imaging by taking advantage of the different resonance frequencies of protons in lipid and water. Fifteen postmortem aortic specimens of the human descending aorta and the aortae of seven patients with documented peripheral vascular disease were studied at 0.5 T. Spin-echo images were used to localize the lesions before acquisition of the chemical shift images. The specimens were examined histologically, and the lipid distribution in the plaque showed good correlation with the chemical shift data. Validation in vivo and clinical applications remain to be established

  13. Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions

    Energy Technology Data Exchange (ETDEWEB)

    Schumann, Frank H.; Riepl, Hubert [University of Regensburg, Institute of Biophysics and Physical Biochemistry (Germany); Maurer, Till [Boehringer Ingelheim Pharma GmbH and Co. KG, Analytical Sciences Department (Germany); Gronwald, Wolfram [University of Regensburg, Institute of Biophysics and Physical Biochemistry (Germany); Neidig, Klaus-Peter [Bruker BioSpin GmbH, Software Department (Germany); Kalbitzer, Hans Robert [University of Regensburg, Institute of Biophysics and Physical Biochemistry (Germany)], E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de

    2007-12-15

    Protein-protein interactions are often studied by chemical shift mapping using solution NMR spectroscopy. When heteronuclear data are available the interaction interface is usually predicted by combining the chemical shift changes of different nuclei to a single quantity, the combined chemical shift perturbation {delta}{delta}{sub comb}. In this paper different procedures (published and non-published) to calculate {delta}{delta}{sub comb} are examined that include a variety of different functional forms and weighting factors for each nucleus. The predictive power of all shift mapping methods depends on the magnitude of the overlap of the chemical shift distributions of interacting and non-interacting residues and the cut-off criterion used. In general, the quality of the prediction on the basis of chemical shift changes alone is rather unsatisfactory but the combination of chemical shift changes on the basis of the Hamming or the Euclidian distance can improve the result. The corrected standard deviation to zero of the combined chemical shift changes can provide a reasonable cut-off criterion. As we show combined chemical shifts can also be applied for a more reliable quantitative evaluation of titration data.

  14. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

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

  15. Accessible surface area from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

    Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation.

  16. Random coil chemical shift for intrinsically disordered proteins

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Brander, Søren; Poulsen, Flemming Martin

    2011-01-01

    . Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series......, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and pH, systematic biases of the secondary chemical shifts are minimized, which will improve the reliability of detection of transient secondary...

  17. Proton chemical shift imaging after myocardial infarction

    International Nuclear Information System (INIS)

    Bouchard, A.; Doyle, M.; Pohost, G.M.

    1989-01-01

    The present study was undertaken to test whether chemical shift imaging could detect spatially the lipids known to accumulate in myocardium after an ischemic insult. Seven dogs underwent a 24-hour coronary artery occlusion. Hearts were removed and imaged ex vivo by the Dixon method (1.5 T), and myocardial samples were obtained for high-resolution H-1 spectroscopy. Lipid images revealed regions of increased signal intensity in the periphery f the myocardial infarction. The zones of high lipid signal corresponded to zones with elevated mobile lipids as detected by H-1 spectroscopy

  18. The calculation of proton chemical shifts in hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, Raymond J [Liverpool Univ. (United Kingdom). Dept. of Chemistry

    1994-12-31

    Novel extension of the CHARGE3 semi-empirical calculation of the partial atomic charges in molecules are described which allow the accurate calculation of the proton chemical shifts of a variety of acyclic alkanes. This simple scheme predicts the proton chemical shifts of all the simple alkanes, cyclohexane and methyl cyclohexanes, norbornane, trans-decalin and trans perhydrophenanthrene, comprising a range of chemical shifts from 0.3 to 2.2 {delta} with the known substituent chemical shifts of other functional groups this could allow the general prediction of proton chemical shifts in a simple and useful format. (author) 13 refs., 2 figs.

  19. PACSY, a relational database management system for protein structure and chemical shift analysis.

    Science.gov (United States)

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

    2012-10-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

  20. PACSY, a relational database management system for protein structure and chemical shift analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States); Yu, Wookyung [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Kim, Suhkmann [Pusan National University, Department of Chemistry and Chemistry Institute for Functional Materials (Korea, Republic of); Chang, Iksoo [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Yonsei University, Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry (Korea, Republic of); Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States)

    2012-10-15

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.eduhttp://pacsy.nmrfam.wisc.edu.

  1. PACSY, a relational database management system for protein structure and chemical shift analysis

    Science.gov (United States)

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

    2012-01-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

  2. PACSY, a relational database management system for protein structure and chemical shift analysis

    International Nuclear Information System (INIS)

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L.

    2012-01-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.eduhttp://pacsy.nmrfam.wisc.edu.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-15

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

  4. De novo protein structure generation from incomplete chemical shift assignments

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vernon, Robert; Baker, David [University of Washington, Department of Biochemistry and Howard Hughes Medical Institute (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

    2009-02-15

    NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

  5. 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

  6. Using chemical shift perturbation to characterise ligand binding.

    Science.gov (United States)

    Williamson, Mike P

    2013-08-01

    Chemical shift perturbation (CSP, chemical shift mapping or complexation-induced changes in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is added, and uses these to determine the location of the binding site, the affinity of the ligand, and/or possibly the structure of the complex. A key factor in determining the appearance of spectra during a titration is the exchange rate between free and bound, or more specifically the off-rate koff. When koff is greater than the chemical shift difference between free and bound, which typically equates to an affinity Kd weaker than about 3μM, then exchange is fast on the chemical shift timescale. Under these circumstances, the observed shift is the population-weighted average of free and bound, which allows Kd to be determined from measurement of peak positions, provided the measurements are made appropriately. (1)H shifts are influenced to a large extent by through-space interactions, whereas (13)Cα and (13)Cβ shifts are influenced more by through-bond effects. (15)N and (13)C' shifts are influenced both by through-bond and by through-space (hydrogen bonding) interactions. For determining the location of a bound ligand on the basis of shift change, the most appropriate method is therefore usually to measure (15)N HSQC spectra, calculate the geometrical distance moved by the peak, weighting (15)N shifts by a factor of about 0.14 compared to (1)H shifts, and select those residues for which the weighted shift change is larger than the standard deviation of the shift for all residues. Other methods are discussed, in particular the measurement of (13)CH3 signals. Slow to intermediate exchange rates lead to line broadening, and make Kd values very difficult to obtain. There is no good way to distinguish changes in chemical shift due to direct binding of the ligand from changes in chemical shift due to allosteric change. Ligand binding at multiple sites can often be characterised, by

  7. Rapid and reliable protein structure determination via chemical shift threading.

    Science.gov (United States)

    Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

    2018-01-01

    Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

  8. Relative Configuration of Natural Products Using NMR Chemical Shifts

    Science.gov (United States)

    By comparing calculated with experimental NMR chemical shifts, we were able to determine the relative configurations of three monoterpene diastereomers produced by the walkingstick Anisomorpha buprestoides. The combined RMSDs of both 1H and 13C quantum chemically calculated shifts were able to predi...

  9. A probabilistic approach for validating protein NMR chemical shift assignments

    International Nuclear Information System (INIS)

    Wang Bowei; Wang, Yunjun; Wishart, David S.

    2010-01-01

    It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called 'Probabilistic Approach for protein Nmr Assignment Validation (PANAV)' and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAVhttp://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

  10. Validation of archived chemical shifts through atomic coordinates

    Science.gov (United States)

    Rieping, Wolfgang; Vranken, Wim F

    2010-01-01

    The public archives containing protein information in the form of NMR chemical shift data at the BioMagResBank (BMRB) and of 3D structure coordinates at the Protein Data Bank are continuously expanding. The quality of the data contained in these archives, however, varies. The main issue for chemical shift values is that they are determined relative to a reference frequency. When this reference frequency is set incorrectly, all related chemical shift values are systematically offset. Such wrongly referenced chemical shift values, as well as other problems such as chemical shift values that are assigned to the wrong atom, are not easily distinguished from correct values and effectively reduce the usefulness of the archive. We describe a new method to correct and validate protein chemical shift values in relation to their 3D structure coordinates. This method classifies atoms using two parameters: the per-atom solvent accessible surface area (as calculated from the coordinates) and the secondary structure of the parent amino acid. Through the use of Gaussian statistics based on a large database of 3220 BMRB entries, we obtain per-entry chemical shift corrections as well as Z scores for the individual chemical shift values. In addition, information on the error of the correction value itself is available, and the method can retain only dependable correction values. We provide an online resource with chemical shift, atom exposure, and secondary structure information for all relevant BMRB entries (http://www.ebi.ac.uk/pdbe/nmr/vasco) and hope this data will aid the development of new chemical shift-based methods in NMR. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20602353

  11. Probabilistic validation of protein NMR chemical shift assignments

    International Nuclear Information System (INIS)

    Dashti, Hesam; Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel; Ulrich, Eldon L.; Markley, John L.

    2016-01-01

    Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/

  12. Probabilistic validation of protein NMR chemical shift assignments

    Energy Technology Data Exchange (ETDEWEB)

    Dashti, Hesam [University of Wisconsin-Madison, Graduate Program in Biophysics, Biochemistry Department (United States); Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States); Ulrich, Eldon L. [University of Wisconsin-Madison, BioMagResBank, Biochemistry Department (United States); Markley, John L., E-mail: markley@nmrfam.wisc.edu, E-mail: jmarkley@wisc.edu [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States)

    2016-01-15

    Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/.

  13. Is the Lamb shift chemically significant?

    Science.gov (United States)

    Dyall, Kenneth G.; Bauschlicher, Charles W., Jr.; Schwenke, David W.; Pyykko, Pekka; Arnold, James (Technical Monitor)

    2001-01-01

    The contribution of the Lamb shift to the atomization energies of some prototype molecules, BF3, AlF3, and GaF3, is estimated by a perturbation procedure. It is found to be in the range of 3-5% of the one-electron scalar relativistic contribution to the atomization energy. The maximum absolute value is 0.2 kcal/mol for GaF3. These sample calculations indicate that the Lamb shift is probably small enough to be neglected for energetics of molecules containing light atoms if the target accuracy is 1 kcal/mol, but for higher accuracy calculations and for molecules containing heavy elements it must be considered.

  14. Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

    Science.gov (United States)

    Borowski, Piotr

    2012-01-01

    Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

  15. Chemical shifts of oxygen-17 NMR in polyoxotungstates

    International Nuclear Information System (INIS)

    Kazanskij, L.P.; Fedotov, M.A.; Spitsyn, V.I.

    1977-01-01

    17 O NMR spectra of aqueous solutions containing paratungstate BH 2 W 12 O 42 10- and metatungstate H 2 W 12 O 40 6- anions have been measured. On the basis of the obtained data a scale of chemical shifts for oxygen atoms connected by various bonds with tungsten atoms is suggested. The obtained data are compared with the Raman spectra of crystalline salts and their aqueous solutions. Chemical shifts of 17 O NMR spectra have been also measured in other heteropolyanions

  16. Chemical Shift Imaging (CSI) by precise object displacement

    OpenAIRE

    Leclerc, Sebastien; Trausch, Gregory; Cordier, Benoit; Grandclaude, Denis; Retournard, Alain; Fraissard, Jacques; Canet, Daniel

    2006-01-01

    International audience; A mechanical device (NMR lift) has been built for displacing vertically an object (typically a NMR sample tube) inside the NMR probe with an accuracy of 1 Μm. A series of single pulse experiments are performed for incremented vertical positions of the sample. With a sufficiently spatially selective rf field, one obtains chemical shift information along the displacement direction (one dimensional Chemical Shift Imaging – CSI). Knowing the vertical radio-frequency (rf) f...

  17. Electronic torsional sound in linear atomic chains: Chemical energy transport at 1000 km/s

    Energy Technology Data Exchange (ETDEWEB)

    Kurnosov, Arkady A.; Rubtsov, Igor V.; Maksymov, Andrii O.; Burin, Alexander L., E-mail: aburin@tulane.edu [Department of Chemistry, Tulane University, New Orleans, Louisiana 70118 (United States)

    2016-07-21

    We investigate entirely electronic torsional vibrational modes in linear cumulene chains. The carbon nuclei of a cumulene are positioned along the primary axis so that they can participate only in the transverse and longitudinal motions. However, the interatomic electronic clouds behave as a torsion spring with remarkable torsional stiffness. The collective dynamics of these clouds can be described in terms of electronic vibrational quanta, which we name torsitons. It is shown that the group velocity of the wavepacket of torsitons is much higher than the typical speed of sound, because of the small mass of participating electrons compared to the atomic mass. For the same reason, the maximum energy of the torsitons in cumulenes is as high as a few electronvolts, while the minimum possible energy is evaluated as a few hundred wavenumbers and this minimum is associated with asymmetry of zero point atomic vibrations. Theory predictions are consistent with the time-dependent density functional theory calculations. Molecular systems for experimental evaluation of the predictions are proposed.

  18. Electronic torsional sound in linear atomic chains: Chemical energy transport at 1000 km/s

    Science.gov (United States)

    Kurnosov, Arkady A.; Rubtsov, Igor V.; Maksymov, Andrii O.; Burin, Alexander L.

    2016-07-01

    We investigate entirely electronic torsional vibrational modes in linear cumulene chains. The carbon nuclei of a cumulene are positioned along the primary axis so that they can participate only in the transverse and longitudinal motions. However, the interatomic electronic clouds behave as a torsion spring with remarkable torsional stiffness. The collective dynamics of these clouds can be described in terms of electronic vibrational quanta, which we name torsitons. It is shown that the group velocity of the wavepacket of torsitons is much higher than the typical speed of sound, because of the small mass of participating electrons compared to the atomic mass. For the same reason, the maximum energy of the torsitons in cumulenes is as high as a few electronvolts, while the minimum possible energy is evaluated as a few hundred wavenumbers and this minimum is associated with asymmetry of zero point atomic vibrations. Theory predictions are consistent with the time-dependent density functional theory calculations. Molecular systems for experimental evaluation of the predictions are proposed.

  19. Counterion influence on chemical shifts in strychnine salts

    Energy Technology Data Exchange (ETDEWEB)

    Metaxas, Athena E.; Cort, John R.

    2013-05-01

    The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here we characterize the relative influence of different counterions on 1H and 13C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD) and chloroform-d (CDCl3) solvents. In organic solvents, but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. The observed effects are much greater in organic solvents than in water. Slight concentration-dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared to the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts.

  20. Evaluating amber force fields using computed NMR chemical shifts.

    Science.gov (United States)

    Koes, David R; Vries, John K

    2017-10-01

    NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

  1. A Core-Offset Mach Zehnder Interferometer Based on A Non-Zero Dispersion-Shifted Fiber and Its Torsion Sensing Application

    Directory of Open Access Journals (Sweden)

    Eduardo Huerta-Mascotte

    2016-06-01

    Full Text Available In this paper, an all-fiber Mach-Zehnder interferometer (MZI based on a non-zero dispersion-shifted fiber (NZ-DSF is presented. The MZI was implemented by core-offset fusion splicing one section of a NZ-DSF fiber between two pieces of single mode fibers (SMFs. Here, the NZ-DSF core and cladding were used as the arms of the MZI, while the core-offset sections acted as optical fiber couplers. Thus, a MZI interference spectrum with a fringe contrast (FC of about 20 dB was observed. Moreover, its response spectrum was experimentally characterized to the torsion parameter and a sensitivity of 0.070 nm/° was achieved. Finally, these MZIs can be implemented in a compact size and low cost.

  2. Appendicular Torsion

    Directory of Open Access Journals (Sweden)

    Siddharth Pramod Dubhashi

    2016-01-01

    Full Text Available Torsion of the vermiform appendix is a rare condition detectable only at operation. It can be primary or secondary. This is a case report of 52-year-old female with 180° anti-clockwise rotation of the appendix. Torsion can further leads to strangulation and infarction of the organ. Appendicular torsion could be included in the differential diagnosis of pain in right iliac fossa.

  3. Nucleic acid helix structure determination from NMR proton chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

    2013-06-15

    We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

  4. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

    2013-09-15

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

  5. Anisotropy of the fluorine chemical shift tensor in UF6

    International Nuclear Information System (INIS)

    Rigny, P.

    1965-04-01

    An 19 F magnetic resonance study of polycrystalline UF 6 is presented. The low temperature complex line can be analyzed as the superposition of two distinct lines, which is attributed to a distortion of the UF 6 octahedron in the solid. The shape of the two components is studied. Their width is much larger than the theoretical dipolar width, and must be explained by large anisotropies of the fluorine chemical shift tensors. The resulting shape functions of the powder spectra are determined. The values of the parameters of the chemical shift tensors yield estimates of the characters of the U-F bonds, and this gives some information on the ground state electronic wave function of the UF 6 molecule in the solid. (author) [fr

  6. Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy

    International Nuclear Information System (INIS)

    Herbst, Christian

    2010-01-01

    The basic aim of the thesis was the development and improvement of homo- and heteronuclear feedback sequences for the generation of correlation spectra of the chemical shift. In a first step the possibility of the acquisition of 13 C- 13 correlation spectra of the chemical shift by means of inversion pulses with low RF power factor was studied. Furthermore it was shown that broad-band phase-modulated inversion and universal rotational pulses can be constructed by means of global optimization procedures like the genetic algorithms under regardment of the available RF field strength. By inversion, universal rotational, and 360 pulses as starting values of the optimization efficient homonuclear CN n ν and RN n ν mixing sequences as well as heteronuclear RN n ν s ,ν k feedback sequences were generated. The satisfactory power of the numerically optimized sequences was shown by means of the simulation as well by means of correlation experiments of the chemical shift of L-histidine, L-arginine, and the (CUG) 97 -RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN n ν s ,ν k pulse sequences both 15 N- 13 C and 13 C- 15 N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D- 15 N- 13 C- 13 C and 13 C- 15 N-( 1 H)- 1 H correlation spectra is possible. By this in only one measurement process resonance assignments can be met and studies of the global folding performed. A further application of several receivers is the simultaneous acquisition of CHHC, NHHN, NHHC, as well as CHHN spectra. By such experiments it is possible to characterize the hydrogen-bonding pattern and the glycosidic torsion angle χ in RNA. This was demonstrated by means of the (CUG) 97 -RNA. The simultaneous acquisition of all relevant crossing signals of the correlation spectra leads not only to an essential time saving, but

  7. Solvent Effects on Oxygen-17 Chemical Shifts in Amides. Quantitative Linear Solvation Shift Relationships

    Science.gov (United States)

    Díez, Ernesto; Fabián, Jesús San; Gerothanassis, Ioannis P.; Esteban, Angel L.; Abboud, José-Luis M.; Contreras, Ruben H.; de Kowalewski, Dora G.

    1997-01-01

    A multiple-linear-regression analysis (MLRA) has been carried out using the Kamlet-Abboud-Taft (KAT) solvatochromic parameters in order to elucidate and quantify the solvent effects on the17O chemical shifts ofN-methylformamide (NMF),N,N-dimethylformamide (DMF),N-methylacetamide (NMA), andN,N-dimethylacetamide (DMA). The chemical shifts of the four molecules show the same dependence (in ppm) on the solvent polarity-polarizability, i.e., -22π*. The influence of the solvent hydrogen-bond-donor (HBD) acidities is slightly larger for the acetamides NMA and DMA, i.e., -48α, than for the formamides NMF and DMF, i.e., -42α. The influence of the solvent hydrogen-bond-acceptor (HBA) basicities is negligible for the nonprotic molecules DMF and DMA but significant for the protic molecules NMF and NMA, i.e., -9β. The effect of substituting the N-H hydrogen by a methyl group amounts to -5.9 ppm in NMF and 5.4 ppm in NMA. The effect of substituting the O=C-H hydrogen amounts to 5.5 ppm in NMF and 16.8 ppm in DMF. The model of specific hydration sites of amides by I. P. Gerothanassis and C. Vakka [J. Org. Chem.59,2341 (1994)] is settled in a more quantitative basis and the model by M. I. Burgar, T. E. St. Amour, and D. Fiat [J. Phys. Chem.85,502 (1981)] is critically evaluated.17O hydration shifts have been calculated for formamide (FOR) by the ab initio LORG method at the 6-31G* level. For a formamide surrounded by the four in-plane molecules of water in the first hydration shell, the calculated17O shift change due to the four hydrogen bonds, -83.2 ppm, is smaller than the empirical hydration shift, -100 ppm. The17O shift change from each out-of-plane water molecule hydrogen-bonded to the amide oxygen is -18.0 ppm. These LORG results support the conclusion that no more than four water molecules are hydrogen-bonded to the amide oxygen in formamide.

  8. NMR chemical shifts in amino acids: Effects of environments, electric field, and amine group rotation

    International Nuclear Information System (INIS)

    Yoon, Young-Gui; Pfrommer, Bernd G.; Louie, Steven G.; Canning, Andrew

    2002-01-01

    The authors present calculations of NMR chemical shifts in crystalline phases of some representative amino acids such as glycine, alanine, and alanyl-alanine. To get an insight on how different environments affect the chemical shifts, they study the transition from the crystalline phase to completely isolated molecules of glycine. In the crystalline limit, the shifts are dominated by intermolecular hydrogen-bonds. In the molecular limit, however, dipole electric field effects dominate the behavior of the chemical shifts. They show that it is necessary to average the chemical shifts in glycine over geometries. Tensor components are analyzed to get the angle dependent proton chemical shifts, which is a more refined characterization method

  9. Appendicular Torsion

    African Journals Online (AJOL)

    A‑2/103, Shivranjan Towers, Someshwarwadi, Pashan, Pune ‑ 411 008,. Maharashtra, India. E‑mail: spdubhashi@gmail.com. INTRODUCTION. Acute appendicitis presents with pain in right iliac fossa. Torsion of the vermiform appendix, though rare, also presents in a similar fashion, and it is detectable only at operation.[1].

  10. Role of quantitative chemical shift magnetic resonance imaging and chemical shift subtraction technique in discriminating adenomatous from non adenomatous adrenal solid lesions

    Directory of Open Access Journals (Sweden)

    Ahmed H. Afifi

    2017-03-01

    Conclusion: The signal intensity index and adrenal to spleen ratio are the most reliable quantitative chemical shift MRI methods in differentiation of adrenal adenomas from other non-adenomatous adrenal solid lesions. Chemical shift subtraction MRI is a recent technique that gives highly confident discrimination between two categories of pathology without using of any reference organ.

  11. Testicular torsion

    DEFF Research Database (Denmark)

    Brasso, K; Andersen, L; Kay, L

    1993-01-01

    Thirty-five patients were examined 6-11 years after operation for torsion of the testis. Loss of testicular tissue was significantly associated with long preoperative duration of symptoms and with low postoperative sperm counts. The sex hormones were normal in the majority of patients...... to the sperm count and concentration. Measurement of carnitine levels in seminal plasma, as a sign of vas deferens obstruction or dysfunction of epididymis, and of autoantibodies against spermatozoa revealed no significant findings....

  12. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

    International Nuclear Information System (INIS)

    Ginzinger, Simon W.; Coles, Murray

    2009-01-01

    We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods

  13. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

    Energy Technology Data Exchange (ETDEWEB)

    Ginzinger, Simon W. [Center of Applied Molecular Engineering, University of Salzburg, Department of Molecular Biology, Division of Bioinformatics (Austria)], E-mail: simon@came.sbg.ac.at; Coles, Murray [Max-Planck-Institute for Developmental Biology, Department of Protein Evolution (Germany)], E-mail: Murray.Coles@tuebingen.mpg.de

    2009-03-15

    We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods.

  14. Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

    Science.gov (United States)

    Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

    2018-01-01

    Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

  15. Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView

    International Nuclear Information System (INIS)

    Schwarzinger, Stephan; Kroon, Gerard J.A.; Foss, Ted R.; Wright, Peter E.; Dyson, H. Jane

    2000-01-01

    Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best

  16. Applications of Chemical Shift Imaging to Marine Sciences

    Directory of Open Access Journals (Sweden)

    Haakil Lee

    2010-08-01

    Full Text Available The successful applications of magnetic resonance imaging (MRI in medicine are mostly due to the non-invasive and non-destructive nature of MRI techniques. Longitudinal studies of humans and animals are easily accomplished, taking advantage of the fact that MRI does not use harmful radiation that would be needed for plain film radiographic, computerized tomography (CT or positron emission (PET scans. Routine anatomic and functional studies using the strong signal from the most abundant magnetic nucleus, the proton, can also provide metabolic information when combined with in vivo magnetic resonance spectroscopy (MRS. MRS can be performed using either protons or hetero-nuclei (meaning any magnetic nuclei other than protons or 1H including carbon (13C or phosphorus (31P. In vivo MR spectra can be obtained from single region ofinterest (ROI or voxel or multiple ROIs simultaneously using the technique typically called chemical shift imaging (CSI. Here we report applications of CSI to marine samples and describe a technique to study in vivo glycine metabolism in oysters using 13C MRS 12 h after immersion in a sea water chamber dosed with [2-13C]-glycine. This is the first report of 13C CSI in a marine organism.

  17. MR chemical shift imaging and spectroscopy of atherosclerotic plaque

    International Nuclear Information System (INIS)

    Vinitski, S.; Consigny, P.M.; Shapiro, M.J.; Janes, N.; Smullens, S.N.; Rifkin, M.D.

    1989-01-01

    The purpose of this study was to develop a technique for in vivo imaging and characterization of atherosclerotic plaque. The authors used a spin-echo technique with a short echo time (TE) of 11 msec. Lipid/water suppression was achieved by means of hybrid chemical shift imaging. Lesions were induced in three rabbits by a combination of balloon denudation of the abdominal aorta and a high-cholesterol diet. Following in vivo imaging of these rabbit aortas and human carotid arteries (1.5 T), the animals were killed or carotid endarterectomy was performed so that the plaques could be excised. The plaques were then analyzed in vitro both histologically and with high-resolution spectroscopy (8.5 T). Use of the short TE improved lesion visualization. The fat/water suppression showed only a small amount of mobile lipids in plaque. Both MR spectroscopic and histologic analysis corroborated these images. The composition of atherosclerotic plaques in both humans and rabbits was demonstrated to be heterogeneous, with predominantly nonmobile lipids. These results suggest that the combination of short TE MR imaging and fat/water suppression can identify plaque and delineate areas containing mobile lipids

  18. Diagnostic value of chemical shift artifact in distinguishing benign lymphadenopathy

    Energy Technology Data Exchange (ETDEWEB)

    Farshchian, Nazanin, E-mail: farshchian.n@gmail.com [Department of Radiology, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Tamari, Saghar; Farshchian, Negin [Department of Radiology, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Madani, Hamid [Department of Pathology, Imam-Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Rezaie, Mansour [Department of Biostatistics, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Mohammadi-Motlagh, Hamid-Reza, E-mail: mohammadimotlagh@gmail.com [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

    2011-11-15

    Purpose: Today, distinguishing metastatic lymph nodes from secondary benign inflammatory ones via using non-invasive methods is increasingly favorable. In this study, the diagnostic value of chemical shift artifact (CSA) in magnetic resonance imaging (MRI) was evaluated to distinguish benign lymphadenopathy. Subjects and methods: A prospective intraindividual internal review board-approved study was carried out on 15 men and 15 women having lymphadenopathic lesions in different locations of the body who underwent contrast-enhanced dynamic MR imaging at 1.5 T. Then, the imaging findings were compared with pathology reports, using the statistics analyses. Results: Due to the findings of the CSA existence in MRI, a total of 56.7% of the studied lesions (17 of 30) were identified as benign lesions and the rest were malignant, whereas the pathology reports distinguished twelve malignant and eighteen benign cases. Furthermore, the CSA findings comparing the pathology reports indicated that CSA, with confidence of 79.5%, has a significant diagnostic value to differentiate benign lesions from malignant ones. Conclusion: Our study demonstrated that CSA in MR imaging has a suitable diagnostic potential nearing readiness for clinical trials. Furthermore, CSA seems to be a feasible tool to differentiate benign lymph nodes from malignant ones; however, further studies including larger numbers of patients are required to confirm our results.

  19. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    Science.gov (United States)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

  20. The PROSECCO server for chemical shift predictions in ordered and disordered proteins.

    Science.gov (United States)

    Sanz-Hernández, Máximo; De Simone, Alfonso

    2017-11-01

    The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences. Our sequence-based approach, protein sequences and chemical shift correlations (PROSECCO), achieves the accuracy of the most advanced structure-based methods in the characterization of chemical shifts of folded proteins and improves the state of the art in the study of disordered proteins. Our analyses revealed fundamental insights on the structural information carried by NMR chemical shifts of structured and unstructured protein states.

  1. Temperature dependence of 1H NMR chemical shifts and its influence on estimated metabolite concentrations.

    Science.gov (United States)

    Wermter, Felizitas C; Mitschke, Nico; Bock, Christian; Dreher, Wolfgang

    2017-12-01

    Temperature dependent chemical shifts of important brain metabolites measured by localised 1 H MRS were investigated to test how the use of incorrect prior knowledge on chemical shifts impairs the quantification of metabolite concentrations. Phantom measurements on solutions containing 11 metabolites were performed on a 7 T scanner between 1 and 43 °C. The temperature dependence of the chemical shift differences was fitted by a linear model. Spectra were simulated for different temperatures and analysed by the AQSES program (jMRUI 5.2) using model functions with chemical shift values for 37 °C. Large differences in the temperature dependence of the chemical shift differences were determined with a maximum slope of about ±7.5 × 10 -4  ppm/K. For 32-40 °C, only minor quantification errors resulted from using incorrect chemical shifts, with the exception of Cr and PCr. For 1-10 °C considerable quantification errors occurred if the temperature dependence of the chemical shifts was neglected. If 1 H MRS measurements are not performed at 37 °C, for which the published chemical shift values have been determined, the temperature dependence of chemical shifts should be considered to avoid systematic quantification errors, particularly for measurements on animal models at lower temperatures.

  2. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

    International Nuclear Information System (INIS)

    Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei

    2013-01-01

    We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  3. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

    Energy Technology Data Exchange (ETDEWEB)

    Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

    2013-06-15

    We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  4. Empirical correlation between protein backbone {sup 15}N and {sup 13}C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

    Energy Technology Data Exchange (ETDEWEB)

    Wang Liya [Cold Spring Harbor Laboratory (United States); Markley, John L. [University of Wisconsin, Biochemistry Department (United States)], E-mail: markley@nmrfam.wisc.edu

    2009-06-15

    The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting {sup 13}C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to {sup 15}N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary {sup 15}N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta {sup 13}C chemical shifts are available (their difference is referencing error-free), the {sup 15}N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have {delta}{sup 15}N values mis-referenced by over 0.7 ppm and over 25% of them have {delta}{sup 1}H{sup N} values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone {sup 15}N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself.

  5. A procedure to validate and correct the {sup 13}C chemical shift calibration of RNA datasets

    Energy Technology Data Exchange (ETDEWEB)

    Aeschbacher, Thomas; Schubert, Mario, E-mail: schubert@mol.biol.ethz.ch; Allain, Frederic H.-T., E-mail: allain@mol.biol.ethz.ch [ETH Zuerich, Institute for Molecular Biology and Biophysics (Switzerland)

    2012-02-15

    Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of {sup 13}C NMR data of RNAs. Our procedure uses five {sup 13}C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the {sup 13}C calibration and detect errors or inconsistencies in RNA {sup 13}C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure-{sup 13}C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable {sup 13}C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure-chemical shift relationships with this improved list of {sup 13}C chemical shift data. This is demonstrated by a clear relationship between ribose {sup 13}C shifts and the sugar pucker, which can be used to predict a C2 Prime - or C3 Prime -endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.

  6. Deuterium isotope effects on 13C chemical shifts of 10-Hydroxybenzo[h]quinolines

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Kamounah, Fadhil S.; Gryko, Daniel T.

    2013-01-01

    Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found to be nega...

  7. Measurements of relative chemical shift tensor orientations in solid-state NMR: new slow magic angle spinning dipolar recoupling experiments.

    Science.gov (United States)

    Jurd, Andrew P S; Titman, Jeremy J

    2009-08-28

    Solid-state NMR experiments can be used to determine conformational parameters, such as interatomic distances and torsion angles. The latter can be obtained from measurements of the relative orientation of two chemical shift tensors, if the orientation of these with respect to the surrounding bonds is known. In this paper, a new rotor-synchronized magic angle spinning (MAS) dipolar correlation experiment is described which can be used in this way. Because the experiment requires slow MAS rates, a novel recoupling sequence, designed using symmetry principles, is incorporated into the mixing period. This recoupling sequence is based in turn on a new composite cyclic pulse referred to as COAST (for combined offset and anisotropy stabilization). The new COAST-C7(2)(1) sequence is shown to give good theoretical and experimental recoupling efficiency, even when the CSA far exceeds the MAS rate. In this regime, previous recoupling sequences, such as POST-C7(2)(1), exhibit poor recoupling performance. The effectiveness of the new method has been explored by a study of the dipeptide L-phenylalanyl-L-phenylalanine.

  8. Protein backbone angle restraints from searching a database for chemical shift and sequence homology

    Energy Technology Data Exchange (ETDEWEB)

    Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    1999-03-15

    Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

  9. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)

    2015-01-15

    There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-15

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

  11. Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis

    Energy Technology Data Exchange (ETDEWEB)

    Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

    2017-02-15

    Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H{sup δ21} and H{sup ε21}, respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

  12. Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

    International Nuclear Information System (INIS)

    Cromsigt, Jenny A.M.T.C.; Hilbers, Cees W.; Wijmenga, Sybren S.

    2001-01-01

    An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1 H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1 H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

  13. Relation between chemical shift artifact and infiltration on MR imaging of renal cell carcinoma

    International Nuclear Information System (INIS)

    Yoshigoe, Fukuo; Makino, Hideki; Yanada, Syuichi; Ohishi, Yukihiko; Mashima, Yasuoki; Yamada, Hideo.

    1994-01-01

    Retrospective study on the relation between existence of the interruption and disturbance of chemical shift artifact and tumor infiltration at the periphery of the kidney on MR imaging was evaluated in 28 cases with renal cell carcinoma. Judgement was possible in 9 out of the 11 cases with pathological stage below pT2 and 14 cases out of 17 pT3 cases. Judgement was impracticable in 5 cases because the peripheral fat tissue of the kidney was too less to observe chemical shift artifact and the tumor was spreading at the side opposite to the chemical shift artifact. Chemical shift artifact on MRI in this study correlated well with renal tumor infiltration. (author)

  14. PPM-One: a static protein structure based chemical shift predictor

    International Nuclear Information System (INIS)

    Li, Dawei; Brüschweiler, Rafael

    2015-01-01

    We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs

  15. Theoretical Study of the NMR Chemical Shift of Xe in Supercritical Condition

    DEFF Research Database (Denmark)

    Lacerda Junior, Evanildo Gomes; Sauer, Stephan P. A.; Mikkelsen, Kurt Valentin

    2018-01-01

    In this work we investigate the level of theory necessary for reproducing the non-linear variation of the 129Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the 129Xe chemical shift depends under these conditions...... on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xen...... this approach we obtain very good agreement with the experimental data, showing that the chemical shift of 129Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects....

  16. 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

  17. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Joshua D.; Summers, Michael F. [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [University of Maryland Baltimore County, Department of Chemistry and Biochemistry (United States)

    2015-09-15

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR and {sup 13}C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and {sup 1}H and {sup 13}C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA {sup 1}H and {sup 13}C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

  18. Chemical shift MRI can aid in the diagnosis of indeterminate skeletal lesions of the spine

    Energy Technology Data Exchange (ETDEWEB)

    Douis, H. [University Hospital Birmingham, Department of Radiology, Birmingham (United Kingdom); Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Davies, A.M. [Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Jeys, L. [Royal Orthopaedic Hospital, Department of Orthopaedic Oncology, Birmingham (United Kingdom); Sian, P. [Royal Orthopaedic Hospital, Department of Spinal Surgery and Spinal Oncology, Birmingham (United Kingdom)

    2016-04-15

    To evaluate the role of chemical shift MRI in the characterisation of indeterminate skeletal lesions of the spine as benign or malignant. Fifty-five patients (mean age 54.7 years) with 57 indeterminate skeletal lesions of the spine were included in this retrospective study. In addition to conventional MRI at 3 T which included at least sagittal T1WI and T2WI/STIR sequences, patients underwent chemical shift MRI. A cut-off value with a signal drop-out of 20 % was used to differentiate benign lesions from malignant lesions (signal drop-out <20 % being malignant). There were 45 benign lesions and 12 malignant lesions. Chemical shift imaging correctly diagnosed 33 of 45 lesions as benign and 11 of 12 lesions as malignant. In contrast, there were 12 false positive cases and 1 false negative case based on chemical shift MRI. This yielded a sensitivity of 91.7 %, a specificity of 73.3 %, a negative predictive value of 97.1 %, a positive predictive value of 47.8 % and a diagnostic accuracy of 82.5 %. Chemical shift MRI can aid in the characterisation of indeterminate skeletal lesions of the spine in view of its high sensitivity in diagnosing malignant lesions. Chemical shift MRI can potentially avoid biopsy in a considerable percentage of patients with benign skeletal lesions of the spine. (orig.)

  19. Cyclohexanecarbonitriles: Assigning Configurations at Quaternary Centers From 13C NMR CN Chemical Shifts.1

    Science.gov (United States)

    Wei, Guoqing

    2009-01-01

    13C NMR chemical shifts of the nitrile carbon in cyclohexanecarbonitriles directly correlate with the configuration of the quaternary, nitrile-bearing stereocenter. Comparing 13C NMR chemical shifts for over 200 cyclohexanecarbonitriles reveals that equatorially oriented nitriles resonate 3.3 ppm downfield, on average, from their axial counterparts. Pairs of axial/equatorial diastereomers varying only at the nitrile-bearing carbon consistently exhibit downfield shifts of δ 0.4–7.2 for the equatorial nitrile carbon, even in angularly substituted decalins and hydrindanes. PMID:19348434

  20. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

    International Nuclear Information System (INIS)

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

    2015-01-01

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), 1 H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong 1 H– 1 H homonuclear dipolar couplings and narrow 1 H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) 1 H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about 1 H– 1 H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic-level structural and dynamical

  1. Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

    Energy Technology Data Exchange (ETDEWEB)

    Harris, R.K. [University of Durham, Durham (United Kingdom). Dept. of Chemistry; Becker, E.D. [National Institutes of Health, Bethesda, MD (United States); Menezes, S.M. Cabral de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Granger, P. [University Louis Pasteur, Strasbourg (France). Inst. of Chemistry; Hoffman, R.E. [The Hebrew University of Jerusalem, Safra Campus, Jerusalem (Israel). Dept. of Organic Chemistry; Zilm, K.W., E-mail: r.k.harris@durham.ac.uk [Yale University, New Haven, CT (United States). Dept. of Chemistry

    2008-07-01

    IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the {sup 1}H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating {sup 13}C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

  2. Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

    International Nuclear Information System (INIS)

    Harris, R.K.; Menezes, S.M. Cabral de; Granger, P.; Hoffman, R.E.; Zilm, K.W.

    2008-01-01

    IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the 1 H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating 13 C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

  3. 29Si NMR Chemical Shift Calculation for Silicate Species by Gaussian Software

    Science.gov (United States)

    Azizi, S. N.; Rostami, A. A.; Godarzian, A.

    2005-05-01

    Hartree-Fock self-consistent-field (HF-SCF) theory and the Gauge-including atomic orbital (GIAO) methods are used in the calculation of 29Si NMR chemical shifts for ABOUT 90 units of 19 compounds of various silicate species of precursors for zeolites. Calculations have been performed at geometries optimized at the AM1 semi-empirical method. The GIAO-HF-SCF calculations were carried out with using three different basis sets: 6-31G*, 6-31+G** and 6-311+G(2d,p). To demonstrate the quality of the calculations the calculated chemical shifts, δ, were compared with the corresponding experimental values for the compounds in study. The results, especially with 6-31+g** are in excellent agreement with experimental values. The calculated chemical shifts, in practical point of view, appear to be accurate enough to aid in experimental peak assignments. The difference between the experimental and calculated 29Si chemical shift values not only depends on the Qn units but also it seems that basis set effects and the level of theory is more important. For the series of molecules studied here, the standard deviations and mean absolute errors for 29Si chemical shifts relative to TMS determined using Hartree--Fock 6-31+G** basis is nearly in all cases smaller than the errors for shifts determined using HF/6-311+G(2d,p).

  4. 1H NMR spectra part 31: 1H chemical shifts of amides in DMSO solvent.

    Science.gov (United States)

    Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

    2014-07-01

    The (1)H chemical shifts of 48 amides in DMSO solvent are assigned and presented. The solvent shifts Δδ (DMSO-CDCl3 ) are large (1-2 ppm) for the NH protons but smaller and negative (-0.1 to -0.2 ppm) for close range protons. A selection of the observed solvent shifts is compared with calculated shifts from the present model and from GIAO calculations. Those for the NH protons agree with both calculations, but other solvent shifts such as Δδ(CHO) are not well reproduced by the GIAO calculations. The (1)H chemical shifts of the amides in DMSO were analysed using a functional approach for near ( ≤ 3 bonds removed) protons and the electric field, magnetic anisotropy and steric effect of the amide group for more distant protons. The chemical shifts of the NH protons of acetanilide and benzamide vary linearly with the π density on the αN and βC atoms, respectively. The C=O anisotropy and steric effect are in general little changed from the values in CDCl3. The effects of substituents F, Cl, Me on the NH proton shifts are reproduced. The electric field coefficient for the protons in DMSO is 90% of that in CDCl3. There is no steric effect of the C=O oxygen on the NH proton in an NH…O=C hydrogen bond. The observed deshielding is due to the electric field effect. The calculated chemical shifts agree well with the observed shifts (RMS error of 0.106 ppm for the data set of 257 entries). Copyright © 2014 John Wiley & Sons, Ltd.

  5. Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen

    to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....

  6. Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)

    2010-03-15

    We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and {sup 13}C{sup {beta}} chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-{sup 13}C{sup {gamma}}, Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-{sup 13}C{sup {gamma}} assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and {sup 13}C{sup {beta}} chemical shifts.

  7. Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

    Science.gov (United States)

    Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

    2015-04-01

    In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

  8. DFT/GIAO calculations of the relative contributions of hyperconjugation to the chemical shifts of ethanol

    International Nuclear Information System (INIS)

    Carneiro, J. Walkimar de M.; Dias, Jacques F.; Seidl, Peter R.; Tostes, J. Glauco R.

    2002-01-01

    Our previous DFT/GIAO calculations on different types of alcohols reveal that the rotation of the hydroxyl group can affect the chemical shift of carbons and hydrogens close to the substituent in different ways. Besides the steric and electrostatic effects that have been widely studied, hyperconjugation with the lone pairs on oxygen of the hydroxyl group leads to changes in bond lengths and angles as well as to different charge distributions. As all three of these factors also affect chemical shifts, we undertook a systematic investigation of their relative contributions to the chemical shifts of ethanol, a molecule in which there is minimum interference among these factors. Calculations by the B3LYP method at the 6-31G(d) level for ethanol conformers corresponding to a rotation around the carbon-oxygen bond at 30 dec increments are used to show how relative contributions vary with the dihedral angle formed between the carbon-carbon and oxygen-hydrogen bonds (C-C-O-H). Largest contributions to carbon chemical shifts can be attributed to changes in bond lengths while for hydrogen chemical shifts also contribute significantly differences in charge distribution. (author)

  9. Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

    Science.gov (United States)

    Boomsma, Wouter; Tian, Pengfei; Frellsen, Jes; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Lindorff-Larsen, Kresten; Vendruscolo, Michele

    2014-09-23

    Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.

  10. Resolution of NMR chemical shift images into real and imaginary components

    International Nuclear Information System (INIS)

    Yamamoto, E.; Kohno, H.

    1986-01-01

    Fast chemical shift imaging of two-line materials is described using a modified spin-echo sequence. The method resolves the two chemical shift images into real and imaginary components representing the reconstructed image. The measuring time is reduced to half of that for the conventional method proposed by Dixon et al, and quantitative evaluation of the images becomes possible. Reference material with a single resonant line is used to eliminate the phase error caused by static field inhomogeneity and the inherent apparatus offset phase. Experiments are conducted using acetone and benzene with a medium-bore superconductive magnet operating at 0.5T. From these experiments, two chemical shift images are obtained. These images are then superimposed to produce a conventional density image. (author)

  11. /sup 1/H-NMR chemical shift imaging suitable for low field systems

    Energy Technology Data Exchange (ETDEWEB)

    Yamamoto, Etsuji; Onodera, Takashi; Shiono, Hidemi; Kohno, Hideki

    1986-12-01

    An echo-time encoding proton NMR chemical shift imaging proposed by Dixon is extended to be applicable to low filed systems. The method utilizes the small phase angle between magnetic vectors of water and lipid protons to decrease the signal decays with spin-spin relaxation. The inevitable phase error caused by the static field inhomogeneity is corrected by using phase images of phantom measured under the same conditions as the actual measurements. The experiments were carried out using CuSO/sub 4/ doped water and vegetable oil at 0.5 T. Two chemical shift images could be clearly resolved with only one scan when the field inhomogeneity was larger than the chemical shift difference.

  12. What can we learn by computing 13Cα chemical shifts for X-ray protein models?

    International Nuclear Information System (INIS)

    Arnautova, Yelena A.; Vila, Jorge A.; Martin, Osvaldo A.; Scheraga, Harold A.

    2009-01-01

    The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. The room-temperature X-ray structures of ubiquitin and of the RNA-binding domain of nonstructural protein 1 of influenza A virus solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R free factors similar to those of the deposited X-ray structure, the 13 C α chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13 C α chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13 C α chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13 C α chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13 C α chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with

  13. Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin

    2011-01-01

    Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues....... The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we...... in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve...

  14. Investigation of DOTA-Metal Chelation Effects on the Chemical Shift of 129 Xe

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, K; Slack, CC; Vassiliou, CC; Dao, P; Gomes, MD; Kennedy, DJ; Truxal, AE; Sperling, LJ; Francis, MB; Wemmer, DE; Pines, A

    2015-09-17

    Recent work has shown that xenon chemical shifts in cryptophane-cage sensors are affected when tethered chelators bind to metals. Here in this paper, we explore the xenon shifts in response to a wide range of metal ions binding to diastereomeric forms of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) linked to cryptophane-A. The shifts induced by the binding of Ca2+, Cu2+, Ce3+, Zn2+, Cd2+, Ni2+, Co2+, Cr2+, Fe3+, and Hg2+ are distinct. In addition, the different responses of the diastereomers for the same metal ion indicate that shifts are affected by partial folding with a correlation between the expected coordination number of the metal in the DOTA complex and the chemical shift of 129Xe. Lastly, these sensors may be used to detect and quantify many important metal ions, and a better understanding of the basis for the induced shifts could enhance future designs.

  15. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

  16. Identification of helix capping and {beta}-turn motifs from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2012-03-15

    We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and {beta}-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7-0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

  17. Identify Beta-Hairpin Motifs with Quadratic Discriminant Algorithm Based on the Chemical Shifts.

    Directory of Open Access Journals (Sweden)

    Feng YongE

    Full Text Available Successful prediction of the beta-hairpin motif will be helpful for understanding the of the fold recognition. Some algorithms have been proposed for the prediction of beta-hairpin motifs. However, the parameters used by these methods were primarily based on the amino acid sequences. Here, we proposed a novel model for predicting beta-hairpin structure based on the chemical shift. Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in not beta-hairpin and beta-hairpin motifs. Secondly, we used these chemical shifts as features combined with three algorithms to predict beta-hairpin structure. Finally, we achieved the best prediction, namely sensitivity of 92%, the specificity of 94% with 0.85 of Mathew's correlation coefficient using quadratic discriminant analysis algorithm, which is clearly superior to the same method for the prediction of beta-hairpin structure from 20 amino acid compositions in the three-fold cross-validation. Our finding showed that the chemical shift is an effective parameter for beta-hairpin prediction, suggesting the quadratic discriminant analysis is a powerful algorithm for the prediction of beta-hairpin.

  18. Chemical shift of Mn and Cr K-edges in X-ray absorption

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Bulletin of Materials Science; Volume 36; Issue 6. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation. D Joseph A K Yadav S N Jha D Bhattacharyya. Volume 36 Issue 6 November 2013 pp ...

  19. Database proton NMR chemical shifts for RNA signal assignment and validation

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Shawn; Heng Xiao [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce@onemoonscientific.com [University of Maryland, Baltimore County, Department of Chemistry and Biochemistry (United States); Summers, Michael F., E-mail: summers@hhmi.umbc.edu [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States)

    2013-01-15

    The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson-Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 4{sup 3} possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA {sup 1}H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

  20. Skeletal and chlorine effects on 13C-NMR chemical shifts of chlorinated polycyclic systems

    Directory of Open Access Journals (Sweden)

    Costa V.E.U.

    1999-01-01

    Full Text Available In order to establish a comparative analysis of chemical shifts caused by ring compression effects or by the presence of a chlorine atom on strained chlorinated carbons, a series of the chlorinated and dechlorinated polycyclic structures derived from "aldrin" (5 and "isodrin" (14 was studied. Compounds were classified in four different groups, according to their conformation and number of ring such as: endo-exo and endo-endo tetracyclics, pentacyclics and hexacyclics. The 13C chemical shift comparison between the chlorinated and dechlorinated compounds showed that when C-9 and C-10 are olefinic carbons, it occurs a shielding of 0.5-2.4 ppm for endo-endo tetracyclics and of 4.7-7.6 ppm for endo-exo tetracyclic. The chemical shift variation for C-11 reaches 49-53 ppm for endo-exo and endo-endo tetracyclics, 54 ppm for pentacyclic and 56-59 ppm for hexacyclic compounds. From these data, it was possible to observe the influence of ring compression on the chemical shifts.

  1. Identification of helix capping and β-turn motifs from NMR chemical shifts

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2012-01-01

    We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13 C β chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7–0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

  2. H-1 chemical shift imaging characterization of human brain tumor and edema

    NARCIS (Netherlands)

    Sijens, PE; Oudkerk, M

    Longitudinal (T1) and transverse (T2) relaxation times of metabolites in human brain tumor, peritumoral edema, and unaffected brain tissue were assessed from point resolved spectroscopy (PRESS) H-1 chemical shift imaging results at different repetition times (TR = 1500 and 5000 ms; T1: n = 19) and

  3. Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene.

    Science.gov (United States)

    Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

    2018-07-01

    Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. Graphical Abstract ᅟ.

  4. Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene

    Science.gov (United States)

    Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

    2018-04-01

    Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. [Figure not available: see fulltext.

  5. Intermittent Testicular Torsion

    African Journals Online (AJOL)

    2017-06-02

    Jun 2, 2017 ... had prior episodes of testicular pain, suggesting that they may have had intermittent torsion before .... None of the patients had antecedent history of sexual exposure, fever, or urinary tract infection .... torsion of the spermatic cord portends an increased risk of acute testicular infarction. J Urol 2008;180 4 ...

  6. Pressure-dependent {sup 13}C chemical shifts in proteins: origins and applications

    Energy Technology Data Exchange (ETDEWEB)

    Wilton, David J. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom); Kitahara, Ryo [Ritsumeikan University, College of Pharmaceutical Sciences (Japan); Akasaka, Kazuyuki [Kinki University, Department of Biotechnological Science, School of Biology-Oriented Science and Technology (Japan); Williamson, Mike P. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom)], E-mail: m.williamson@sheffield.ac.uk

    2009-05-15

    Pressure-dependent {sup 13}C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH{sub 3}, CH{sub 2} and CH carbon shifts change on average by +0.23, -0.09 and -0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the {gamma}-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual {sup 13}C{alpha} shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas {sup 13}C{beta} shifts retain significant dependence on local compression, making them less useful as structural restraints.

  7. Evaluation of the application of chemical shift for the detection of lipid in brain lesion

    Energy Technology Data Exchange (ETDEWEB)

    Lim, C.J. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ng, K.H., E-mail: ngkh@um.edu.m [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ramli, N.; Azman, R.R. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia)

    2011-02-15

    Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

  8. Evaluation of the application of chemical shift for the detection of lipid in brain lesion

    International Nuclear Information System (INIS)

    Lim, C.J.; Ng, K.H.; Ramli, N.; Azman, R.R.

    2011-01-01

    Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

  9. Coronary artery atherosclerosis associated with shift work in chemical plant workers by using coronary CT angiography.

    Science.gov (United States)

    Kang, WonYang; Park, Won-Ju; Jang, Keun-Ho; Kim, Soo-Hyeon; Gwon, Do-Hyeong; Lim, Hyeong-Min; Ahn, Ji-Sung; Moon, Jai-Dong

    2016-08-01

    The aim of this study was to investigate whether shift work is related to elevated risk of coronary artery disease (CAD) by determining the coronary artery calcium (CAC) score and the presence of coronary artery stenosis by using coronary artery CT angiography (CCTA). In this study, 110 male workers participated and underwent a CCTA examination for CAC scoring, which represents coronary artery plaque, and were evaluated for luminal stenosis. All of the participants were working in the same chemical plant, of whom 70 worked day shifts and 40 worked rotating shifts. In a multivariate logistic regression analysis, including age, smoking status, alcohol consumption, regular exercise and waist circumference, shift work was associated with a 2.89-fold increase in the odds of developing coronary plaque compared with day work (OR, 2.89; 95% CI 1.07 to 7.82). The association between shift work and coronary plaque was strong after adjustment for age, low-density lipoprotein cholesterol, hypertension and diabetes mellitus (OR, 2.92; 95% CI 1.02 to 8.33). In addition, the number of years of shift work employment was associated with coronary plaque. However, no association was found between shift work and coronary artery stenosis. Shift work could induce CAD onset via the atherosclerotic process, and shift work employment duration was associated with an increased risk of atherosclerosis in male workers. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  10. Isotope effects on chemical shifts in tautomeric systems with double proton transfer. Citronin

    International Nuclear Information System (INIS)

    Hansen, P.E.; Langgard, M.; Bolvig, S.

    1998-01-01

    Primary and secondary deuterium isotope effects on 1 H and 13 C chemical shifts are measured in citrinin, a tautomeric compound with an unusual doubly intramolecularly hydrogen bonded structure. The isotope effects are to a large extent dominated by equilibrium contributions and deuteration leads to more of the deuterated enol forms rather than the deuterated acid form. 1 H 13 C and 17 O nuclear shieldings are calculated using density functional ab initio methods. A very good correlation between calculated nuclear shieldings and experimental 1 H and 13 C chemical shifts is obtained. The tautomeric equilibrium can be analyzed based on the isotope effects on B-6 and C-8 carbons and shows an increase in the o-quinone form on lowering the temperature. Furthermore, upon deuteration the largest equilibrium shift is found for deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration is increasing at lower temperature. (author)

  11. 13C NMR Chemical Shifts of the Triclinic and Monoclinic Crystal forms of Valinomycin

    International Nuclear Information System (INIS)

    Kameda, Tsunenori; McGeorge, Gary; Orendt, Anita M.; Grant, David M.

    2004-01-01

    Two different crystalline polymorphs of valinomycin, the triclinic and monoclinic forms, have been studied by high resolution, solid state 13 C CP-MAS NMR spectroscopy. Although the two polymorphs of the crystal are remarkably similar, there are distinct differences in the isotropic chemical shifts between the two spectra. For the triclinic form, the carbon chemical shift tensor components for the alpha carbons adjacent to oxygen in the lactic acid and hydroxyisovaleric acid residues and the ester carbonyls of the valine residue were obtained using the FIREMAT experiment. From the measured components, it was found that the behavior of the isotropic chemical shift, δ iso , for valine residue ester carbonyl carbons is predominately influenced by the intermediate component, δ 22 . Additionally it was found that the smallest shift component, δ 33 , for the L-lactic acid (L-Lac) and D-α-hydroxyisovaleric acid (D-Hyi) C α -O carbon was significantly displaced depending upon the nature of individual amino acid residues, and it is the δ 33 component that governs the behavior of δ iso in these alpha carbons

  12. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations

    Energy Technology Data Exchange (ETDEWEB)

    Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

    2012-12-15

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K{sub D}) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K{sub D} value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of {sup 1}H-{sup 15}N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k{sub off}). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k{sub off} {approx} 3,000 s{sup -1} in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k{sub off} from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k{sub off} values over a wide range, from 100 to 15,000 s{sup -1}. The validity of line shape analysis for k{sub off} values approaching intermediate exchange ({approx}100 s{sup -1}), may be facilitated by

  13. Accuracy and precision of protein–ligand interaction kinetics determined from chemical shift titrations

    International Nuclear Information System (INIS)

    Markin, Craig J.; Spyracopoulos, Leo

    2012-01-01

    NMR-monitored chemical shift titrations for the study of weak protein–ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K D ) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K D value of a 1:1 protein–ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125–138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of 1 H– 15 N 2D HSQC NMR spectra acquired using precise protein–ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k off ). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k off ∼ 3,000 s −1 in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k off from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k off values over a wide range, from 100 to 15,000 s −1 . The validity of line shape analysis for k off values approaching intermediate exchange (∼100 s −1 ), may be facilitated by more accurate K D measurements from NMR

  14. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

    Science.gov (United States)

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

  15. Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine.

    Science.gov (United States)

    Tredwell, Gregory D; Bundy, Jacob G; De Iorio, Maria; Ebbels, Timothy M D

    2016-01-01

    Despite the use of buffering agents the 1 H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. To investigate the acid, base and metal ion dependent 1 H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl 2 , MgCl 2 , NaCl or KCl, and their 1 H NMR spectra were acquired. Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na + , K + , Ca 2+ and Mg 2+ , were also measured. These data will be a valuable resource for 1 H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1 H NMR spectra.

  16. Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

    Science.gov (United States)

    Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

    2014-04-23

    We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2H)ethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T) level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

  17. Identifying Stereoisomers by ab-initio Calculation of Secondary Isotope Shifts on NMR Chemical Shieldings

    Directory of Open Access Journals (Sweden)

    Karl-Heinz Böhm

    2014-04-01

    Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

  18. Cα and Cβ Carbon-13 Chemical Shifts in Proteins From an Empirical Database

    International Nuclear Information System (INIS)

    Iwadate, Mitsuo; Asakura, Tetsuo; Williamson, Michael P.

    1999-01-01

    We have constructed an extensive database of 13C Cα and Cβ chemical shifts in proteins of solution, for proteins of which a high-resolution crystal structure exists, and for which the crystal structure has been shown to be essentially identical to the solution structure. There is no systematic effect of temperature, reference compound, or pH on reported shifts, but there appear to be differences in reported shifts arising from referencing differences of up to 4.2 ppm. The major factor affecting chemical shifts is the backbone geometry, which causes differences of ca. 4 ppm between typical α- helix and β-sheet geometries for Cα, and of ca. 2 ppm for Cβ. The side-chain dihedral angle χ1 has an effect of up to 0.5 ppm on the Cα shift, particularly for amino acids with branched side-chains at Cβ. Hydrogen bonding to main-chain atoms has an effect of up to 0.9 ppm, which depends on the main- chain conformation. The sequence of the protein and ring-current shifts from aromatic rings have an insignificant effect (except for residues following proline). There are significant differences between different amino acid types in the backbone geometry dependence; the amino acids can be grouped together into five different groups with different φ,ψ shielding surfaces. The overall fit of individual residues to a single non-residue-specific surface, incorporating the effects of hydrogen bonding and χ1 angle, is 0.96 ppm for both Cα and Cβ. The results from this study are broadly similar to those from ab initio studies, but there are some differences which could merit further attention

  19. An extrapolation scheme for solid-state NMR chemical shift calculations

    Science.gov (United States)

    Nakajima, Takahito

    2017-06-01

    Conventional quantum chemical and solid-state physical approaches include several problems to accurately calculate solid-state nuclear magnetic resonance (NMR) properties. We propose a reliable computational scheme for solid-state NMR chemical shifts using an extrapolation scheme that retains the advantages of these approaches but reduces their disadvantages. Our scheme can satisfactorily yield solid-state NMR magnetic shielding constants. The estimated values have only a small dependence on the low-level density functional theory calculation with the extrapolation scheme. Thus, our approach is efficient because the rough calculation can be performed in the extrapolation scheme.

  20. Measuring 13Cβ chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy

    International Nuclear Information System (INIS)

    Lundstroem, Patrik; Lin Hong; Kay, Lewis E.

    2009-01-01

    A labeling scheme is introduced that facilitates the measurement of accurate 13 C β chemical shifts of invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. The approach makes use of protein over-expression in a strain of E. coli in which the TCA cycle enzyme succinate dehydrogenase is knocked out, leading to the production of samples with high levels of 13 C enrichment (30-40%) at C β side-chain carbon positions for 15 of the amino acids with little 13 C label at positions one bond removed (∼5%). A pair of samples are produced using [1- 13 C]-glucose/NaH 12 CO 3 or [2- 13 C]-glucose as carbon sources with isolated and enriched (>30%) 13 C β positions for 11 and 4 residues, respectively. The efficacy of the labeling procedure is established by NMR spectroscopy. The utility of such samples for measurement of 13 C β chemical shifts of invisible, excited states in exchange with visible, ground conformations is confirmed by relaxation dispersion studies of a protein-ligand binding exchange reaction in which the extracted chemical shift differences from dispersion profiles compare favorably with those obtained directly from measurements on ligand free and fully bound protein samples

  1. Effects of Protein-pheromone Complexation on Correlated Chemical Shift Modulations

    International Nuclear Information System (INIS)

    Perazzolo, Chiara; Wist, Julien; Loth, Karine; Poggi, Luisa; Homans, Steve; Bodenhausen, Geoffrey

    2005-01-01

    Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{C'N} and DQC{C'N}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand)

  2. Effects of Protein-pheromone Complexation on Correlated Chemical Shift Modulations

    Energy Technology Data Exchange (ETDEWEB)

    Perazzolo, Chiara; Wist, Julien [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland); Loth, Karine; Poggi, Luisa [Ecole Normale Superieure, Departement de chimie, associe au CNRS (France); Homans, Steve [University of Leeds, School of Biochemistry and Microbiology (United Kingdom); Bodenhausen, Geoffrey [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland)], E-mail: Geoffrey.Bodenhausen@ens.fr

    2005-12-15

    Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{l_brace}C'N{r_brace} and DQC{l_brace}C'N{r_brace}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand)

  3. Some torsion potentials

    Energy Technology Data Exchange (ETDEWEB)

    Grundberg, J; Lindstrom, U

    1986-10-01

    Using the notion of torsion potentials, the duality between antisymmetric tensor fields and scalar fields is discussed. First-order actions with these fields, the connection and the metric as independent variables are presented.

  4. Testicular Torsion (For Parents)

    Science.gov (United States)

    ... Parents Kids Teens Hernias Ultrasound: Scrotum Undescended Testicles Male Reproductive System PQ: I have a lump on one of ... to Do a Testicular Self-Exam (Slideshow) Varicocele Male Reproductive System Testicular Torsion View more About Us Contact Us ...

  5. Induced quantum torsion

    International Nuclear Information System (INIS)

    Denardo, G.; Spallucci, E.

    1985-07-01

    We study pregeometry in the framework of a Poincare gauge field theory. The Riemann-Cartan space-time is shown to be an ''effective geometry'' for this model in the low energy limit. By using Heat Kernel techniques we find the induced action for curvature and torsion. We obtain in this way the usual Einstein-Hilbert action plus an axial Maxwell term describing the propagation of a massless, axial vector torsion field. (author)

  6. Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

    Science.gov (United States)

    Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

    2014-02-11

    An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

  7. Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

    Science.gov (United States)

    Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

    2012-03-07

    Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

  8. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    International Nuclear Information System (INIS)

    Fritzsching, Keith J.; Hong, Mei; Schmidt-Rohr, Klaus

    2016-01-01

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ( 13 C– 13 C, 15 N– 13 C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13 C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the 13 C NMR data and almost all 15 N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the 13 C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a

  9. Carbon 13 nuclear magnetic resonance chemical shifts empiric calculations of polymers by multi linear regression and molecular modeling

    International Nuclear Information System (INIS)

    Da Silva Pinto, P.S.; Eustache, R.P.; Audenaert, M.; Bernassau, J.M.

    1996-01-01

    This work deals with carbon 13 nuclear magnetic resonance chemical shifts empiric calculations by multi linear regression and molecular modeling. The multi linear regression is indeed one way to obtain an equation able to describe the behaviour of the chemical shift for some molecules which are in the data base (rigid molecules with carbons). The methodology consists of structures describer parameters definition which can be bound to carbon 13 chemical shift known for these molecules. Then, the linear regression is used to determine the equation significant parameters. This one can be extrapolated to molecules which presents some resemblances with those of the data base. (O.L.). 20 refs., 4 figs., 1 tab

  10. Elucidation of the substitution pattern of 9,10-anthraquinones through the chemical shifts of peri-hydroxyl protons

    DEFF Research Database (Denmark)

    Schripsema, Jan; Danigno, Denise

    1996-01-01

    In 9,10-anthraquinones the chemical shift of a peri-hydroxyl proton is affected by the substituents in the other benzenoid ring. These effects are additive. They are useful for the determination of substitution patterns and have been used to revise the structures of six previously reported...... anthraquinones containing methoxyl, hydroxyl, methylenedioxy and beta-methyl substituents. Because the chemical shifts of the other protons are hardly affected by substitutions in the other ring, the characteristic chemical shifts for a wide variety of substitution patterns could be derived....

  11. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    Energy Technology Data Exchange (ETDEWEB)

    Fritzsching, Keith J., E-mail: kfritzsc@brandeis.edu [Brandeis University, Department of Chemistry (United States); Hong, Mei [Massachusetts Institute of Technology, Department of Chemistry (United States); Schmidt-Rohr, Klaus, E-mail: srohr@brandeis.edu [Brandeis University, Department of Chemistry (United States)

    2016-02-15

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ({sup 13}C–{sup 13}C, {sup 15}N–{sup 13}C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 {sup 13}C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the {sup 13}C NMR data and almost all {sup 15}N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the {sup 13}C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra

  12. Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy; Korrelationen der chemischen Verschiebung an schnell rotierenden biologischen Festkoerpern mittels NMR-Spektroskopie

    Energy Technology Data Exchange (ETDEWEB)

    Herbst, Christian

    2010-04-27

    The basic aim of the thesis was the development and improvement of homo- and heteronuclear feedback sequences for the generation of correlation spectra of the chemical shift. In a first step the possibility of the acquisition of {sup 13}C-{sup 13} correlation spectra of the chemical shift by means of inversion pulses with low RF power factor was studied. Furthermore it was shown that broad-band phase-modulated inversion and universal rotational pulses can be constructed by means of global optimization procedures like the genetic algorithms under regardment of the available RF field strength. By inversion, universal rotational, and 360 pulses as starting values of the optimization efficient homonuclear CN{sub n}{sup {nu}} and RN{sub n}{sup {nu}} mixing sequences as well as heteronuclear RN{sub n}{sup {nu}{sub s},{nu}{sub k}} feedback sequences were generated. The satisfactory power of the numerically optimized sequences was shown by means of the simulation as well by means of correlation experiments of the chemical shift of L-histidine, L-arginine, and the (CUG){sub 97}-RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN{sub n}{sup {nu}{sub s},{nu}{sub k}} pulse sequences both {sup 15}N-{sup 13}C and {sup 13}C-{sup 15}N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D-{sup 15}N-{sup 13}C-{sup 13}C and {sup 13}C-{sup 15}N-({sup 1}H)-{sup 1}H correlation spectra is possible. By this in only one measurement process resonance assignments can be met and studies of the global folding performed. A further application of several receivers is the simultaneous acquisition of CHHC, NHHN, NHHC, as well as CHHN spectra. By such experiments it is possible to characterize the hydrogen-bonding pattern and the glycosidic torsion angle {sup {chi}} in RNA. This was demonstrated by means of the (CUG){sub 97

  13. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2010-09-15

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and {sup 13}C{sup {beta}} chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and {sup 13}C{sup {beta}} atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for {delta}{sup 15}N, {delta}{sup 13}C', {delta}{sup 13}C{sup {alpha}}, {delta}{sup 13}C{sup {beta}}, {delta}{sup 1}H{sup {alpha}} and {delta}{sup 1}H{sup N}, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

  14. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2010-01-01

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13 C β chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and 13 C β atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ 15 N, δ 13 C', δ 13 C α , δ 13 C β , δ 1 H α and δ 1 H N , respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

  15. Quantitative chemical shift-encoded MRI is an accurate method to quantify hepatic steatosis.

    Science.gov (United States)

    Kühn, Jens-Peter; Hernando, Diego; Mensel, Birger; Krüger, Paul C; Ittermann, Till; Mayerle, Julia; Hosten, Norbert; Reeder, Scott B

    2014-06-01

    To compare the accuracy of liver fat quantification using a three-echo chemical shift-encoded magnetic resonance imaging (MRI) technique without and with correction for confounders with spectroscopy (MRS) as the reference standard. Fifty patients (23 women, mean age 56.6 ± 13.2 years) with fatty liver disease were enrolled. Patients underwent T2-corrected single-voxel MRS and a three-echo chemical shift-encoded gradient echo (GRE) sequence at 3.0T. MRI fat fraction (FF) was calculated without and with T2* and T1 correction and multispectral modeling of fat and compared with MRS-FF using linear regression. The spectroscopic range of liver fat was 0.11%-38.7%. Excellent correlation between MRS-FF and MRI-FF was observed when using T2* correction (R(2)  = 0.96). With use of T2* correction alone, the slope was significantly different from 1 (1.16 ± 0.03, P fat were addressed, the results showed equivalence between fat quantification using MRI and MRS (slope: 1.02 ± 0.03, P = 0.528; intercept: 0.26% ± 0.46%, P = 0.572). Complex three-echo chemical shift-encoded MRI is equivalent to MRS for quantifying liver fat, but only with correction for T2* decay and T1 recovery and use of spectral modeling of fat. This is necessary because T2* decay, T1 recovery, and multispectral complexity of fat are processes which may otherwise bias the measurements. Copyright © 2013 Wiley Periodicals, Inc.

  16. Study of chemical shifts of the chloroform complexes with cyclic donors of electrons

    International Nuclear Information System (INIS)

    Blaszkiewicz, B.; Pajak, Z.

    1973-01-01

    Chemical shifts of chloroform complexes with the heterocyclic electron donors: pyridine, piperidine, alpha-picoline and gamma-picoline have been studied using the high resolution (5.10 -9 ) spectrometer operating at 80 MHz. An attempt has also been made to study the three - component solutions of : chloroform, a heterocyclic donor of electrons and carbon tetrachloride. The results, which have been obtained, indicate that the complex-forming power of pyridine and other electron donors is greater in carbon tetrachloride than in other solvents. (S.B.)

  17. Isomer shifts and chemical bonding in crystalline Sn(II) and Sn(IV) compounds

    International Nuclear Information System (INIS)

    Terra, J.; Guenzburger, D.

    1991-01-01

    First-principles self-consistent Local Density calculations of the electronic structure of clusters representing Sn(II) (SnO, SnF 2 , SnS, SnSe) and Sn(IV) (SnO 2 , SnF 4 ) crystalline compounds were performed. Values of the electron density at the Sn nucleus were obtained and related to measured values of the Moessbauer Isomer Shifts reported in the literature. The nuclear parameter of 119 Sn derived was ΔR/R=(1.58±0.14)x10 -4 . The chemical bonding in the solids was analysed and related to the electron densities obtained. (author)

  18. Performance test of multicomponent quantum mechanical calculation with polarizable continuum model for proton chemical shift.

    Science.gov (United States)

    Kanematsu, Yusuke; Tachikawa, Masanori

    2015-05-21

    Multicomponent quantum mechanical (MC_QM) calculations with polarizable continuum model (PCM) have been tested against liquid (1)H NMR chemical shifts for a test set of 80 molecules. Improvement from conventional quantum mechanical calculations was achieved for MC_QM calculations. The advantage of the multicomponent scheme could be attributed to the geometrical change from the equilibrium geometry by the incorporation of the hydrogen nuclear quantum effect, while that of PCM can be attributed to the change of the electronic structure according to the polarization by solvent effects.

  19. Parameter-free calculation of K alpha chemical shifts for Al, Si, and Ge oxides

    DEFF Research Database (Denmark)

    Lægsgaard, Jesper

    2001-01-01

    The chemical shifts of the K alpha radiation line from Al, Si, and Ge ions between their elemental and oxide forms are calculated within the framework of density functional theory using ultrasoft pseudopotentials. It is demonstrated that this theoretical approach yields quantitatively accurate...... results fur the systems investigated, provided that relaxations of the valence electrons upon the core-hole transition are properly accounted for. Therefore, such calculations provide a powerful tool for identification of impurity states based on x-ray fluorescence data. Results for an Al impurity...

  20. Combined echo offset (Dixon) and line volume chemical shift imaging as a clinical imaging protocol

    International Nuclear Information System (INIS)

    Listerud, J.; Chan, T.; Lenkinski, R.E.; Kressel, H.Y.; Chao, P.W.

    1989-01-01

    The authors have studied the sensitivity and specificity of the line-volume chemical-shift imaging (CSI) method as compared with the Dixon method they have recently implemented on a Signa, which supports a variety of options. Potential sources or error for the Dixon method include line broadening due to susceptibility, field inhomogeneity, and errors form olefinic resonances associated with fat, which behave like water in the Dixon regime. The authors investigate whether a combined Dixon/line-volume CSI method could be used to improve the placement of the line volume and to provide higher sensitivity and specificity than does the Dixon method alone

  1. Calculation of NMR chemical shifts. 7. Gauge-invariant INDO method

    Science.gov (United States)

    Fukui, H.; Miura, K.; Hirai, A.

    A gauge-invariant INDO method based on the coupled Hartree-Fuck perturbation theory is presented and applied to the calculation of 1H and 13C chemical shifts of hydrocarbons including ring compounds. Invariance of the diamagnetic and paramagnetic shieldings with respect to displacement of the coordinate origin is discussed. Comparison between calculated and experimental results exhibits fairly good agreement, provided that the INDO parameters of Ellis et al. (J. Am. Chem. Soc.94, 4069 (1972)) are used with the inclusion of all multicenter one-electron integrals.

  2. Determination of hydration numbers of electrolytes from temperature dependence of PMR chemical shifts

    International Nuclear Information System (INIS)

    Subramanian, N.

    1979-01-01

    The method proposed by Malinowski et al. for the determination of effective hydration numbers (h) of electrolytes leads to a consistent incrrease in the observed values of 'h' with increase in solution concentration. An attempt is made to rationalize the experimental results by cosidering the simultaneous effects of temperature and concentration on the proton chemical shift. It is suggested that Malinowski's technique might yeld 'h' values very close to the true value for those ions for which there is a fortuitous cancellation of structure-making and structure-breaking properties. (Author) [pt

  3. Higher Franz-Reidemeister torsion

    CERN Document Server

    Igusa, Kiyoshi

    2002-01-01

    The book is devoted to the theory of topological higher Franz-Reidemeister torsion in K-theory. The author defines the higher Franz-Reidemeister torsion based on Volodin's K-theory and Borel's regulator map. He describes its properties and generalizations and studies the relation between the higher Franz-Reidemeister torsion and other torsions used in K-theory: Whitehead torsion and Ray-Singer torsion. He also presents methods of computing higher Franz-Reidemeister torsion, illustrates them with numerous examples, and describes various applications of higher Franz-Reidemeister torsion, particularly for the study of homology of mapping class groups. Packed with up-to-date information, the book provides a unique research and reference tool for specialists working in algebraic topology and K-theory.

  4. Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging

    DEFF Research Database (Denmark)

    Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A

    2000-01-01

    Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations co...

  5. Gallbladder torsion. Case report

    DEFF Research Database (Denmark)

    Brasso, K; Rasmussen, O V

    1991-01-01

    Gallbladder torsion is a rare surgical emergency occurring primarily in elderly women. The anatomical background is a variation in the attachment of the gallbladder to the inferior margin of the liver. Increasing life span will probably lead to an increasing number of cases, and gallbladder torsion...... must be kept in mind in patients with sudden onset of pain in the upper right quadrant, nausea, vomiting, and a palpable mass. None of the laboratory routines or non-invasive examinations enables one to make the right preoperative diagnosis. Treatment is cholecystectomy. Promptly treated, the prognosis...

  6. Torsional heterotic geometries

    International Nuclear Information System (INIS)

    Becker, Katrin; Sethi, Savdeep

    2009-01-01

    We construct new examples of torsional heterotic backgrounds using duality with orientifold flux compactifications. We explain how duality provides a perturbative solution to the type I/heterotic string Bianchi identity. The choice of connection used in the Bianchi identity plays an important role in the construction. We propose the existence of a much larger landscape of compact torsional geometries using string duality. Finally, we present some quantum exact metrics that correspond to NS5-branes placed on an elliptic space. These metrics describe how torus isometries are broken by NS flux.

  7. Physical basis of the effect of hemoglobin on the 31P NMR chemical shifts of various phosphoryl compounds

    International Nuclear Information System (INIS)

    Kirk, K.; Kuchel, P.W.

    1988-01-01

    The marked difference between the intra- and extracellular 31 P NMR chemical shifts of various phosphoryl compounds when added to a red cell suspension may be largely understood in terms of the effects of hemoglobin on the 31 P NMR chemical shifts. The presence of [oxy- or (carbonmonoxy)-] hemoglobin inside the red cell causes the bulk magnetic susceptibility of the cell cytoplasm to be significantly less than that of the external solution. This difference is sufficient to account for the difference in the intra- and extracellular chemical shifts of the two phosphate esters trimethyl phosphate and triethyl phosphate. However, in the case of the compounds dimethyl methylphosphonate, diethyl methylphosphonate, and trimethylphosphine oxide as well as the hypophosphite, phenylphosphinate, and diphenylphosphinate ions, hemoglobin exerts an additional, much larger, effect, causing the 31 P NMR resonances to shift to lower frequency in a manner that cannot be accounted for in terms of magnetic susceptibility. Lysozyme is a protein structurally unrelated to hemoglobin and was shown to cause similar shifts to lower frequency of the resonances of these six compounds; this suggests that the mechanism may involve a property of proteins in general and not a specific property of hemoglobin. The effect of different solvents on the chemical shifts of the eight phosphoryl compounds provided an insight into the possible physical basis of the effect. It is proposed that, in addition to magnetic susceptibility effects, hemoglobin exerts its influence on phosphoryl chemical shifts by disrupting the hydrogen bonding of the phosphoryl group to solvent water

  8. Solvation effects on chemical shifts by embedded cluster integral equation theory.

    Science.gov (United States)

    Frach, Roland; Kast, Stefan M

    2014-12-11

    The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

  9. Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: 1H and 13C chemical shift assignments

    International Nuclear Information System (INIS)

    Facundo, Valdir A.; Morais, Selene M.; Braz Filho, Raimundo

    2004-01-01

    In an ethanolic extract of leaves of Ottonia corcovadensis (Piperaceae) were identified sixteen terpenoids of essential oil and the three flavonoids 3',4',5,5',7-penta methoxyflavone (1), 3',4',5,7-tetra methoxyflavone (2) and 5-hydroxy-3',4',5',7-tetra methoxyflavone (3) and cafeic acid (4). Two amides (5 and 6) were isolated from an ethanolic extract of the roots. The structures were established by spectral analysis, meanly NMR (1D and 2D) and mass spectra. Extensive NMR analysis was also used to complete 1 H and 13 C chemical shift assignments of the flavonoids and amides. The components of the essential oil were identified by computer library search, retention indices and visual interpretation of mass spectra. (author)

  10. Criteria to average out the chemical shift anisotropy in solid-state NMR when irradiated with BABA I, BABA II, and C7 radiofrequency pulse sequences.

    Science.gov (United States)

    Stephane Mananga, Eugene

    2013-01-01

    Floquet-Magnus expansion is used to study the effect of chemical shift anisotropy in solid-state NMR of rotating solids. The chemical shift interaction is irradiated with two types of radiofrequency pulse sequences: BABA and C7. The criteria for the chemical shift anisotropy to be averaged out in each rotor period are obtained. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Torsion in superstrings

    International Nuclear Information System (INIS)

    Bars, I.; Nemeschansky, D.; Yankielowicz, S.

    1986-01-01

    In this paper the authors discuss string theories on a background manifold with torsion. In the first part, candidate vacuum configurations for ten-dimensional superstrings are discussed. The authors compactify these on M/sub 4/xK, where M/sub 4/ is four-dimensional and K some compact six-dimensional manifold. In particular they are interested in investigating the existence of solutions with non-zero torsion on K. The compactification problem is approached both from the effective field theory point of view and directly using string considerations. The second part of the talk is devoted to the construction of string theories in curved space with torsion. The authors discuss both the Neveu-Schwarz-Ramond type string and the Green-Schwarz type string. Particular emphasis is put on the resulting constraints on space-time supersymmetry in the Green-Schwarz approach. This study uses two-dimensional non-linear sigma models to describe the propagation of strings in background geometries with torsion. The background field can be understood as arising from condensation of infinite number of strings

  12. Torsion induces gravity

    International Nuclear Information System (INIS)

    Aros, Rodrigo; Contreras, Mauricio

    2006-01-01

    In this work the Poincare-Chern-Simons and anti-de Sitter-Chern-Simons gravities are studied. For both, a solution that can be cast as a black hole with manifest torsion is found. Those solutions resemble Schwarzschild and Schwarzschild-AdS solutions, respectively

  13. Testicular torsion repair

    Science.gov (United States)

    ... the Procedure is Performed Testicular torsion is an emergency. In most cases, surgery is needed right away to relieve pain ... RM, Hockberger RS, Gausche-Hill M, eds. Rosen's Emergency Medicine: Concepts and Clinical Practice . 9th ed. Philadelphia, PA: Elsevier; 2018:chap ...

  14. Tibiotalar torsion: bioengineering paradigm.

    Science.gov (United States)

    Michele, A A; Nielsen, P M

    1976-10-01

    1. Medial tibiotalar torsion is the most common disorder peculiar to mankind. 2. The pathogonomic findings are (a) an axial medially rotated and adducted distal third of the shaft of the tibia, (b) the plafond of the tibia with its mortise containing the "track-bound" talus, which is deflected strongly toward the tibial side, (c) an exaggerated midtarsal equinus, (d) ostensible restriction of dorsiflexion of the hindfoot against the tibia, (e) mild separation of the distal tibiofibular articulation, and (f) forward displacement of the gravitational axis to the naviculocunei-form joint. 3. Faulty leg crossing in utero resulting in an abnormal pelvofemoral-tibial design is discussed and its important consequences in the vulnerable 40 per cent of the population are emphasized. 4. The kinesiomechanics of the leg, ankle and foot is reviewed. 5. The radiographic parameters of medial tibiotalar torsion are presented, as well as the multiple facets of the clinical examination. 6. Methods of treatment depending on age and severity of the disorder are recommended. Surgery, detortional casts, and corrective footwear are discussed. Shoes presently available are inadequate for tibiotalar torsion and therefore engineering principles must be applied in the design and construction of all footwear, including sneakers and sportswear. This can be done only if the pathological biomechanics of this group of disorders is recognized. Biplane proximal tibial osteotomy is recommended in refractory cases, especially when tibiotalar torsion is demonstrated. 7. After 30 years of experience, the author finds that results with these patients have been uniformly good to excellent, depending on age and mode of treatment. 8. In medial tibiotalar torsion, the consequent adaptive changes are readily observed, but rarely are they recognized as the inevitable sequelae of medial tibiotalar torsion. 9. Adaptive compensating disorders are identified and their mechanism described. 10. The management of

  15. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

    Science.gov (United States)

    Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

    2015-01-01

    An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

  16. Experimental investigation of torsional vibration isolation using Magneto Rheological Elastomer

    Directory of Open Access Journals (Sweden)

    Praveen Shenoy K

    2018-01-01

    Full Text Available Rotating systems suffer from lateral and torsional vibrations which have detrimental effect on the roto-dynamic performance. Many available technologies such as vibration isolators and vibration absorbers deal with the torsional vibrations to a certain extent, however passive isolators and absorbers find less application when the input conditions are dynamic. The present work discusses use of a smart material called as Magneto Rheological Elastomer (MRE, whose properties can be changed based on magnetic field input, as a potential isolator for torsional vibrations under dynamic loading conditions. Carbonyl Iron Particles (CIP of average size 5 μm were mixed with RTV Silicone rubber to form the MRE. The effect of magnetic field on the system parameters was comprehended under impulse loading conditions using a custom built in-house system. Series arrangement of accelerometers were used to differentiate between the torsional and the bending modes of vibration of the system. Impact hammer tests were carried out on the torsional system to study its response, in the presence and absence of magnetic field. The tests revealed a shift in torsional frequency in the presence of magnetic field which elucidates the ability of MRE to work as a potential vibration isolator for torsional systems.

  17. The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

    2011-01-01

    and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

  18. Improvement of chemical shift selective saturation (CHESS) pulse for MR angiography

    International Nuclear Information System (INIS)

    Ishimori, Yoshiyuki; Sashie, Hiroyuki; Hiraga, Akira; Matsuda, Tsuyoshi

    2000-01-01

    We improved the fat suppression technique based on chemical shift selective saturation (CHESS). To do this, we shortened the duration of the CHESS pulse to achieve a short repetition time (TR) for MR angiography (MRA). A short-duration CHESS pulse causes broad frequency band saturation, creating extensive offset from the resonance frequency of water. In our phantom experiment, the best parameters of the short-duration CHESS pulse were 3.84 ms in duration, -650 Hz in offset frequency from water resonance, and had a 130-degree flip angle. With this technique, MRA will be able to be carried out without a significant increase in TR. Thus, better vessel contrast will be maintained in time-of-flight (TOF) MRA or contrast-enhanced MRA when using the maximum intensity projection (MIP) method. (author)

  19. Chemical shift assignments of the partially deuterated Fyn SH2-SH3 domain.

    Science.gov (United States)

    Kieken, Fabien; Loth, Karine; van Nuland, Nico; Tompa, Peter; Lenaerts, Tom

    2018-04-01

    Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1 H, 15 N and 13 C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.

  20. Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

    Science.gov (United States)

    Hanni, Matti; Lantto, Perttu; Vaara, Juha

    2011-08-14

    Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

  1. On the Confounding Effect of Temperature on Chemical Shift-Encoded Fat Quantification

    Science.gov (United States)

    Hernando, Diego; Sharma, Samir D.; Kramer, Harald; Reeder, Scott B.

    2014-01-01

    Purpose To characterize the confounding effect of temperature on chemical shift-encoded (CSE) fat quantification. Methods The proton resonance frequency of water, unlike triglycerides, depends on temperature. This leads to a temperature dependence of the spectral models of fat (relative to water) that are commonly used by CSE-MRI methods. Simulation analysis was performed for 1.5 Tesla CSE fat–water signals at various temperatures and echo time combinations. Oil–water phantoms were constructed and scanned at temperatures between 0 and 40°C using spectroscopy and CSE imaging at three echo time combinations. An explanted human liver, rejected for transplantation due to steatosis, was scanned using spectroscopy and CSE imaging. Fat–water reconstructions were performed using four different techniques: magnitude and complex fitting, with standard or temperature-corrected signal modeling. Results In all experiments, magnitude fitting with standard signal modeling resulted in large fat quantification errors. Errors were largest for echo time combinations near TEinit ≈ 1.3 ms, ΔTE ≈ 2.2 ms. Errors in fat quantification caused by temperature-related frequency shifts were smaller with complex fitting, and were avoided using a temperature-corrected signal model. Conclusion Temperature is a confounding factor for fat quantification. If not accounted for, it can result in large errors in fat quantifications in phantom and ex vivo acquisitions. PMID:24123362

  2. Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations

    Energy Technology Data Exchange (ETDEWEB)

    Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

    2012-06-15

    NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from {approx}2 {mu}M to {approx}1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K{sub D}) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K{sub D}, and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K{sub D} and the maximum chemical shift change ({Delta}{delta}{sub max}). During a typical NMR titration, the initial protein concentration, [P{sub 0}], is held nearly constant. For this condition, to determine the most accurate parameters for K{sub D} and {Delta}{delta}{sub max} from nonlinear least squares analyses requires initial protein concentrations that are {approx}0.5 Multiplication-Sign K{sub D}, and a maximum concentration for the ligand, or titrant, of {approx}10 Multiplication-Sign [P{sub 0}]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K{sub D} and {Delta}{delta}{sub max} values when [P{sub 0}] > K{sub D}. Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K{sub D} and {Delta}{delta}{sub max}) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.

  3. The contribution of chemical shift imaging with digital subtracting images to the diagnosis of steatohepatitis

    International Nuclear Information System (INIS)

    Guo Xinghua; Wang Juanping; Zhang Chongjie; Zheng Guofang; Fan Ruiqiang; Zhu Sumei; Liu Qiwang

    2006-01-01

    Objective: To investigate the diagnosis value of chemical shift imaging with digital subtracting in steatohepatitis. Methods: The in-phase images were subtracted by the out-phase ones in 34 cases of steatohepatitis, and the CNR were measured on these subtracted images to estimate the steatosis of the liver. The relationship of CT grade of steatohepatitis and CNR from the subtracted images was analyzed to evaluate the relationship between CNR and the degree of hepatic steatosis. The sensitivity and specificity of the subtracting and eyeballing methods were compared with chi-square test. Results: On the subtracted images, the liver and spleen were seen nearly the same aspects as low signals, CNR=0.98±0.06, meanwhile the spongy vertebra and the subcutaneous or abdominal lipid were seen as obvious higher signals in 52 normal cases. On the 34 steatohepatitis, scattered high signals were seen in the liver, which made the signal of liver higher than that of spleen, CNR=3.25±0.91--14.35±6.10. There was positive correlation between CNR and CT grade in the 34 cases of steatohepatitis, r=0.893, P<0.01. The sensitivity and specificity of the subtracting method were 88.24% and 94. 23%, significantly higher than that of the eyeballing results, 32.35% and 80.77%, P<0.01 and P<0.05. Conclusion: Chemical shift imaging with digital subtracting is a sensitive, specific, objective method to diagnose steatohepatitis and it is of potential ability for quantitative diagnosis. (authors)

  4. Clinical application of 1H-chemical-shift imaging (CSI) to brain diseases

    International Nuclear Information System (INIS)

    Naruse, Shoji; Furuya, Seiichi; Ide, Mariko

    1992-01-01

    An H-1 chemical shift imaging (CSI) was developed as part of the clinical MRI system, by which magnetic resonance spectra (MRS) can be obtained from multiple small voxels and metabolite distribution in the brain can be visualized. The present study was to determine the feasibility and clinical potential of using an H-1 CSI. The device used was a Magnetom H 15 apparatus. The study population was comprised of 25 healthy subjects, 20 patients with brain tumor, 4 with ischemic disease, and 6 with miscellaneous degenerative disease. The H-1 CSI was obtained by the 3-dimensional Fourier transformation. After suppressing the lipid signal by the inversion-recovery method and the water signal by the chemical-shift selective pulse with a following dephasing gradient, 2-directional 16 x 16 phase encodings were applied to the 16 x 16∼18 x 18 cm field of view, in which a 8 x 8 x 2∼10 x 10 x 2 cm area was selected by the stimulated echo or spin-echo method. The metabolite mapping and its contour mapping were created by using the curve-fitted area, with interpolation to the 256 x 256 matrix. In the healthy group, high resolution spectra for N-acetyl aspartate (NAA), creatine, choline (Cho), and glutamine/glutamate were obtained from each voxel; and metabolite mapping and contour mapping also clearly showed metabolite distribution in the brain. In the group of brain tumor, an increased Cho and lactate and loss of NAA were observed, along with heterogeneity within the tumor and changes in the surrounding tissue; and there was a good correlation between lactate peak and tumor malignancy. The group of ischemic and degenerative disease had a decreased NAA and increased lactate on both spectra and metabolite mapping, depending on disease stage. These findings indicated that H-1 CSI is helpful for detecting spectra over the whole brain, as well as for determining metabolite distribution. (N.K.)

  5. Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

    Science.gov (United States)

    Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

    2014-01-14

    The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

  6. Binding energies and chemical shifts of least bound core electron excitations in cubic Asub(N)Bsub(8-N) semiconductors

    International Nuclear Information System (INIS)

    Bechstedt, F.; Enderlein, R.; Wischnewski, R.

    1981-01-01

    Core electron binding energies Esup(B) with respect to the vacuum level and their chemical shifts are calculated for the least bound core levels of cations and anions of cubic Asub(N)Bsub(8-N) semiconductors. Starting from the HF-binding energy of the free atom absolute values of Esup(B) are obtained by adding core level shifts and relaxation energies. Core level shifts are calculated by means of an electrostatic model with ionic and bond charges according to Phillips' bond charge model. For the calculation of relaxation energies the linear dielectric theory of electronic polarization is applied. Valence and core electrons, and diagonal and non-diagonal screening are taken into account. The theoretical results for chemical shifts of binding energies are compared with experimental values from XPS-measurements corrected by work function data. Good agreement is obtained in all cases within the error limit of about one eV. Chemical and atomic trends of core level shifts, relaxation energies, and binding energies are discussed in terms of changes of atomic and solid state parameters. Chemical shifts and relaxation energies are predicted for various ternary Asub(N)Bsub(8-N) compounds. (author)

  7. Resolution of torsional vibration issue for large turbine generators

    International Nuclear Information System (INIS)

    Evans, D.G.; Giesecke, H.D.; Willman, E.C.; Moffitt, S.P.

    1995-01-01

    The excitation of turbine generator torsional natural frequencies in the region near 120 Hz by electrical transients in the power system has resulted in blade failures for several large 1,800 rpm nuclear turbines. At Cleveland Electric's Perry Nuclear Power plant a combination of advanced measurement techniques and analyses were used to identify and resolve a potential torsional vibration problem without adverse impact on the plant availability. The Perry turbine generator consists of a high pressure turbine, three low pressure turbines with 43 inch last stage blades, and a 1,250 MWe four pole generator operating at 1,800 rpm. Torsional vibration measurements obtained from random vibration during operation were acquired just prior to the 1994 refueling outage. The measurements indicated that the 26th torsional mode of vibration was just under 120 Hz and within the range of frequencies for which the manufacturer recommends modifying the unit to shift the problem torsional natural frequency. Extensive analytical modeling was used to design a modification to shift the torsional natural frequencies away from 120 Hertz and the modification was implemented during the refueling outage without affecting outage critical path. An off-line ramp test and additional on-line monitoring performed at the conclusion of the outage confirmed that the on-line method provided accurate measurements of the torsional natural frequencies and demonstrated that, with the modification, the torsional natural frequencies were sufficiently removed from 120 Hertz to allow turbine generator operation. The modification, which involved brazing of the tie wires on all last stage blades, also significantly reduces the stress on the last stage blades that result from negative sequence currents, further increasing the operating margin of the turbine generator with respect to electrical transients and faults

  8. Fragment-based {sup 13}C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, Joshua D.; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu [Department of Chemistry, University of California, Riverside, California 92521 (United States); Monaco, Stephen; Schatschneider, Bohdan [The Pennsylvania State University, The Eberly Campus, 2201 University Dr, Lemont Furnace, Pennsylvania 15456 (United States)

    2015-09-14

    We assess the quality of fragment-based ab initio isotropic {sup 13}C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic {sup 13}C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits.

  9. Spin-echo based diagonal peak suppression in solid-state MAS NMR homonuclear chemical shift correlation spectra

    Science.gov (United States)

    Wang, Kaiyu; Zhang, Zhiyong; Ding, Xiaoyan; Tian, Fang; Huang, Yuqing; Chen, Zhong; Fu, Riqiang

    2018-02-01

    The feasibility of using the spin-echo based diagonal peak suppression method in solid-state MAS NMR homonuclear chemical shift correlation experiments is demonstrated. A complete phase cycling is designed in such a way that in the indirect dimension only the spin diffused signals are evolved, while all signals not involved in polarization transfer are refocused for cancellation. A data processing procedure is further introduced to reconstruct this acquired spectrum into a conventional two-dimensional homonuclear chemical shift correlation spectrum. A uniformly 13C, 15N labeled Fmoc-valine sample and the transmembrane domain of a human protein, LR11 (sorLA), in native Escherichia coli membranes have been used to illustrate the capability of the proposed method in comparison with standard 13C-13C chemical shift correlation experiments.

  10. Quantum-Chemical Approach to NMR Chemical Shifts in Paramagnetic Solids Applied to LiFePO4 and LiCoPO4.

    Science.gov (United States)

    Mondal, Arobendo; Kaupp, Martin

    2018-04-05

    A novel protocol to compute and analyze NMR chemical shifts for extended paramagnetic solids, accounting comprehensively for Fermi-contact (FC), pseudocontact (PC), and orbital shifts, is reported and applied to the important lithium ion battery cathode materials LiFePO 4 and LiCoPO 4 . Using an EPR-parameter-based ansatz, the approach combines periodic (hybrid) DFT computation of hyperfine and orbital-shielding tensors with an incremental cluster model for g- and zero-field-splitting (ZFS) D-tensors. The cluster model allows the use of advanced multireference wave function methods (such as CASSCF or NEVPT2). Application of this protocol shows that the 7 Li shifts in the high-voltage cathode material LiCoPO 4 are dominated by spin-orbit-induced PC contributions, in contrast with previous assumptions, fundamentally changing interpretations of the shifts in terms of covalency. PC contributions are smaller for the 7 Li shifts of the related LiFePO 4 , where FC and orbital shifts dominate. The 31 P shifts of both materials finally are almost pure FC shifts. Nevertheless, large ZFS contributions can give rise to non-Curie temperature dependences for both 7 Li and 31 P shifts.

  11. Experimental and DFT evaluation of the 1H and 13C NMR chemical shifts for calix[4]arenes

    Science.gov (United States)

    Guzzo, Rodrigo N.; Rezende, Michelle Jakeline Cunha; Kartnaller, Vinicius; Carneiro, José Walkimar de M.; Stoyanov, Stanislav R.; Costa, Leonardo Moreira da

    2018-04-01

    The density functional theory is employed to determine the efficiency of 11 exchange-correlation (XC) functionals to compute the 1H and 13C NMR chemical shifts of p-tert-butylcalix[4]arene (ptcx4, R1 = C(CH3)3) and congeners using the 6-31G(d,p) basis set. The statistical analysis shows that B3LYP, B3PW91 and PBE1PBE are the best XC functionals for the calculation of 1H chemical shifts. Moreover, the best results for the 13C chemical shifts are obtained using the LC-WPBE, M06-2X and wB97X-D functionals. The performance of these XC functionals is tested for three other calix[4]arenes: p-sulfonic acid calix[4]arene (sfxcx4 - R1 = SO3H), p-nitro-calix[4]arene (ncx4, R1 = NO2) and calix[4]arene (cx4 - R1 = H). For 1H chemical shifts B3LYP, B3PW91 and PBE1PBE yield similar results, although B3PW91 shows more consistency in the calculated error for the different structures. For 13C NMR chemical shifts, the XC functional that stood out as best is LC-WPBE. Indeed, the three functionals selected for each of 1H and 13C show good accuracy and can be used in future studies involving the prediction of 1H and 13C chemical shifts for this type of compounds.

  12. Shifts in Plant Chemical Defenses of Chile Pepper (Capsicum annuum L. Due to Domestication in Mesoamerica

    Directory of Open Access Journals (Sweden)

    Jose de Jesus Luna-Ruiz

    2018-04-01

    Full Text Available We propose that comparisons of wild and domesticated Capsicum species can serve as a model system for elucidating how crop domestication influences biotic and abiotic interactions mediated by plant chemical defenses. Perhaps no set of secondary metabolites (SMs used for plant defenses and human health have been better studied in the wild and in milpa agro-habitats than those found in Capsicum species. However, very few scientific studies on SM variation have been conducted in both the domesticated landraces of chile peppers and in their wild relatives in the Neotropics. In particular, capsaicinoids in Capsicum fruits and on their seeds differ in the specificity of their ecological effects from broad-spectrum toxins in other members of the Solanaceae. They do so in a manner that mediates specific ecological interactions with a variety of sympatric Neotropical vertebrates, invertebrates, nurse plants and microbes. Specifically, capsaicin is a secondary metabolite (SM in the placental tissues of the chile fruit that mediates interactions with seed dispersers such as birds, and with seed predators, ranging from fungi to insects and rodents. As with other Solanaceae, a wide range of SMs in Capsicum spp. function to ecologically mediate the effects of a variety of biotic and abiotic stresses on wild chile peppers in certain tropical and subtropical habitats. However, species in the genus Capsicum are the only ones found within any solanaceous genus that utilize capsaicinoids as their primary means of chemical defense. We demonstrate how exploring in tandem the evolutionary ecology and the ethnobotany of human-chile interactions can generate and test novel hypotheses with regard to how the domestication process shifts plant chemical defense strategies in a variety of tropical crops. To do so, we draw upon recent advances regarding the chemical ecology of a number of wild Capsicum species found in the Neotropics. We articulate three hypotheses regarding

  13. Multiparametric fat-water separation method for fast chemical-shift imaging guidance of thermal therapies.

    Science.gov (United States)

    Lin, Jonathan S; Hwang, Ken-Pin; Jackson, Edward F; Hazle, John D; Stafford, R Jason; Taylor, Brian A

    2013-10-01

    A k-means-based classification algorithm is investigated to assess suitability for rapidly separating and classifying fat/water spectral peaks from a fast chemical shift imaging technique for magnetic resonance temperature imaging. Algorithm testing is performed in simulated mathematical phantoms and agar gel phantoms containing mixed fat/water regions. Proton resonance frequencies (PRFs), apparent spin-spin relaxation (T2*) times, and T1-weighted (T1-W) amplitude values were calculated for each voxel using a single-peak autoregressive moving average (ARMA) signal model. These parameters were then used as criteria for k-means sorting, with the results used to determine PRF ranges of each chemical species cluster for further classification. To detect the presence of secondary chemical species, spectral parameters were recalculated when needed using a two-peak ARMA signal model during the subsequent classification steps. Mathematical phantom simulations involved the modulation of signal-to-noise ratios (SNR), maximum PRF shift (MPS) values, analysis window sizes, and frequency expansion factor sizes in order to characterize the algorithm performance across a variety of conditions. In agar, images were collected on a 1.5T clinical MR scanner using acquisition parameters close to simulation, and algorithm performance was assessed by comparing classification results to manually segmented maps of the fat/water regions. Performance was characterized quantitatively using the Dice Similarity Coefficient (DSC), sensitivity, and specificity. The simulated mathematical phantom experiments demonstrated good fat/water separation depending on conditions, specifically high SNR, moderate MPS value, small analysis window size, and low but nonzero frequency expansion factor size. Physical phantom results demonstrated good identification for both water (0.997 ± 0.001, 0.999 ± 0.001, and 0.986 ± 0.001 for DSC, sensitivity, and specificity, respectively) and fat (0.763 ± 0.006, 0

  14. The 40th anniversary of the discovery of NMR-chemical shift and nuclear spin-spin coupling

    International Nuclear Information System (INIS)

    Zhu Zhenghe; Gou Qingquan

    1989-01-01

    After the discovery of NMR Phenomenon in the physics laboratories of E.M.Purcell at Harvard and F.Bloch at Stanford in 1946, W.G.Proctor and F.C.Yu made the successful discovery of NMR-chemical shift and nuclear spin-spin coupling at Stanford in 1950, Which brought NMR spectroscopy from the physics laboratory to the laboratories of many different fields. This is worth memorizing. Retrospecting the past 40 years, it is sure that chemical shift theory will be much more prosperous prospects

  15. Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics.

    Science.gov (United States)

    Klukowski, Piotr; Schubert, Mario

    2018-06-15

    A better understanding of oligosaccharides and their wide-ranging functions in almost every aspect of biology and medicine promises to uncover hidden layers of biology and will support the development of better therapies. Elucidating the chemical structure of an unknown oligosaccharide is still a challenge. Efficient tools are required for non-targeted glycomics. Chemical shifts are a rich source of information about the topology and configuration of biomolecules, whose potential is however not fully explored for oligosaccharides. We hypothesize that the chemical shifts of each monosaccharide are unique for each saccharide type with a certain linkage pattern, so that correlated data measured by NMR spectroscopy can be used to identify the chemical nature of a carbohydrate. We present here an efficient search algorithm, GlycoNMRSearch, that matches either a subset or the entire set of chemical shifts of an unidentified monosaccharide spin system to all spin systems in an NMR database. The search output is much more precise than earlier search functions and highly similar matches suggest the chemical structure of the spin system within the oligosaccharide. Thus searching for connected chemical shift correlations within all electronically available NMR data of oligosaccharides is a very efficient way of identifying the chemical structure of unknown oligosaccharides. With an improved database in the future, GlycoNMRSearch will be even more efficient deducing chemical structures of oligosaccharides and there is a high chance that it becomes an indispensable technique for glycomics. The search algorithm presented here, together with a graphical user interface, is available at http://glyconmrsearch.santos.pwr.edu.pl. Supplementary data are available at Bioinformatics online.

  16. Stability in quadratic torsion theories

    Energy Technology Data Exchange (ETDEWEB)

    Vasilev, Teodor Borislavov; Cembranos, Jose A.R.; Gigante Valcarcel, Jorge; Martin-Moruno, Prado [Universidad Complutense de Madrid, Departamento de Fisica Teorica I, Madrid (Spain)

    2017-11-15

    We revisit the definition and some of the characteristics of quadratic theories of gravity with torsion. We start from a Lagrangian density quadratic in the curvature and torsion tensors. By assuming that General Relativity should be recovered when the torsion vanishes and investigating the behaviour of the vector and pseudo-vector torsion fields in the weak-gravity regime, we present a set of necessary conditions for the stability of these theories. Moreover, we explicitly obtain the gravitational field equations using the Palatini variational principle with the metricity condition implemented via a Lagrange multiplier. (orig.)

  17. Stability in quadratic torsion theories

    International Nuclear Information System (INIS)

    Vasilev, Teodor Borislavov; Cembranos, Jose A.R.; Gigante Valcarcel, Jorge; Martin-Moruno, Prado

    2017-01-01

    We revisit the definition and some of the characteristics of quadratic theories of gravity with torsion. We start from a Lagrangian density quadratic in the curvature and torsion tensors. By assuming that General Relativity should be recovered when the torsion vanishes and investigating the behaviour of the vector and pseudo-vector torsion fields in the weak-gravity regime, we present a set of necessary conditions for the stability of these theories. Moreover, we explicitly obtain the gravitational field equations using the Palatini variational principle with the metricity condition implemented via a Lagrange multiplier. (orig.)

  18. Orientation-dependent surface core-level shifts and chemical shifts on clean and H 2S-covered GaAs

    Science.gov (United States)

    Ranke, W.; Finster, J.; Kuhr, H. J.

    1987-08-01

    Photoelectron spectra of the As 3d and Ga 3d core levels were studied in situ on a cylindrically shaped GaAs single crystal for the six inequivalent orientations (001), (113), (111), (110), (11¯1) and (11¯3). On the clean surface, prepared by molecular beam epitaxy (MBE), surface core levels are shifted by 0.25 to 0.55 eV towards smaller binding energy (BE) for As 3d and -0.25 to -0.35 eV towards higher BE for Ga, depending on orientation. Additional As causes As 3d contributions shifted between -0.45 and -0.7 eV towards higher BE. The position and intensity of them is influenced by H 2S adsorption. At 150 K, H 2S adsorbs preferentially on As sites. As chemical shifts appear at -0.6 to -0.9 eV towards higher BE. Simultaneously, As accumulation occurs on all orientations with the exception of (110). High temperature adsorption (550 K, 720 K) influences mainly the Ga 3d peaks. Two peaks shifted by about -0.45 and -0.8 eV towards higher Be were found which are attributed to Ga atoms with one or two sulfur ligands, respectively. At 720 K, also As depletion is observed. The compatibility of surface core-level positions and intensities with recent structural models for the (111) and (11¯1) surfaces is discussed.

  19. Atmospheric Peroxy Radical Measurements by Chemical Amplification - Cavity Attenuated Phase Shift Spectroscopy

    Science.gov (United States)

    Wood, E. C.; Charest, J. R.

    2013-12-01

    We present a new chemical amplifier for the detection of peroxy radicals using Cavity Attenuated Phase Shift spectroscopy (CAPS) detection of NO2. The amplification scheme is similar to other chemical amplifiers and involves addition of CO (8%) and NO (3 ppm) to air sampled in a PFA tube. The chain length is quantified by amplification of a known concentration of methyl peroxy radicals (CH3O2) and peroxyacetyl radicals (CH3COO2) sampled by the instrument's reactor. The CH3O2 and CH3COO2 radicals are produced by photolysis of acetone at 254 nm and quantified by conversion to NO2 by reaction with excess NO. The chain length (CL) in dry air is over 200 and constant at RO2 concentrations under 500 ppt. The CL decreases by 55% at a relative humidity of 50%. A 0.95 cm (3/8') ID PFA tube, a 0.32 cm (1/8' ID) PFA tube, and a 0.48 cm ID quartz reactor give near-identical chain lengths and RH dependence, demonstrating the small importance of wall reactions (for clean tubing) as radical termination steps. The instrument comprises two independent inlets and CAPS detectors, allowing for simultaneous measurements in ROx mode (= NO2 + O3 + RO2 + HO2) and Ox mode (= NO2 + O3) thereby greatly reducing the effect of variations in background [Ox]. The 1σ precision of the instrument at constant background [Ox] and 0% relative humidity is 0.2 ppt ROx with 100 second averaging and increases to 0.3 ppt at an RH of 50%. The absolute uncertainty of the measurements is estimated as 20% and is affected by the accuracy of the NO2 calibration, the precision of the CAPS when calibrating at low RO2 concentrations, and the uncertainty in the photolysis quantum yield for the CH3CO + CH3 channel of acetone photolysis.

  20. Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {in-phase and out-of phase} MR imaging

    International Nuclear Information System (INIS)

    Ragab, Yasser; Emad, Yasser; Gheita, Tamer; Mansour, Maged; Abou-Zeid, A.; Ferrari, Serge; Rasker, Johannes J.

    2009-01-01

    Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

  1. Torsional Rigidity of Minimal Submanifolds

    DEFF Research Database (Denmark)

    Markvorsen, Steen; Palmer, Vicente

    2006-01-01

    We prove explicit upper bounds for the torsional rigidity of extrinsic domains of minimal submanifolds $P^m$ in ambient Riemannian manifolds $N^n$ with a pole $p$. The upper bounds are given in terms of the torsional rigidities of corresponding Schwarz symmetrizations of the domains in warped...

  2. A comparison of chemical shift sensitivity of trifluoromethyl tags: optimizing resolution in {sup 19}F NMR studies of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Libin; Larda, Sacha Thierry; Frank Li, Yi Feng [University of Toronto, UTM, Department of Chemistry (Canada); Manglik, Aashish [Stanford University School of Medicine, Department of Molecular and Cellular Physiology (United States); Prosser, R. Scott, E-mail: scott.prosser@utoronto.ca [University of Toronto, UTM, Department of Chemistry (Canada)

    2015-05-15

    The elucidation of distinct protein conformers or states by fluorine ({sup 19}F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the {sup 19}F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:H{sub 2}O = 4) to polar (MeOH:H{sub 2}O = 0.25). {sup 19}F NMR spectra of the tripeptide, glutathione ((2S)-2-amino-4-{[(1R)-1-[(carboxymethyl)carbamoyl] -2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity.

  3. Oophoropexy for Recurrent Ovarian Torsion

    Directory of Open Access Journals (Sweden)

    Jennifer Hartley

    2018-01-01

    Full Text Available A 31-year-old nulliparous patient presents with a three-day history of right sided colicky abdominal pain and associated nausea. This patient has previously presented twice with right sided ovarian torsion with the background of polycystic ovaries in the last two consecutive years. Blood tests were normal. Due to previous history, there was a high index of clinical suspicion that this may be a further torsion. Therefore, the patient was taken to theatre for a diagnostic laparoscopy and a further right sided ovarian torsion was noted. At this time, oophoropexy was performed to the uterosacral ligament to prevent further torsion in order to preserve the patients’ fertility. In this article, we detail this case and also provide a discussion of ovarian torsion including risk factors, presentation, and current thoughts on management.

  4. Torsion testing of bed joints

    DEFF Research Database (Denmark)

    Hansen, Klavs Feilberg; Pedersen, Carsten Mørk

    2008-01-01

    This paper describes a simple test method for determining the torsion strength of a single bed joint between two bricks and presents results from testing using this test method. The setup for the torsion test is well defined, require minimal preparation of the test specimen and the test can...... be carried out directly in a normal testing machine. The torsion strength is believed to be the most important parameter in out-of-plane resistance of masonry walls subjected to bending about an axis perpendicular to the bed joints. The paper also contains a few test results from bending of small walls about...... an axis perpendicular to the bed joints, which indicate the close connection between these results and results from torsion tests. These characteristics make the torsion strength well suited to act as substitute parameter for the bending strength of masonry about an axis perpendicular to the bed joints....

  5. 1H MR chemical shift imaging detection of phenylalanine in patients suffering from phenylketonuria (PKU)

    International Nuclear Information System (INIS)

    Sijens, Paul E.; Oudkerk, Matthijs; Reijngoud, Dirk-Jan; Spronsen, Francjan J. van; Leenders, Klaas L.; Valk, Harold W. de

    2004-01-01

    Short echo time single voxel methods were used in previous MR spectroscopy studies of phenylalanine (Phe) levels in phenylketonuria (PKU) patients. In this study, apparent T 2 relaxation time of the 7.3-ppm Phe multiplet signal in the brain of PKU patients was assessed in order to establish which echo time would be optimal. 1 H chemical shift imaging (CSI) examinations of a transverse plain above the ventricles of the brain were performed in 10 PKU patients and 11 persons not suffering from PKU at 1.5 T, using four echo times (TE 20, 40, 135 and 270 ms). Phe was detectable only when the signals from all CSI voxels were summarized. In patients suffering from PKU the T 2 relaxation times of choline, creatine and N-acetyl aspartate (NAA) were similar to those previously reported for healthy volunteers (between 200 and 325 ms). The T 2 of Phe in brain tissue was 215±120 ms (standard deviation). In the PKU patients the brain tissue Phe concentrations were 141±69 μM as opposed to 58±23 μM in the persons not suffering from PKU. In the detection of Phe, MR spectroscopy performed at TE 135 or 270 ms is not inferior to that performed at TE 20 or 40 ms (all previous studies). Best results were obtained at TE=135 ms, relating to the fact that at that particular TE, the visibility of a compound with a T 2 of 215 ms still is good, while interfering signals from short-TE compounds are negligible. (orig.)

  6. {sup 1}H MR chemical shift imaging detection of phenylalanine in patients suffering from phenylketonuria (PKU)

    Energy Technology Data Exchange (ETDEWEB)

    Sijens, Paul E.; Oudkerk, Matthijs [University Hospital Groningen, Department of Radiology, Hanzeplein 1, P.O. Box 30001, Groningen (Netherlands); Reijngoud, Dirk-Jan; Spronsen, Francjan J. van [University Hospital Groningen, Department of Pediatrics, Groningen (Netherlands); Leenders, Klaas L. [University Hospital Groningen, Department of Neurology, Groningen (Netherlands); Valk, Harold W. de [University Medical Centre of Utrecht, Department of Internal Medicine, Utrecht (Netherlands)

    2004-10-01

    Short echo time single voxel methods were used in previous MR spectroscopy studies of phenylalanine (Phe) levels in phenylketonuria (PKU) patients. In this study, apparent T{sub 2} relaxation time of the 7.3-ppm Phe multiplet signal in the brain of PKU patients was assessed in order to establish which echo time would be optimal. {sup 1}H chemical shift imaging (CSI) examinations of a transverse plain above the ventricles of the brain were performed in 10 PKU patients and 11 persons not suffering from PKU at 1.5 T, using four echo times (TE 20, 40, 135 and 270 ms). Phe was detectable only when the signals from all CSI voxels were summarized. In patients suffering from PKU the T{sub 2} relaxation times of choline, creatine and N-acetyl aspartate (NAA) were similar to those previously reported for healthy volunteers (between 200 and 325 ms). The T{sub 2} of Phe in brain tissue was 215{+-}120 ms (standard deviation). In the PKU patients the brain tissue Phe concentrations were 141{+-}69 {mu}M as opposed to 58{+-}23 {mu}M in the persons not suffering from PKU. In the detection of Phe, MR spectroscopy performed at TE 135 or 270 ms is not inferior to that performed at TE 20 or 40 ms (all previous studies). Best results were obtained at TE=135 ms, relating to the fact that at that particular TE, the visibility of a compound with a T{sub 2} of 215 ms still is good, while interfering signals from short-TE compounds are negligible. (orig.)

  7. Quantification of fat using chemical shift imaging and 1H-MR spectroscopy in phantom model

    International Nuclear Information System (INIS)

    Peng Xingui; Ju Shenghong; Fang Fang; Teng Gaojun

    2010-01-01

    Objective: To evaluate the accuracy of chemical shift imaging (CSI) and MR spectroscopy (MRS) for fat quantification in phantom model. Methods: Eleven phantoms were made according to the volume percentage of fat ranging from 0 to 100% with an interval of 10%. The fat concentration in the phantoms were measured respectively by CSI and MRS and compared using one-sample t test. The correlation between the two methods was also analyzed. The concentration of saturated fatty acids (FS), unsaturated fatty acids (FU) and the poly, unsaturation degree (PUD) were calculated by using MRS. Results: The fat concentration was (48.0±1.0)%, (57.0±0.5)%, (67.3±0.6)%, (77.3± 0.6)%, (83.3±0.6)% and (91.0±1.0)% respectively with fat volume of 50% to 100% by CSI. The fat concentration was (8.3±0.6)%, (16.3±0.7)%, (27.7±0.6)%, (36.0±1.0)%, (43.5± 0.6)% and (56.5±1.0)% respectively with fat volume of 10% to 60% by MRS, the fat concentration were underestimated by CSI and MRS (P<0.05), and had high linear correlation with the real concentration in phantoms (CSI: r=0.998, MRS: r=0.996, P<0.01). There was also a linear correlation between two methods (r=0.992, P<0.01) but no statistically significant difference (paired- samples t test, t=-0.125, P=0.903). By using MRS, the relative ratio of FS and FU in fat were 0. 15 and 0.85, the PUD was 0.0325, respectively, and highly consistent with these in phantoms. Conclusion: Both CSI and MRS are efficient and accurate methods in fat quantification at 7.0 T MR. (authors)

  8. Changes of brain metabolite concentrations during maturation in different brain regions measured by chemical shift imaging.

    Science.gov (United States)

    Bültmann, Eva; Nägele, Thomas; Lanfermann, Heinrich; Klose, Uwe

    2017-01-01

    We examined the effect of maturation on the regional distribution of brain metabolite concentrations using multivoxel chemical shift imaging. From our pool of pediatric MRI examinations, we retrospectively selected patients showing a normal cerebral MRI scan or no pathologic signal abnormalities at the level of the two-dimensional 1H MRS-CSI sequence and an age-appropriate global neurological development, except for focal neurological deficits. Seventy-one patients (4.5 months-20 years) were identified. Using LC Model, spectra were evaluated from voxels in the white matter, caudate head, and corpus callosum. The concentration of total N-acetylaspartate increased in all regions during infancy and childhood except in the right caudate head where it remained constant. The concentration of total creatine decreased in the caudate nucleus and splenium and minimally in the frontal white matter and genu. It remained largely constant in the parietal white matter. The concentration of choline-containing compounds had the tendency to decrease in all regions except in the parietal white matter where it remained constant. The concentration of myoinositol decreased slightly in the splenium and right frontal white matter, remained constant on the left side and in the caudate nucleus, and rose slightly in the parietal white matter and genu. CSI determined metabolite concentrations in multiple cerebral regions during routine MRI. The obtained data will be helpful in future pediatric CSI measurements deciding whether the ratios of the main metabolites are within the range of normal values or have to be considered as probably pathologic.

  9. Changes of brain metabolite concentrations during maturation in different brain regions measured by chemical shift imaging

    International Nuclear Information System (INIS)

    Bueltmann, Eva; Lanfermann, Heinrich; Naegele, Thomas; Klose, Uwe

    2017-01-01

    We examined the effect of maturation on the regional distribution of brain metabolite concentrations using multivoxel chemical shift imaging. From our pool of pediatric MRI examinations, we retrospectively selected patients showing a normal cerebral MRI scan or no pathologic signal abnormalities at the level of the two-dimensional 1H MRS-CSI sequence and an age-appropriate global neurological development, except for focal neurological deficits. Seventy-one patients (4.5 months-20 years) were identified. Using LC Model, spectra were evaluated from voxels in the white matter, caudate head, and corpus callosum. The concentration of total N-acetylaspartate increased in all regions during infancy and childhood except in the right caudate head where it remained constant. The concentration of total creatine decreased in the caudate nucleus and splenium and minimally in the frontal white matter and genu. It remained largely constant in the parietal white matter. The concentration of choline-containing compounds had the tendency to decrease in all regions except in the parietal white matter where it remained constant. The concentration of myoinositol decreased slightly in the splenium and right frontal white matter, remained constant on the left side and in the caudate nucleus, and rose slightly in the parietal white matter and genu. CSI determined metabolite concentrations in multiple cerebral regions during routine MRI. The obtained data will be helpful in future pediatric CSI measurements deciding whether the ratios of the main metabolites are within the range of normal values or have to be considered as probably pathologic. (orig.)

  10. Quantification of liver fat with respiratory-gated quantitative chemical shift encoded MRI.

    Science.gov (United States)

    Motosugi, Utaroh; Hernando, Diego; Bannas, Peter; Holmes, James H; Wang, Kang; Shimakawa, Ann; Iwadate, Yuji; Taviani, Valentina; Rehm, Jennifer L; Reeder, Scott B

    2015-11-01

    To evaluate free-breathing chemical shift-encoded (CSE) magnetic resonance imaging (MRI) for quantification of hepatic proton density fat-fraction (PDFF). A secondary purpose was to evaluate hepatic R2* values measured using free-breathing quantitative CSE-MRI. Fifty patients (mean age, 56 years) were prospectively recruited and underwent the following four acquisitions to measure PDFF and R2*; 1) conventional breath-hold CSE-MRI (BH-CSE); 2) respiratory-gated CSE-MRI using respiratory bellows (BL-CSE); 3) respiratory-gated CSE-MRI using navigator echoes (NV-CSE); and 4) single voxel MR spectroscopy (MRS) as the reference standard for PDFF. Image quality was evaluated by two radiologists. MRI-PDFF measured from the three CSE-MRI methods were compared with MRS-PDFF using linear regression. The PDFF and R2* values were compared using two one-sided t-test to evaluate statistical equivalence. There was no significant difference in the image quality scores among the three CSE-MRI methods for either PDFF (P = 1.000) or R2* maps (P = 0.359-1.000). Correlation coefficients (95% confidence interval [CI]) for the PDFF comparisons were 0.98 (0.96-0.99) for BH-, 0.99 (0.97-0.99) for BL-, and 0.99 (0.98-0.99) for NV-CSE. The statistical equivalence test revealed that the mean difference in PDFF and R2* between any two of the three CSE-MRI methods was less than ±1 percentage point (pp) and ±5 s(-1) , respectively (P liver PDFF and R2* and are as valid as the standard breath-hold technique. © 2015 Wiley Periodicals, Inc.

  11. Changes of brain metabolite concentrations during maturation in different brain regions measured by chemical shift imaging

    Energy Technology Data Exchange (ETDEWEB)

    Bueltmann, Eva; Lanfermann, Heinrich [Hannover Medical School, Institute of Diagnostic and Interventional Neuroradiology, Hannover (Germany); Naegele, Thomas [University of Tuebingen, Department of Diagnostic and Interventional Neuroradiology, Radiological University Hospital, Tuebingen (Germany); Klose, Uwe [University of Tuebingen, Section of Experimental MR of the CNS, Department of Neuroradiology, Radiological University Hospital, Tuebingen (Germany)

    2017-01-15

    We examined the effect of maturation on the regional distribution of brain metabolite concentrations using multivoxel chemical shift imaging. From our pool of pediatric MRI examinations, we retrospectively selected patients showing a normal cerebral MRI scan or no pathologic signal abnormalities at the level of the two-dimensional 1H MRS-CSI sequence and an age-appropriate global neurological development, except for focal neurological deficits. Seventy-one patients (4.5 months-20 years) were identified. Using LC Model, spectra were evaluated from voxels in the white matter, caudate head, and corpus callosum. The concentration of total N-acetylaspartate increased in all regions during infancy and childhood except in the right caudate head where it remained constant. The concentration of total creatine decreased in the caudate nucleus and splenium and minimally in the frontal white matter and genu. It remained largely constant in the parietal white matter. The concentration of choline-containing compounds had the tendency to decrease in all regions except in the parietal white matter where it remained constant. The concentration of myoinositol decreased slightly in the splenium and right frontal white matter, remained constant on the left side and in the caudate nucleus, and rose slightly in the parietal white matter and genu. CSI determined metabolite concentrations in multiple cerebral regions during routine MRI. The obtained data will be helpful in future pediatric CSI measurements deciding whether the ratios of the main metabolites are within the range of normal values or have to be considered as probably pathologic. (orig.)

  12. Proton magnetic resonance chemical shift imaging (1H CSI)-directed stereotactic biopsy

    International Nuclear Information System (INIS)

    Son, B.-C.; Kim, B.-C.; Kang, J.-K.; Choi, B.-G.; Kim, E.-N.; Baik, H.-M.; Choe, B.-Y.; Naruse, S.

    2001-01-01

    Introduction. To add metabolic information during stereotactic biopsy target selection, the authors adopted proton chemical shift imaging ( 1 H CSI)-directed stereotactic biopsy. Currently, proton single voxel spectroscopy (SVS) technique has been reported in stereotactic biopsy. We performed 1 H CSI in combination with a stereotactic headframe and selected targets according to local metabolic information, and evaluated the pathological results. Patients and Method. The 1 H CSI-directed stereotactic biopsy was performed in four patients. 1 H CSI and conventional Gd-enhancement stereotactic MRI were performed simultaneously after the fitting of a stereotactic frame. After reconstructing the metabolic maps of N-acetylaspartate (NAA)/phosphocreatine (Cr), phosphocholine (Cho)/Cr, and Lactate/Cr ratios, focal areas of increased Cho/Cr ratio and Lac/Cr ratios were selected as target sites in the stereotactic MR images. Result. 1 H CSI is possible with the stereotactic headframe in place. No difficulty was experienced performing 1 H CSI or making a diagnosis. Pathological samples taken from areas of increased Cho/Cr ratios and decreased NAA/Cr ratios provided information upon increased cellularity, mitoses and cellular atypism, and facilitated diagnosis. Pathological samples taken from areas of increased Lac/ Cr ratio snowed predominant feature of necrosis. Conclusion. 1 H CSI was feasible with the stereotactic headframe in place. The final pathological results obtained were concordant with the local metabolic information from 1 H CSI. We believe that 1 H CSI-directed stereotactic biopsy has the potential to significantly improve the accuracy of stereotactic biopsy targeting. (author)

  13. Female sea lamprey shift orientation toward a conspecific chemical cue to escape a sensory trap

    Science.gov (United States)

    Brant, Cory O.; Johnson, Nicholas; Li, Ke; Buchinger, Tyler J.; Li, Weiming

    2016-01-01

    The sensory trap model of signal evolution hypothesizes that signalers adapt to exploit a cue used by the receiver in another context. Although exploitation of receiver biases can result in conflict between the sexes, deceptive signaling systems that are mutually beneficial drive the evolution of stable communication systems. However, female responses in the nonsexual and sexual contexts may become uncoupled if costs are associated with exhibiting a similar response to a trait in both contexts. Male sea lamprey (Petromyzon marinus) signal with a mating pheromone, 3-keto petromyzonol sulfate (3kPZS), which may be a match to a juvenile cue used by females during migration. Upstream movement of migratory lampreys is partially guided by 3kPZS, but females only move toward 3kPZS with proximal accuracy during spawning. Here, we use in-stream behavioral assays paired with gonad histology to document the transition of female preference for juvenile- and male-released 3kPZS that coincides with the functional shift of 3kPZS as a migratory cue to a mating pheromone. Females became increasingly biased toward the source of synthesized 3kPZS as their maturation progressed into the reproductive phase, at which point, a preference for juvenile odor (also containing 3kPZS naturally) ceased to exist. Uncoupling of female responses during migration and spawning makes the 3kPZS communication system a reliable means of synchronizing mate search. The present study offers a rare example of a transition in female responses to a chemical cue between nonsexual and sexual contexts, provides insights into the origins of stable communication signaling systems.

  14. Benchmark fragment-based 1H, 13C, 15N and 17O chemical shift predictions in molecular crystals†

    Science.gov (United States)

    Hartman, Joshua D.; Kudla, Ryan A.; Day, Graeme M.; Mueller, Leonard J.; Beran, Gregory J. O.

    2016-01-01

    The performance of fragment-based ab initio 1H, 13C, 15N and 17O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. 1H, 13C, 15N, and 17O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same 1H, 13C, 15N, and 17O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tertbutyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2. PMID:27431490

  15. Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

    Science.gov (United States)

    Hartman, Joshua D; Kudla, Ryan A; Day, Graeme M; Mueller, Leonard J; Beran, Gregory J O

    2016-08-21

    The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.

  16. Relativistic Spin-Orbit Heavy Atom on the Light Atom NMR Chemical Shifts: General Trends Across the Periodic Table Explained.

    Science.gov (United States)

    Vícha, Jan; Komorovsky, Stanislav; Repisky, Michal; Marek, Radek; Straka, Michal

    2018-05-10

    The importance of relativistic effects on the NMR parameters in heavy-atom (HA) compounds, particularly the SO-HALA (Spin-Orbit Heavy Atom on the Light Atom) effect on NMR chemical shifts, has been known for about 40 years. Yet, a general correlation between the electronic structure and SO-HALA effect has been missing. By analyzing 1 H NMR chemical shifts of the sixth-period hydrides (Cs-At), we discovered general electronic-structure principles and mechanisms that dictate the size and sign of the SO-HALA NMR chemical shifts. In brief, partially occupied HA valence shells induce relativistic shielding at the light atom (LA) nuclei, while empty HA valence shells induce relativistic deshielding. In particular, the LA nucleus is relativistically shielded in 5d 2 -5d 8 and 6p 4 HA hydrides and deshielded in 4f 0 , 5d 0 , 6s 0 , and 6p 0 HA hydrides. This general and intuitive concept explains periodic trends in the 1 H NMR chemical shifts along the sixth-period hydrides (Cs-At) studied in this work. We present substantial evidence that the introduced principles have a general validity across the periodic table and can be extended to nonhydride LAs. The decades-old question of why compounds with occupied frontier π molecular orbitals (MOs) cause SO-HALA shielding at the LA nuclei, while the frontier σ MOs cause deshielding is answered. We further derive connection between the SO-HALA NMR chemical shifts and Spin-Orbit-induced Electron Deformation Density (SO-EDD), a property that can be obtained easily from differential electron densities and can be represented graphically. SO-EDD provides an intuitive understanding of the SO-HALA effect in terms of the depletion/concentration of the electron density at LA nuclei caused by spin-orbit coupling due to HA in the presence of a magnetic field. Using an analogy between the SO-EDD concept and arguments from classic NMR theory, the complex question of the SO-HALA NMR chemical shifts becomes easily understandable for a wide

  17. Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

    Beck Erlach, Markus; Koehler, Joerg; Crusca, Edson; Munte, Claudia E; Kainosho, Masatsune; Kremer, Werner; Kalbitzer, Hans Robert

    2017-10-01

    For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13 C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH 2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For H N , N and C α the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13 C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.

  18. Torsion in extra-dimensions

    International Nuclear Information System (INIS)

    Wali, Kameshwar C

    2010-01-01

    We consider a variant of the 5 dimensional Kaluza-Klein theory within the framework of Einstein-Cartan formalism. By imposing a set of constraints on torsion and Ricci rotation coefficients, we show that the torsion components are completely expressed in terms of the metric. and the Ricci tensor in 5D corresponds exactly to what one would obtain from torsion-free general relativity on a 4D hypersurface. The contributions of the scalar and vector fields of the standard K-K theory to the Ricci tensor and the affine connections are completely nullified by the contributions from the torsion. As a consequence, geodesic motions do not distinguish the torsion free 4D space-time from a hypersurface of 5D space-time with torsion satisfying the constraints. Since torsion is not an independent dynamical variable in this formalism, the modified Einstein equations are different from those in the general Einstein-Cartan theory. This leads to important cosmological consequences such as the emergence of cosmic acceleration.

  19. Ovarian torsion: Echographic discoveries

    International Nuclear Information System (INIS)

    Triana R, Gustavo; Navas O, Claudia

    1994-01-01

    Patient of 31 years who consulted to the even service of urgencies to present of two hours of evolution intense pain in flank and region lumbar left, associated to vomit, present square similar 5 previous days to the entrance in the right side. Go Po, plans with DIU FUR, 8 previous days to the square. It is practiced Tran abdominal pelvic echography that shows left ovary of 6 x 5 x 3 cms, with multiple follicular images, of thick walls, with I liquidate free abdominal, highly suggestive of ovarian torsion although the patient didn't present square of sharp abdomen. It decides to suspend analgesic and to value it, presented sharp abdominal pain, reason why laparotomy was practiced, finding mass of 6 x 6 cms. of necrotic aspect, corresponding to the left ovary, which presented three turns on their axis. It is taken finish left salpingooferectomy

  20. Vanadium NMR Chemical Shifts of (Imido)vanadium(V) Dichloride Complexes with Imidazolin-2-iminato and Imidazolidin-2-iminato Ligands: Cooperation with Quantum-Chemical Calculations and Multiple Linear Regression Analyses.

    Science.gov (United States)

    Yi, Jun; Yang, Wenhong; Sun, Wen-Hua; Nomura, Kotohiro; Hada, Masahiko

    2017-11-30

    The NMR chemical shifts of vanadium ( 51 V) in (imido)vanadium(V) dichloride complexes with imidazolin-2-iminato and imidazolidin-2-iminato ligands were calculated by the density functional theory (DFT) method with GIAO. The calculated 51 V NMR chemical shifts were analyzed by the multiple linear regression (MLR) analysis (MLRA) method with a series of calculated molecular properties. Some of calculated NMR chemical shifts were incorrect using the optimized molecular geometries of the X-ray structures. After the global minimum geometries of all of the molecules were determined, the trend of the observed chemical shifts was well reproduced by the present DFT method. The MLRA method was performed to investigate the correlation between the 51 V NMR chemical shift and the natural charge, band energy gap, and Wiberg bond index of the V═N bond. The 51 V NMR chemical shifts obtained with the present MLR model were well reproduced with a correlation coefficient of 0.97.

  1. Numerical Analysis on Variation of Dynamic Response of Girder Bridges with Torsional Reinforcement Panels

    Directory of Open Access Journals (Sweden)

    Kang Jae-Yoon

    2015-01-01

    Full Text Available The dynamic flexural behaviour of the railway bridge is influenced by its torsional behaviour. Especially, in the case of girder railway bridges, the dynamic response tends to amplify when the natural frequency in flexure (1st vibration mode is close to that in torsion (2nd vibration mode. In order to prevent such situation, it is necessary to adopt a flexural-to-torsional natural frequency ratio larger than 120%. This study proposes a solution shifting the natural frequency in torsion to high frequency range and restraining torsion by installing concrete panels on the bottom flange of the girder so as to prevent the superposition of the responses in the girder bridge. The applicability of this solution is examined by finite element analysis of the shift of the torsional natural frequency and change in the dynamic response according to the installation of the concrete panels. The analytical results for a 30 m-span girder railway bridge indicate that installing the concrete panels increases the natural frequency in torsion by restraining the torsional behaviour and reduces also the overall dynamic response. It is seen that the installation of 100 mm-thick concrete panels along a section of 4 m at both extremities of the girder can reduce the dynamic response by more than 30%.

  2. Re-torsion of the ovaries

    DEFF Research Database (Denmark)

    Hyttel, Trine E W; Bak, Geske S; Larsen, Solveig B

    2015-01-01

    The increasing use of de-torsion of the ovaries may result in re-torsion. This review addresses risk of re-torsion and describes preventive strategies to avoid re-torsion in pre-menarcheal girls, and fertile and pregnant women. We clinically reviewed PubMed, Embase, Trip and Cochrane databases. T...

  3. Hematosalpinx torsion in an adolescent

    Directory of Open Access Journals (Sweden)

    Inês Vaz

    2016-02-01

    Full Text Available Introduction: Isolated fallopian tube torsion is an uncommon cause of acute lower abdominal pain. Ectopic pregnancy, hydro or hematosalpinx, endometriosis, adnexal masses and other causes of adnexal disease are predisposing factors. The diagnosis is difficult and often delayed due to the lack of pathognomonic symptoms, characteristic physical signs, and specific imaging and laboratory studies. Defi nitive diagnosis requires a surgical approach. Case report: The authors present a case of hematosalpinx and its tubal torsion in a virgin teenager with no prior predisposing factors. Discussion: This rare case may highlight a new insight into pathophysiology of tubal torsion and recalls hematosalpinx as a differential diagnosis.

  4. Calculation of the NMR chemical shift for a 4d1 system in a strong crystal field environment of trigonal symmetry with a threefold axis of quantization

    International Nuclear Information System (INIS)

    Ahn, Sang Woon; Oh, Se Woung; Ro, Seung Woo

    1986-01-01

    The NMR chemical shift arising from 4d electron angular momentum and 4d electron angular momentum and 4d electron spin dipolar-nuclear spin angular momentum interactions for a 4d 1 system in a strong crystal field environment of trigonal symmetry, where the threefold axis is chosen to be the axis of quantization axis, has been examined. A general expression using the nonmultipole expansion method (exact method) is derived for the NMR chemical shift. From this expression all the multipolar terms are determined. we observe that along the (100), (010), (110), and (111) axes the NMR chemical shifts are positive while along the (001) axis, it is negative. We observe that the dipolar term (1/R 3 ) is the dominant contribution to the NMR chemical shift except for along the (111) axis. A comparison of the multipolar terms with the exact values shows also that the multipolar results are exactly in agreement with the exact values around R≥0.2 nm. The temperature dependence analysis on the NMR chemical shifts may imply that along the (111) axis the contribution to the NMR chemical shift is dominantly pseudo contact interaction. Separation of the contributions of the Fermi and the pseudo contact interactions would correctly imply that the dipolar interaction is the dominant contribution to the NMR chemical shifts along the (100), (010), (001), and (110) axes, but along the (111) axis the Fermi contact interaction is incorrectly the dominant contribution to the NMR chemical shift. (Author)

  5. Chemical shift of U L3 edges in different uranium compounds ...

    Indian Academy of Sciences (India)

    Administrator

    by X-ray absorption spectroscopy with synchrotron radiation. D JOSEPH†, C NAYAK††, ... Bhabha Atomic Research Centre, Mumbai 400 085, India. MS received 28 .... As has been discussed in the 'Introduction' section, the above edge shift ...

  6. Correlates to sleepiness on night shift among male workers engaged in three-shift work in a chemical plant: its association with sleep practice and job stress.

    Science.gov (United States)

    Kageyama, Takayuki; Kobayashi, Toshio; Abe-Gotoh, Ayano

    2011-01-01

    The purpose of this study was to examine the correlation of sleepiness during night shift (SNS) in male shiftworkers with nonpharmacological self-management (nPSM) practices to facilitate good day sleep, and also with job stress. Sleepiness on the job and possible correlates to SNS among 157 male shiftworkers in a rotating three-shift schedule at a chemical plant were cross-sectionally investigated using a self-administered questionnaire. Multivariate analyses revealed that SNS was positively associated with drinking alcoholic beverages before day sleep, but inversely associated with subjective health status, being of the evening type, abstaining from caffeine before day sleep, having a bath before day sleep, job control, reward from work, feeling suited to the job, and support from colleagues. SNS correlated with certain nPSM practices and also with possible modifiers of job stress. These findings provide clues to developing countermeasures against SNS among shiftworkers. The effects of nPSM practices and job stress management on their day sleep and SNS should be examined in detail.

  7. Development of 19F-NMR chemical shift detection of DNA B-Z equilibrium using 19F-NMR.

    Science.gov (United States)

    Nakamura, S; Yang, H; Hirata, C; Kersaudy, F; Fujimoto, K

    2017-06-28

    Various DNA conformational changes are in correlation with biological events. In particular, DNA B-Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B-Z equilibrium using 19 F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19 F-NMR chemical shift change.

  8. Predicting Heats of Explosion of Nitroaromatic Compounds through NBO Charges and 15N NMR Chemical Shifts of Nitro Groups

    Directory of Open Access Journals (Sweden)

    Ricardo Infante-Castillo

    2012-01-01

    Full Text Available This work presents a new quantitative model to predict the heat of explosion of nitroaromatic compounds using the natural bond orbital (NBO charge and 15N NMR chemical shifts of the nitro groups (15NNitro as structural parameters. The values of the heat of explosion predicted for 21 nitroaromatic compounds using the model described here were compared with experimental data. The prediction ability of the model was assessed by the leave-one-out cross-validation method. The cross-validation results show that the model is significant and stable and that the predicted accuracy is within 0.146 MJ kg−1, with an overall root mean squared error of prediction (RMSEP below 0.183 MJ kg−1. Strong correlations were observed between the heat of explosion and the charges (R2 = 0.9533 and 15N NMR chemical shifts (R2 = 0.9531 of the studied compounds. In addition, the dependence of the heat of explosion on the presence of activating or deactivating groups of nitroaromatic explosives was analyzed. All calculations, including optimizations, NBO charges, and 15NNitro NMR chemical shifts analyses, were performed using density functional theory (DFT and a 6-311+G(2d,p basis set. Based on these results, this practical quantitative model can be used as a tool in the design and development of highly energetic materials (HEM based on nitroaromatic compounds.

  9. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

    Energy Technology Data Exchange (ETDEWEB)

    Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu

    2005-05-15

    We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.

  10. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

    International Nuclear Information System (INIS)

    Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.

    2005-01-01

    We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states

  11. Isolated penile torsion in newborns.

    Science.gov (United States)

    Eroglu, Egemen; Gundogdu, Gokhan

    2015-01-01

    We reported on the incidence of isolated penile torsion among our healthy children and our approach to this anomaly. Between 2011 and 2014, newborn babies with penile torsion were classified according to the angle of torsion. Surgical correction (penile degloving and reattachment for moderate cases and dorsal dartos flap technique in case of resistance) after 6 months was advised to the babies with rotations more than 45°. Among 1000 newborn babies, 200 isolated penile torsions were found, and among these, 43 had torsions more than 45°, and 4 of these had angles greater than 90°. The mean angle of the rotations was found 30.45° (median: 20°). In total, 8 children with 60° torsions were previously circumcised. Surgery was performed on 19 patients, with a mean patient age of 12 ± 2 months. Of these 19, 13 babies were corrected with degloving and reattachment. This technique was not enough on the remaining 6 patients; therefore, derotational dorsal dartos flap was added to correct the torsion. After a mean of 15.6 ± 9.8 months, residual penile rotation, less than 15°, was found only in 2 children. The incidence of isolated penile torsion is 20% in newborns. However, rotation more than 45° angles are seen in 4.3% of male babies. Correction is not necessary in mild degrees, and penile degloving with reattachment is enough in most cases. If the initial correction is insufficient, dorsal dartos flap rotation is easy and effective. Prior circumcision neither disturbs the operative procedure nor affects the outcomes.

  12. Variations of retinal nerve fiber layer thickness and ganglion cell-inner plexiform layer thickness according to the torsion direction of optic disc.

    Science.gov (United States)

    Lee, Kang Hoon; Kim, Chan Yun; Kim, Na Rae

    2014-02-20

    To examine the relationship between the optic disc torsion and peripapillary retinal nerve fiber layer (RNFL) thickness through a comparison with the macular ganglion cell inner plexiform layer complex (GCIPL) thickness measured by Cirrus optical coherence tomography (OCT). Ninety-four eyes of 94 subjects with optic disc torsion and 114 eyes of 114 subjects without optic disc torsion were enrolled prospectively. The participants underwent fundus photography and OCT imaging in peripapillary RNFL mode and macular GCIPL mode. The participants were divided into groups according to the presence or absence of optic disc torsion. The eyes with optic disc torsion were further divided into supranasal torsion and inferotemporal torsion groups according to the direction of optic disc torsion. The mean RNFL and GCIPL thicknesses for the quadrants and subsectors were compared. The superior and inferior peak locations of the RNFL were also measured according to the torsion direction. The temporal RNFL thickness was significantly thicker in inferotemporal torsion, whereas the GCIPL thickness at all segments was unaffected. The inferotemporal optic torsion had more temporally positioned superior peak locations of the RNFL than the nontorsion and supranasal-torted optic disc. Thickening of the temporal RNFL with a temporal shift in the superior peak within the eyes with inferotemporal optic disc torsion can lead to interpretation errors. The ganglion cell analysis algorithm can assist in differentiating eyes with optic disc torsion.

  13. Proton Chemical Shift Imaging of the Brain in Pediatric and Adult Developmental Stuttering.

    Science.gov (United States)

    O'Neill, Joseph; Dong, Zhengchao; Bansal, Ravi; Ivanov, Iliyan; Hao, Xuejun; Desai, Jay; Pozzi, Elena; Peterson, Bradley S

    2017-01-01

    Developmental stuttering is a neuropsychiatric condition of incompletely understood brain origin. Our recent functional magnetic resonance imaging study indicates a possible partial basis of stuttering in circuits enacting self-regulation of motor activity, attention, and emotion. To further characterize the neurophysiology of stuttering through in vivo assay of neurometabolites in suspect brain regions. Proton chemical shift imaging of the brain was performed in a case-control study of children and adults with and without stuttering. Recruitment, assessment, and magnetic resonance imaging were performed in an academic research setting. Ratios of N-acetyl-aspartate plus N-acetyl-aspartyl-glutamate (NAA) to creatine (Cr) and choline compounds (Cho) to Cr in widespread cerebral cortical, white matter, and subcortical regions were analyzed using region of interest and data-driven voxel-based approaches. Forty-seven children and adolescents aged 5 to 17 years (22 with stuttering and 25 without) and 47 adults aged 21 to 51 years (20 with stuttering and 27 without) were recruited between June 2008 and March 2013. The mean (SD) ages of those in the stuttering and control groups were 12.2 (4.2) years and 13.4 (3.2) years, respectively, for the pediatric cohort and 31.4 (7.5) years and 30.5 (9.9) years, respectively, for the adult cohort. Region of interest-based findings included lower group mean NAA:Cr ratio in stuttering than nonstuttering participants in the right inferior frontal cortex (-7.3%; P = .02), inferior frontal white matter (-11.4%; P < .001), and caudate (-10.6%; P = .04), while the Cho:Cr ratio was higher in the bilateral superior temporal cortex (left: +10.0%; P = .03 and right: +10.8%; P = .01), superior temporal white matter (left: +14.6%; P = .003 and right: +9.5%; P = .02), and thalamus (left: +11.6%; P = .002 and right: +11.1%; P = .001). False discovery rate-corrected voxel-based findings were highly consistent

  14. 2H isotope effect on 13C chemical shifts of Nitro-Benzo-9-Crown-3

    International Nuclear Information System (INIS)

    Moghimi, A.; Rastegar, M.; Ghandi, M.; Bijanzadeh, H. R.

    2002-01-01

    Deuterium substitution on two ortho-substituted-OCH 2 fragments in Nitro-Benzo-9 Crown-3 induces low frequency shifts, positive m ''nΔC j, in all 13 C NMR resonances which is an indication of the increased shielding in this crown ether. The magnitude of these shifts vary from 15 ΔC 7=716 to 54 ΔC 3=15 ppb for C 7 and C 3 carbons directly attached to 2 H, respectively. The influences of concentration and solvent, CDCl 3 CD 3 COCD 3 , and C 6 D 6 , on mn ΔC j values were investigated. The mn ΔC j values depended more on the nature of the solvent than on the concentration. The order of induced isotope shifts is 15 Δ, 51 Δ > 24 Δ, 42 Δ> 34 Δ, 43 Δ > 56 Δ, 65 Δ> 45 Δ, 54 Δ. The isotope shifts observed are suggested to be a sum of contributions from low frequency shift due to inductive-type and negative hyperconjugation perturbations. The C-D bond, as a poorer electron acceptor than a C-H bond induced less positive charge on directly attached oxygens O 1 and O 2. This, in turn, causes shielding of C 1 and C 2 in C1O1CD 2 and C 2 0 2 CD 2 fragments. The difference in 34 ΔC 1 and 43 ΔC 2 values is attributed to the conformational dependence of the negative hyperconjugation. The C 1 and C 2, are in fact, not equally affected by the two CD 2 groups by negative hyperconjugation because of the existence of NO 2 group attached to the benzene ring

  15. Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Phoebe Dreux Chappell

    2013-09-01

    Full Text Available Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a three-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a three-month-old Haida eddy remained largely (>80% similar over a two-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response.

  16. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

    Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.

  17. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Erlach, Markus Beck; Koehler, Joerg [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Crusca, Edson [University of São Paulo, Physics Institute of São Carlos (Brazil); Kremer, Werner [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Munte, Claudia E. [University of São Paulo, Physics Institute of São Carlos (Brazil); Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

    2016-06-15

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms {sup 1}H{sup α}, {sup 13}C{sup α} and {sup 13}C′ in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2} (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B{sub 1} and B{sub 2} are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.Graphical Abstract.

  18. Bidirectional shifts of TRPM8 channel gating by temperature and chemical agents modulate the cold sensitivity of mammalian thermoreceptors.

    Science.gov (United States)

    Mälkiä, Annika; Madrid, Rodolfo; Meseguer, Victor; de la Peña, Elvira; Valero, María; Belmonte, Carlos; Viana, Félix

    2007-05-15

    TRPM8, a member of the melastatin subfamily of transient receptor potential (TRP) cation channels, is activated by voltage, low temperatures and cooling compounds. These properties and its restricted expression to small sensory neurons have made it the ion channel with the most advocated role in cold transduction. Recent work suggests that activation of TRPM8 by cold and menthol takes place through shifts in its voltage-activation curve, which cause the channel to open at physiological membrane potentials. By contrast, little is known about the actions of inhibitors on the function of TRPM8. We investigated the chemical and thermal modulation of TRPM8 in transfected HEK293 cells and in cold-sensitive primary sensory neurons. We show that cold-evoked TRPM8 responses are effectively suppressed by inhibitor compounds SKF96365, 4-(3-chloro-pyridin-2-yl)-piperazine-1-carboxylic acid (4-tert-butyl-phenyl)-amide (BCTC) and 1,10-phenanthroline. These antagonists exert their effect by shifting the voltage dependence of TRPM8 activation towards more positive potentials. An opposite shift towards more negative potentials is achieved by the agonist menthol. Functionally, the bidirectional shift in channel gating translates into a change in the apparent temperature threshold of TRPM8-expressing cells. Accordingly, in the presence of the antagonist compounds, the apparent response-threshold temperature of TRPM8 is displaced towards colder temperatures, whereas menthol sensitizes the response, shifting the threshold in the opposite direction. Co-application of agonists and antagonists produces predictable cancellation of these effects, suggesting the convergence on a common molecular process. The potential for half maximal activation of TRPM8 activation by cold was approximately 140 mV more negative in native channels compared to recombinant channels, with a much higher open probability at negative membrane potentials in the former. In functional terms, this difference translates

  19. Torsional carbon nanotube artificial muscles.

    Science.gov (United States)

    Foroughi, Javad; Spinks, Geoffrey M; Wallace, Gordon G; Oh, Jiyoung; Kozlov, Mikhail E; Fang, Shaoli; Mirfakhrai, Tissaphern; Madden, John D W; Shin, Min Kyoon; Kim, Seon Jeong; Baughman, Ray H

    2011-10-28

    Rotary motors of conventional design can be rather complex and are therefore difficult to miniaturize; previous carbon nanotube artificial muscles provide contraction and bending, but not rotation. We show that an electrolyte-filled twist-spun carbon nanotube yarn, much thinner than a human hair, functions as a torsional artificial muscle in a simple three-electrode electrochemical system, providing a reversible 15,000° rotation and 590 revolutions per minute. A hydrostatic actuation mechanism, as seen in muscular hydrostats in nature, explains the simultaneous occurrence of lengthwise contraction and torsional rotation during the yarn volume increase caused by electrochemical double-layer charge injection. The use of a torsional yarn muscle as a mixer for a fluidic chip is demonstrated.

  20. Torsional rigidity, isospectrality and quantum graphs

    International Nuclear Information System (INIS)

    Colladay, Don; McDonald, Patrick; Kaganovskiy, Leon

    2017-01-01

    We study torsional rigidity for graph and quantum graph analogs of well-known pairs of isospectral non-isometric planar domains. We prove that such isospectral pairs are distinguished by torsional rigidity. (paper)

  1. Chemical shift of neutron resonances and some ideas on neutron resonances and scattering theory

    International Nuclear Information System (INIS)

    Ignatovich, V.K.; )

    2002-01-01

    The dependence of positions of neutron resonances in nuclei in condensed matter on chemical environment is considered. A possibility of theoretical description of neutron resonances, different from R-matrix theory is investigated. Some contradictions of standard scattering theory are discussed and a new approach without these contradictions is formulated [ru

  2. Dirac operators and Killing spinors with torsion

    International Nuclear Information System (INIS)

    Becker-Bender, Julia

    2012-01-01

    On a Riemannian spin manifold with parallel skew torsion, we use the twistor operator to obtain an eigenvalue estimate for the Dirac operator with torsion. We consider the equality case in dimensions four and six. In odd dimensions we describe Sasaki manifolds on which equality in the estimate is realized by Killing spinors with torsion. In dimension five we characterize all Killing spinors with torsion and obtain certain naturally reductive spaces as exceptional cases.

  3. NMR chemical shift and J coupling parameterization and quantum mechanical reference spectrum simulation for selected nerve agent degradation products in aqueous conditions.

    Science.gov (United States)

    Koskela, Harri; Anđelković, Boban

    2017-10-01

    The spectral parameters of selected nerve agent degradation products relevant to the Chemical Weapons Convention, namely, ethyl methylphosphonate, isopropyl methylphosphonate, pinacolyl methylphosphonate and methylphosphonic acid, were studied in wide range of pH conditions and selected temperatures. The pH and temperature dependence of chemical shifts and J couplings was parameterized using Henderson-Hasselbalch-based functions. The obtained parameters allowed calculation of precise chemical shifts and J coupling constants in arbitrary pH conditions and typical measurement temperatures, thus facilitating quantum mechanical simulation of reference spectra in the chosen magnetic field strength for chemical verification. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  4. pH-Dependent spin state population and 19F NMR chemical shift via remote ligand protonation in an iron(ii) complex.

    Science.gov (United States)

    Gaudette, Alexandra I; Thorarinsdottir, Agnes E; Harris, T David

    2017-11-30

    An Fe II complex that features a pH-dependent spin state population, by virtue of a variable ligand protonation state, is described. This behavior leads to a highly pH-dependent 19 F NMR chemical shift with a sensitivity of 13.9(5) ppm per pH unit at 37 °C, thereby demonstrating the potential utility of the complex as a 19 F chemical shift-based pH sensor.

  5. The odd side of torsion geometry

    DEFF Research Database (Denmark)

    Conti, Diego; Madsen, Thomas Bruun

    2014-01-01

    We introduce and study a notion of `Sasaki with torsion structure' (ST) as an odd-dimensional analogue of Kähler with torsion geometry (KT). These are normal almost contact metric manifolds that admit a unique compatible connection with 3-form torsion. Any odd-dimensional compact Lie group is sho...

  6. Pediatric ovarian torsion: an uncommon clinical entity

    OpenAIRE

    Rajwani, Kapil M; Mahomed, Anies

    2014-01-01

    Key Clinical Message Pediatric ovarian torsion is an infrequent diagnosis and it often mimics acute appendicitis. Most cases are due to underlying ovarian pathology and if left untreated, ovarian torsion may eventually cause peritonitis. Emergency exploratory laparoscopy represents a valuable diagnostic and therapeutic tool in suspected ovarian torsion.

  7. SHIFTING WEED COMPOSITIONS AND BIOMASS PRODUCTION IN SWEET CORN FIELD TREATED WITH ORGANIC COMPOSTS AND CHEMICAL WEED CONTROLS

    Directory of Open Access Journals (Sweden)

    Marulak Simarmata

    2015-10-01

    Full Text Available The objectives of the research were to study the shift of weed compositions in sweet corn field treated with organic compost and chemical weed controls and to compare the effect of treatment combinations on weed growth, weed biomass and sweet corn biomass. The research was conducted in Bengkulu, Indonesia, from April to July 2014. Results showed that the number of weed species decreased after the trials from 14 to 13. There was a shift in weed compositions because 5 species of weeds did not emerge after the trials, but 4 new species were found. Chemical weed control used a herbiside mixture of atrazine and mesotrione applied during postemergence was the most effective method to control weeds, which was observed on decreased weed emergence and weed biomass down to 22.33 and 25.00 percent of control, respectively. Subsequently, biomass production of sweet corn increased up to 195.64 percent at the same trials. Biomass of weeds and sweet corn were also affected by the organic composts. Weed biomass was inhibited by treatment of composted empty fruith bunches of oil palm, whereas significantly increased of sweet corn biomass were observed in the plots of organic manure.

  8. A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

    Energy Technology Data Exchange (ETDEWEB)

    Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

    2007-01-15

    Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

  9. NMR Chemical Shift of a Helium Atom as a Probe for Electronic Structure of FH, F-, (FHF)-, and FH2.

    Science.gov (United States)

    Tupikina, E Yu; Efimova, A A; Denisov, G S; Tolstoy, P M

    2017-12-21

    In this work, we present the first results of outer electronic shell visualization by using a 3 He atom as a probe particle. As model objects we have chosen F - , FH, and FH 2 + species, as well as the hydrogen-bonded complex FH···F - at various H···F - distances (3.0, 2.5, 2.0, and 1.5 Å and equilibrium at ca. 1.14 Å). The interaction energy of investigated objects with helium atom (CCSD/aug-cc-pVTZ) and helium atom chemical shift (B3LYP/pcS-2) surfaces were calculated, and their topological analysis was performed. For comparison, the results of standard quantum mechanical approaches to electronic shell visualization were presented (ESP, ELF, ED, ∇ 2 ED). We show that the Laplacian of helium chemical shift, ∇ 2 δ He , is sensitive to fluorine atom lone pair localization regions, and it can be used for the visualization of the outer electronic shell, which could be used to evaluate the proton accepting ability. The sensitivity of ∇ 2 δ He to lone pairs is preserved at distances as large as 2.0-2.5 Å from the fluorine nucleus (in comparison with the distance to ESP minima, located at 1.0-1.5 Å or maxima of ELF, which are as close as 0.6 Å to the fluorine nucleus).

  10. Heat Integration of the Water-Gas Shift Reaction System for Carbon Sequestration Ready IGCC Process with Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

    Juan M. Salazara; Stephen E. Zitney; Urmila M. Diwekara

    2010-01-01

    Integrated gasification combined cycle (IGCC) technology has been considered as an important alternative for efficient power systems that can reduce fuel consumption and CO2 emissions. One of the technological schemes combines water-gas shift reaction and chemical-looping combustion as post gasification techniques in order to produce sequestration-ready CO2 and potentially reduce the size of the gas turbine. However, these schemes have not been energetically integrated and process synthesis techniques can be applied to obtain an optimal flowsheet. This work studies the heat exchange network synthesis (HENS) for the water-gas shift reaction train employing a set of alternative designs provided by Aspen energy analyzer (AEA) and combined in a process superstructure that was simulated in Aspen Plus (AP). This approach allows a rigorous evaluation of the alternative designs and their combinations avoiding all the AEA simplifications (linearized models of heat exchangers). A CAPE-OPEN compliant capability which makes use of a MINLP algorithm for sequential modular simulators was employed to obtain a heat exchange network that provided a cost of energy that was 27% lower than the base case. Highly influential parameters for the pos gasification technologies (i.e. CO/steam ratio, gasifier temperature and pressure) were calculated to obtain the minimum cost of energy while chemical looping parameters (oxidation and reduction temperature) were ensured to be satisfied.

  11. Quantitative analysis of deuterium using the isotopic effect on quaternary {sup 13}C NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Darwish, Tamim A., E-mail: tamim.darwish@ansto.gov.au [National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Locked Bag 21, Kirrawee DC, NSW 2232 (Australia); Yepuri, Nageshwar Rao; Holden, Peter J. [National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Locked Bag 21, Kirrawee DC, NSW 2232 (Australia); James, Michael [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia)

    2016-07-13

    Quantitative analysis of specifically deuterated compounds can be achieved by a number of conventional methods, such as mass spectroscopy, or by quantifying the residual {sup 1}H NMR signals compared to signals from internal standards. However, site specific quantification using these methods becomes challenging when dealing with non-specifically or randomly deuterated compounds that are produced by metal catalyzed hydrothermal reactions in D{sub 2}O, one of the most convenient deuteration methods. In this study, deuterium-induced NMR isotope shifts of quaternary {sup 13}C resonances neighboring deuterated sites have been utilized to quantify the degree of isotope labeling of molecular sites in non-specifically deuterated molecules. By probing {sup 13}C NMR signals while decoupling both proton and deuterium nuclei, it is possible to resolve {sup 13}C resonances of the different isotopologues based on the isotopic shifts and the degree of deuteration of the carbon atoms. We demonstrate that in different isotopologues, the same quaternary carbon, neighboring partially deuterated carbon atoms, are affected to an equal extent by relaxation. Decoupling both nuclei ({sup 1}H, {sup 2}H) resolves closely separated quaternary {sup 13}C signals of the different isotopologues, and allows their accurate integration and quantification under short relaxation delays (D1 = 1 s) and hence fast accumulative spectral acquisition. We have performed a number of approaches to quantify the deuterium content at different specific sites to demonstrate a convenient and generic analysis method for use in randomly deuterated molecules, or in cases of specifically deuterated molecules where back-exchange processes may take place during work up. - Graphical abstract: The relative intensities of quaternary {sup 13}C {"1H,"2H} resonances are equal despite the different relaxation delays, allowing the relative abundance of the different deuterated isotopologues to be calculated using NMR fast

  12. Saccular impact on ocular torsion

    NARCIS (Netherlands)

    Graaf, B. de; Bos, J.E.; Groen, E.L.

    1996-01-01

    When someone is tilted laterally the sheer force on the maculae of the utriculus and the sacculus is described by the sine and the cosine of the angle of tilt, respectively. So both the sacculus and the utriculus are stimulated, but in the litera-ture ocular torsion is normally attributed to

  13. Torsion (volvulus) of the lung

    International Nuclear Information System (INIS)

    Felson, B.

    1986-01-01

    Torsion or volvulus of the lung is a relatively rare but serious condition that can often be recognized or at least suspected radiographically. It occurs under three different sets of circumstances: spontaneously, usually in association with some other pulmonary abnormality; with traumatic pneumothorax; and as a complication of thoracic surgery. The author studied nine cases of torsion of the lung, including examples from each of these categories. The radiographic signs of torsion are as follows: a collapsed or consolidated lobe that occupies an unusual position, hilar displacement in a direction inappropriate for an apparently collapsed lobe, alteration of the normal position and sweep of the pulmonary vasculature, raid opacification of an ipsilateral lobe after trauma or lobectomy, marked change in position of an opacified lobe on sequential films, bronchial cutoff with no evidence of a mass, abnormal position of an affected lobe (shown on CT, angiography, or bronchography), and lobar air trapping. Mortality is high if the torsion goes unrecognized and operation is delayed

  14. Application of the Fenske-Hall molecular orbital method to the calculation of 11B NMR chemical shifts. Antipodal substituent effects in deltahedral clusters

    International Nuclear Information System (INIS)

    Fehlner, T.P.; Czech, P.T.; Fenske, R.F.

    1990-01-01

    Utilizing Fenske-Hall wave functions and eigenvalues combined with the Ramsey sum over states (SOS) approximation, it is demonstrated that the sign and magnitude of the paramagnetic contribution to the shielding correlates well with the observed 11 B chemical shifts of a substantial variety of boron- and metal-containing compounds. Analysis of the molecular orbital (MO) contributions in the SOS approximation leads to an explanation of the large downfield shifts associated with metal-rich metallaboranes. A similar analysis demonstrates the importance of selected cluster occupied and unoccupied MO's in explaining both exo-cage substituent effects in which the antipodal boron resonance is shifted upfield and endo-cage substituent effects (interchange of isolobal fragments within the cage framework) in which the antipodal boron resonance is shifted downfield. Exo- and endo-cage substitution perturbs these MO's in an understandable fashion, leading to an internally consistent explanation of the observed chemical shift changes. 36 refs., 8 figs., 4 tabs

  15. Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

    Science.gov (United States)

    Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

    2018-03-22

    Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

  16. TORSION OF THE VERMIFORM APPENDIX: A CASE REPORT

    Directory of Open Access Journals (Sweden)

    Dr. Imtiaz Wani

    2009-07-01

    Full Text Available Torsion of the vermiform appendix is a rare condition with few cases reported in the literature. Various factors predispose to torsion. Various factors predispose to torsion. We report a case of primary torsion of the vermiform appendix. The clinical presentation was indistinguishable from acute appendicitis and the diagnosis was made at operation. Appendix was preileal in position and the direction of torsion was anticlockwise. There was intrinsic torsion with no obvious factor for torsion identified. Appendectomy was performed.

  17. Backbone and stereospecific (13)C methyl Ile (δ1), Leu and Val side-chain chemical shift assignments of Crc.

    Science.gov (United States)

    Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W.

  18. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution

    DEFF Research Database (Denmark)

    Eriksen, Janus J.; Olsen, Jógvan Magnus H.; Aidas, Kestutis

    2011-01-01

    to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations......In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers...... using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute–solvent configurations extracted from the MD simulation at 300 K are found to be inferior...

  19. Comparison of brown and white adipose tissues in infants and children with chemical-shift-encoded water-fat MRI.

    Science.gov (United States)

    Hu, Houchun H; Yin, Larry; Aggabao, Patricia C; Perkins, Thomas G; Chia, Jonathan M; Gilsanz, Vicente

    2013-10-01

    To compare fat-signal fractions (FFs) and T2* values between brown (BAT) and white (WAT) adipose tissue located within the supraclavicular fossa and subcutaneous depots, respectively. Twelve infants and 39 children were studied. Children were divided into lean and overweight/obese subgroups. Chemical-shift-encoded water-fat magnetic resonance imaging (MRI) was used to quantify FFs and T2* metrics in the supraclavicular and adjacent subcutaneous adipose tissue depots. Linear regression and t-tests were performed. Infants had lower supraclavicular FFs than children (P children exhibited lower supraclavicular FFs and T2* values than overweight children (P children, but not in infants. FFs in both depots were positively correlated with age and weight in infants (P children, they were correlated with weight and body mass index (BMI) (P children (P children, which are potentially indicative of physiological differences in adipose tissue fat content, amount, and metabolic activity. Copyright © 2013 Wiley Periodicals, Inc.

  20. Hepatic fat quantification using automated six-point Dixon: Comparison with conventional chemical shift based sequences and computed tomography.

    Science.gov (United States)

    Shimizu, Kie; Namimoto, Tomohiro; Nakagawa, Masataka; Morita, Kosuke; Oda, Seitaro; Nakaura, Takeshi; Utsunomiya, Daisuke; Yamashita, Yasuyuki

    To compare automated six-point Dixon (6-p-Dixon) MRI comparing with dual-echo chemical-shift-imaging (CSI) and CT for hepatic fat fraction in phantoms and clinical study. Phantoms and fifty-nine patients were examined both MRI and CT for quantitative fat measurements. In phantom study, linear regression between fat concentration and 6-p-Dixon showed good agreement. In clinical study, linear regression between 6-p-Dixon and dual-echo CSI showed good agreement. CT attenuation value was strongly correlated with 6-p-Dixon (R 2 =0.852; PDixon and dual-echo CSI were accurate correlation with CT attenuation value of liver parenchyma. 6-p-Dixon has the potential for automated hepatic fat quantification. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Structural analysis of flavonoids in solution through DFT 1H NMR chemical shift calculations: Epigallocatechin, Kaempferol and Quercetin

    Science.gov (United States)

    De Souza, Leonardo A.; Tavares, Wagner M. G.; Lopes, Ana Paula M.; Soeiro, Malucia M.; De Almeida, Wagner B.

    2017-05-01

    In this work, we showed that comparison between experimental and theoretical 1H NMR chemical shift patterns, calculated using Density Functional Theory (DFT), can be used for the prediction of molecular structure of flavonoids in solution, what is experimentally accessible for gas phase (electron diffraction methods) and solid samples (X-ray diffraction). The best match between B3LYP/6-31G(d,p)-PCM 1H NMR calculations for B ring rotated structures and experimental spectra can provide information on the conformation adopted by polyphenols in solution (usually DMSO-d6, acetone-d6 as solvents), which may differ from solid state and gas phase observed structures, and also DFT optimized geometry in the vacuum.

  2. 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough.

    Science.gov (United States)

    Garcin, Edwige B; Bornet, Olivier; Pieulle, Laetitia; Guerlesquin, Françoise; Sebban-Kreuzer, Corinne

    2011-10-01

    Thioredoxins are ubiquitous key antioxidant enzymes which play an essential role in cell defense against oxidative stress. They maintain the redox homeostasis owing to the regulation of thiol-disulfide exchange. In the present paper, we report the full resonance assignments of (1)H, (13)C and (15)N atoms for the reduced and oxidized forms of Desulfovibrio vulgaris Hildenborough thioredoxin 1 (Trx1). 2D and 3D heteronuclear NMR experiments were performed using uniformly (15)N-, (13)C-labelled Trx1. Chemical shifts of 97% of the backbone and 90% of the side chain atoms were obtained for the oxidized and reduced form (BMRB deposits with accession number 17299 and 17300, respectively).

  3. Quantitative evaluation of vertebral marrow adipose tissue in postmenopausal female using MRI chemical shift-based water–fat separation

    International Nuclear Information System (INIS)

    Li, G.-W.; Xu, Z.; Chen, Q.-W.; Tian, Y.-N.; Wang, X.-Y.; Zhou, L.; Chang, S.-X.

    2014-01-01

    Aim: To investigate the feasibility of assessing vertebral marrow adipose tissue using a magnetic resonance imaging (MRI) chemical shift-based water–fat separation technique at 3 T. Material and methods: A modified Dixon technique was performed to obtain the vertebral marrow fat fraction (FF) in a study of 58 postmenopausal females (age range 49.2–77.4 years), including 24 normal bone density, 19 osteopaenia, and 15 osteoporosis as documented with dual-energy X-ray absorptiometry. The reliability of FF measurements performed by two radiologists independently was evaluated with the intraclass correlation coefficient (ICC). Ten participants were scanned twice to assess the reproducibility of FF measurements. FF values were compared between each vertebral level and between groups. Results: The mean coefficient of variation of FF measurements was 2.1%. According to the ICC, the measurements were reliable (ICC = 0.900 for normal bone density, ICC = 0.937 for osteopaenia and ICC = 0.909 for osteoporosis, p < 0.001 for all). There was an inverse association between mean FF at L1–L4 vertebrae and lumbar spine BMD (r = −0.459, p = 0.006), which remained significant even after controlling for confounders (age, height, and body weight). FF values at different vertebral levels were significantly correlated to each other (r = 0.703–0.921, p < 0.05 for all). There was a general trend toward increased marrow adiposity for more inferior vertebral bodies. Patients with osteopaenia and osteoporosis had a higher marrow fat content compared with normal bone mass after adjusting for confounders, although no significant differences in each vertebral level and average marrow fat content were found between the osteopaenia and osteoporosis groups. Conclusion: Chemical shift-based water–fat separation enables the quantitation of vertebral marrow adiposity with excellent reproducibility, which appears to be a useful method to provide complementary information to osteoporosis

  4. Volumetric spiral chemical shift imaging of hyperpolarized [2-(13) c]pyruvate in a rat c6 glioma model.

    Science.gov (United States)

    Park, Jae Mo; Josan, Sonal; Jang, Taichang; Merchant, Milton; Watkins, Ron; Hurd, Ralph E; Recht, Lawrence D; Mayer, Dirk; Spielman, Daniel M

    2016-03-01

    MRS of hyperpolarized [2-(13)C]pyruvate can be used to assess multiple metabolic pathways within mitochondria as the (13)C label is not lost with the conversion of pyruvate to acetyl-CoA. This study presents the first MR spectroscopic imaging of hyperpolarized [2-(13)C]pyruvate in glioma-bearing brain. Spiral chemical shift imaging with spectrally undersampling scheme (1042 Hz) and a hard-pulse excitation was exploited to simultaneously image [2-(13)C]pyruvate, [2-(13)C]lactate, and [5-(13)C]glutamate, the metabolites known to be produced in brain after an injection of hyperpolarized [2-(13)C]pyruvate, without chemical shift displacement artifacts. A separate undersampling scheme (890 Hz) was also used to image [1-(13)C]acetyl-carnitine. Healthy and C6 glioma-implanted rat brains were imaged at baseline and after dichloroacetate administration, a drug that modulates pyruvate dehydrogenase kinase activity. The baseline metabolite maps showed higher lactate and lower glutamate in tumor as compared to normal-appearing brain. Dichloroacetate led to an increase in glutamate in both tumor and normal-appearing brain. Dichloroacetate-induced %-decrease of lactate/glutamate was comparable to the lactate/bicarbonate decrease from hyperpolarized [1-(13)C]pyruvate studies. Acetyl-carnitine was observed in the muscle/fat tissue surrounding the brain. Robust volumetric imaging with hyperpolarized [2-(13)C]pyruvate and downstream products was performed in glioma-bearing rat brains, demonstrating changes in mitochondrial metabolism with dichloroacetate. © 2015 Wiley Periodicals, Inc.

  5. Chemical shifts as a novel measure of interactions between two binding sites of symmetric dialkyldimethylammonium bromides to α-cyclodextrin

    International Nuclear Information System (INIS)

    Funasaki, Noriaki; Ishikawa, Seiji; Hirota, Shun

    2006-01-01

    Complex formation of α-cyclodextrin (α-CD) with decyltrimethylammonium (DeTAB), N,N-dioctyldimethylammonium (DOAB), and N,N-didecyldimethylammonium bromides (DDeAB) was investigated by proton NMR spectroscopy. Analysis of chemical shifts yielded macroscopic 1:1 and 1:2 binding constants (K 1 and K 2 ) and chemical shift differences (Δδ SD and Δδ SD2 ) for the 1:1 and 1:2 complexes of DeTAB, DOAB, and DDeAB with α-CD. The K 1 and K 2 values of DDeAB were quantitatively explained on the basis of the assumption that the microscopic 1:1 binding constant of DDeAB is identical to the observed K 1 value of DeTAB. The K 2 value of DDeAB was also explained in terms of its observed K 1 value and the independent binding of two alkyl chains. Furthermore, the Δδ SD and Δδ SD2 values for protons of DDeAB and α-CD were quantitatively explained on the basis of the assumption that the geometry of the decyl group of DDeAB in an α-CD cavity is identical to that of DeTAB. The Δδ SD value was also explicable on the basis of the same geometric assumption and the observed Δδ SD2 value for this system. Similar results were obtained for the 1:1 and 1:2 DOAB-α-CD complexes

  6. Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

    Science.gov (United States)

    Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

    2016-04-01

    A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  7. Torsional oscillations of the sun

    International Nuclear Information System (INIS)

    Snodgrass, H.B.; Howard, R.; National Solar Observatory, Tucson, AZ)

    1985-01-01

    The sun's differential rotation has a cyclic pattern of change that is tightly correlated with the sunspot, or magnetic activity, cycle. This pattern can be described as a torsional oscillation, in which the solar rotation is periodically sped up or slowed down in certain zones of latitude while elsewhere the rotation remains essentially steady. The zones of anomalous rotation move on the sun in wavelike fashion, keeping pace with and flanking the zones of magnetic activity. It is uncertain whether this torsional oscillation is a globally coherent ringing of the sun or whether it is a local pattern caused by and causing local changes in the magnetic fields. In either case, it may be an important link in the connection between the rotation and the cycle that is widely believed to exist but is not yet understood. 46 references

  8. Torsions of 3-dimensional manifolds

    CERN Document Server

    Wurzbacher, T

    2002-01-01

    From the reviews: "This is an excellent exposition about abelian Reidemeister torsions for three-manifolds." ―Zentralblatt Math "This monograph contains a wealth of information many topologists will find very handy. …Many of the new points of view pioneered by Turaev are gradually becoming mainstream and are spreading beyond the pure topology world. This monograph is a timely and very useful addition to the scientific literature." ―Mathematical Reviews

  9. Moduli space of torsional manifolds

    International Nuclear Information System (INIS)

    Becker, Melanie; Tseng, L.-S.; Yau, S.-T.

    2007-01-01

    We characterize the geometric moduli of non-Kaehler manifolds with torsion. Heterotic supersymmetric flux compactifications require that the six-dimensional internal manifold be balanced, the gauge bundle be Hermitian Yang-Mills, and also the anomaly cancellation be satisfied. We perform the linearized variation of these constraints to derive the defining equations for the local moduli. We explicitly determine the metric deformations of the smooth flux solution corresponding to a torus bundle over K3

  10. 31P NMR Chemical Shifts of Phosphorus Probes as Reliable and Practical Acidity Scales for Solid and Liquid Catalysts.

    Science.gov (United States)

    Zheng, Anmin; Liu, Shang-Bin; Deng, Feng

    2017-10-11

    Acid-base catalytic reaction, either in heterogeneous or homogeneous systems, is one of the most important chemical reactions that has provoked a wide variety of industrial catalytic processes for production of chemicals and petrochemicals over the past few decades. In view of the fact that the catalytic performances (e.g., activity, selectivity, and reaction mechanism) of acid-catalyzed reactions over acidic catalysts are mostly dictated by detailed acidic features, viz. type (Brønsted vs Lewis acidity), amount (concentration), strength, and local environments (location) of acid sites, information on and manipulation of their structure-activity correlation are crucial for optimization of catalytic performances as well as innovative design of novel effective catalysts. This review aims to summarize recent developments on acidity characterization of solid and liquid catalysts by means of experimental 31 P nuclear magnetic resonance (NMR) spectroscopy using phosphorus probe molecules such as trialkylphosphine (TMP) and trialkylphosphine oxides (R 3 PO). In particular, correlations between the observed 31 P chemical shifts (δ 31 P) of phosphorus (P)-containing probes and acidic strengths have been established in conjuction with density functional theory (DFT) calculations, rendering practical and reliable acidity scales for Brønsted and Lewis acidities at the atomic level. As illustrated for a variety of different solid and liquid acid systems, such as microporous zeolites, mesoporous molecular sieves, and metal oxides, the 31 P NMR probe approaches were shown to provide important acid features of various catalysts, surpassing most conventional methods such as titration, pH measurement, Hammett acidity function, and some other commonly used physicochemical techniques, such as calorimetry, temperature-programmed desorption of ammonia (NH 3 -TPD), Fourier transformed infrared (FT-IR), and 1 H NMR spectroscopies.

  11. Dynamics-based selective 2D 1H/1H chemical shift correlation spectroscopy under ultrafast MAS conditions

    Science.gov (United States)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-05-01

    Dynamics plays important roles in determining the physical, chemical, and functional properties of a variety of chemical and biological materials. However, a material (such as a polymer) generally has mobile and rigid regions in order to have high strength and toughness at the same time. Therefore, it is difficult to measure the role of mobile phase without being affected by the rigid components. Herein, we propose a highly sensitive solid-state NMR approach that utilizes a dipolar-coupling based filter (composed of 12 equally spaced 90° RF pulses) to selectively measure the correlation of 1H chemical shifts from the mobile regions of a material. It is interesting to find that the rotor-synchronized dipolar filter strength decreases with increasing inter-pulse delay between the 90° pulses, whereas the dipolar filter strength increases with increasing inter-pulse delay under static conditions. In this study, we also demonstrate the unique advantages of proton-detection under ultrafast magic-angle-spinning conditions to enhance the spectral resolution and sensitivity for studies on small molecules as well as multi-phase polymers. Our results further demonstrate the use of finite-pulse radio-frequency driven recoupling pulse sequence to efficiently recouple weak proton-proton dipolar couplings in the dynamic regions of a molecule and to facilitate the fast acquisition of 1H/1H correlation spectrum compared to the traditional 2D NOESY (Nuclear Overhauser effect spectroscopy) experiment. We believe that the proposed approach is beneficial to study mobile components in multi-phase systems, such as block copolymers, polymer blends, nanocomposites, heterogeneous amyloid mixture of oligomers and fibers, and other materials.

  12. Dynamics-based selective 2D 1H/1H chemical shift correlation spectroscopy under ultrafast MAS conditions

    International Nuclear Information System (INIS)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-01-01

    Dynamics plays important roles in determining the physical, chemical, and functional properties of a variety of chemical and biological materials. However, a material (such as a polymer) generally has mobile and rigid regions in order to have high strength and toughness at the same time. Therefore, it is difficult to measure the role of mobile phase without being affected by the rigid components. Herein, we propose a highly sensitive solid-state NMR approach that utilizes a dipolar-coupling based filter (composed of 12 equally spaced 90° RF pulses) to selectively measure the correlation of 1 H chemical shifts from the mobile regions of a material. It is interesting to find that the rotor-synchronized dipolar filter strength decreases with increasing inter-pulse delay between the 90° pulses, whereas the dipolar filter strength increases with increasing inter-pulse delay under static conditions. In this study, we also demonstrate the unique advantages of proton-detection under ultrafast magic-angle-spinning conditions to enhance the spectral resolution and sensitivity for studies on small molecules as well as multi-phase polymers. Our results further demonstrate the use of finite-pulse radio-frequency driven recoupling pulse sequence to efficiently recouple weak proton-proton dipolar couplings in the dynamic regions of a molecule and to facilitate the fast acquisition of 1 H/ 1 H correlation spectrum compared to the traditional 2D NOESY (Nuclear Overhauser effect spectroscopy) experiment. We believe that the proposed approach is beneficial to study mobile components in multi-phase systems, such as block copolymers, polymer blends, nanocomposites, heterogeneous amyloid mixture of oligomers and fibers, and other materials

  13. Using torsion to manipulate spin currents

    Science.gov (United States)

    Fumeron, Sébastien; Berche, Bertrand; Medina, Ernesto; Santos, Fernando A. N.; Moraes, Fernando

    2017-02-01

    We address the problem of quantum particles moving on a manifold characterised by the presence of torsion along a preferential axis. In fact, such a torsion may be taylored by the presence of a single screw dislocation, whose Burgers vector measures the torsion amplitude. The problem, first treated in the relativistic limit describing fermions that couple minimally to torsion, is then analysed in the Pauli limit. We show that torsion induces a geometric potential and also that it couples generically to the phase of the wave function, giving rise to the possibility of using torsion to manipulate spin currents in the case of spinor wave functions. These results emerge as an alternative strategy for using screw dislocations in the design of spintronic-based devices.

  14. Newton-Cartan gravity and torsion

    Science.gov (United States)

    Bergshoeff, Eric; Chatzistavrakidis, Athanasios; Romano, Luca; Rosseel, Jan

    2017-10-01

    We compare the gauging of the Bargmann algebra, for the case of arbitrary torsion, with the result that one obtains from a null-reduction of General Relativity. Whereas the two procedures lead to the same result for Newton-Cartan geometry with arbitrary torsion, the null-reduction of the Einstein equations necessarily leads to Newton-Cartan gravity with zero torsion. We show, for three space-time dimensions, how Newton-Cartan gravity with arbitrary torsion can be obtained by starting from a Schrödinger field theory with dynamical exponent z = 2 for a complex compensating scalar and next coupling this field theory to a z = 2 Schrödinger geometry with arbitrary torsion. The latter theory can be obtained from either a gauging of the Schrödinger algebra, for arbitrary torsion, or from a null-reduction of conformal gravity.

  15. Experiments with a cryogenic torsion balance

    International Nuclear Information System (INIS)

    Newman, R.D.

    1983-01-01

    The torsion balance is a remarkably capable instrument for the measurement of slowly varying exceedingly small forces; indeed its potential abilities are still largely untapped. The author outlines some of the virtues (and limitations) of the torsion balance, and presents a menu of gravitation-related experiments to which it may be applied. He discusses plans for developing torsion balances operating at cryogenic temperatures, and describes an experiment to search for anomalous long-range interactions associated with intrinsic spin. (Auth.)

  16. Dirac operators and Killing spinors with torsion; Dirac-Operatoren und Killing-Spinoren mit Torsion

    Energy Technology Data Exchange (ETDEWEB)

    Becker-Bender, Julia

    2012-12-17

    On a Riemannian spin manifold with parallel skew torsion, we use the twistor operator to obtain an eigenvalue estimate for the Dirac operator with torsion. We consider the equality case in dimensions four and six. In odd dimensions we describe Sasaki manifolds on which equality in the estimate is realized by Killing spinors with torsion. In dimension five we characterize all Killing spinors with torsion and obtain certain naturally reductive spaces as exceptional cases.

  17. Primary splenic torsion in a Boston terrier.

    Science.gov (United States)

    OHTA, Hiroshi; TAKAGI, Satoshi; MURAKAMI, Masahiro; SASAKI, Noboru; YOSHIKAWA, Muneyoshi; NAKAMURA, Kensuke; HWANG, Shiang-Jyi; YAMASAKI, Masahiro; TAKIGUCHI, Mitsuyoshi

    2009-11-01

    A 7-year-old female Boston terrier was referred to Hokkaido University Veterinary Teaching Hospital with a history of hemoglobinuria and anemia for several days. Abdominal radiographs showed splenomegaly, and ultrasonography revealed a hypoechoic splenic parenchyma with interspersed linear echoes consistent with the ultrasonographic appearance of splenic torsion. Ultrasonography and computed tomography (CT) indicated a C-shaped spleen. Exploratory laparotomy confirmed the diagnosis of splenic torsion. A splenectomy was performed, and the dog recovered well without complications. This is the first report of splenic torsion in Boston terriers, and the usefulness of ultrasonographic and CT findings of the splenic torsion was also confirmed.

  18. Primary splenic torsion in a Boston terrier

    International Nuclear Information System (INIS)

    Ohta, H.; Takagi, S.; Murakami, M.; Sasaki, N.; Yoshikawa, M.; Nakamura, K.; Hwang, S.J.; Yamasaki, M.; Takiguchi, M.

    2009-01-01

    A 7-year-old female Boston terrier was referred to Hokkaido University Veterinary Teaching Hospital with a history of hemoglobinuria and anemia for several days. Abdominal radiographs showed splenomegaly, and ultrasonography revealed a hypoechoic splenic parenchyma with interspersed linear echoes consistent with the ultrasonographic appearance of splenic torsion. Ultrasonography and computed tomography (CT) indicated a C-shaped spleen. Exploratory laparotomy confirmed the diagnosis of splenic torsion. A splenectomy was performed, and the dog recovered well without complications. This is the first report of splenic torsion in Boston terriers, and the usefulness of ultrasonographic and CT findings of the splenic torsion was also confirmed

  19. Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

    Science.gov (United States)

    Maeda, M.; Yamamoto, K.; Mizokawa, T.; Saini, N. L.; Arita, M.; Namatame, H.; Taniguchi, M.; Tan, G.; Zhao, L. D.; Kanatzidis, M. G.

    2018-03-01

    We have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. The large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

  20. NMR spectroscopy of organic compounds of selenium and tellurium. Communication 9. Chemical shifts of /sup 13/C in isological series of unsaturated ethers, sulfides, selenides and tellurides

    Energy Technology Data Exchange (ETDEWEB)

    Kalabin, G.A.; Bzhezovskii, V.M.; Kushnarev, D.F.; Proidakov, A.G. (Irkutskii Gosudarstvennyj Univ. (USSR))

    1981-06-01

    The effects of heteroatoms Eh(Eh=O, S, Se, Te) on /sup 13/C chemical shifts in eleven isological series of R/sup 1/-Eh-R/sup 2/ unsaturated compounds are compared. A linear relation between /sup 13/C nuclei screening and tEh electronegativity is observed. An assumption is suggested that both likeness of the effects of 6A and 7A group elements on /sup 13/C chemical shifts of R/sup 1/ and R/sup 2/ substituents and their difference for elements of the 4A group are caused by unbonded interactions of the substituents with unshared electron pairs of heteroatoms.

  1. Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and (13)C NMR Chemical Shift Tensors.

    Science.gov (United States)

    Bouzková, Kateřina; Babinský, Martin; Novosadová, Lucie; Marek, Radek

    2013-06-11

    An understanding of the role of intermolecular interactions in crystal formation is essential to control the generation of diverse crystalline forms which is an important concern for pharmaceutical industry. Very recently, we reported a new approach to interpret the relationships between intermolecular hydrogen bonding, redistribution of electron density in the system, and NMR chemical shifts (Babinský et al. J. Phys. Chem. A, 2013, 117, 497). Here, we employ this approach to characterize a full set of crystal interactions in a sample of anhydrous theobromine as reflected in (13)C NMR chemical shift tensors (CSTs). The important intermolecular contacts are identified by comparing the DFT-calculated NMR CSTs for an isolated theobromine molecule and for clusters composed of several molecules as selected from the available X-ray diffraction data. Furthermore, electron deformation density (EDD) and shielding deformation density (SDD) in the proximity of the nuclei involved in the proposed interactions are calculated and visualized. In addition to the recently reported observations for hydrogen bonding, we focus here particularly on the stacking interactions. Although the principal relations between the EDD and CST for hydrogen bonding (HB) and stacking interactions are similar, the real-space consequences are rather different. Whereas the C-H···X hydrogen bonding influences predominantly and significantly the in-plane principal component of the (13)C CST perpendicular to the HB path and the C═O···H hydrogen bonding modulates both in-plane components of the carbonyl (13)C CST, the stacking modulates the out-of-plane electron density resulting in weak deshielding (2-8 ppm) of both in-plane principal components of the CST and weak shielding (∼ 5 ppm) of the out-of-plane component. The hydrogen-bonding and stacking interactions may add to or subtract from one another to produce total values observed experimentally. On the example of theobromine, we demonstrate

  2. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D., E-mail: jdfv2009@gmail.com [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Grupo de Ressonância Magnética Nuclear e Química Medicinal

    2017-07-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  3. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    International Nuclear Information System (INIS)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D.

    2017-01-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  4. Noninvasive measurements of cardiac high-energy phosphate metabolites in dilated cardiomyopathy by using 31P spectroscopic chemical shift imaging

    International Nuclear Information System (INIS)

    Hansch, A.; Rzanny, R.; Heyne, J.-P.; Reichenbach, J.R.; Kaiser, W.A.; Leder, U.

    2005-01-01

    Dilated cardiomyopathy (DCM) is accompanied by an impaired cardiac energy metabolism. The aim of this study was to investigate metabolic ratios in patients with DCM compared to controls by using spectroscopic two-dimensional chemical shift imaging (2D-CSI). Twenty volunteers and 15 patients with severe symptoms (left ventricular ejection fraction, LVEF 30%) of DCM were investigated. Cardiac 31 P MR 2D-CSI measurements (voxel size: 40 x 40 x 100 mm 3 ) were performed with a 1.5 T whole-body scanner. Measurement time ranged from 15 min to 30 min. Peak areas and ratios of different metabolites were evaluated, including high-energy phosphates (PCr, ATP), 2,3-diphosphoglycerate (2,3-DPG) and phosphodiesters (PDE). In addition, we evaluated how PCr/ATP ratios correlate with LVEF as an established prognostic factor of heart failure. The PCr/γ-ATP ratio was significantly decreased in patients with moderate and severe DCM and showed a linear correlation with reduced LVEFs. PDE/ATP ratios were significantly increased only in patients with severe DCM as compared to volunteers. Applying 31 P MRS with commonly-available 2D-CSI sequences is a valuable technique to evaluate DCM by determining PCr/ATP ratios noninvasively. In addition to reduced PCr/ATP ratios observed in patients suffering from DCM, significantly-increased PDE/ATP ratios were found in patients with severe DCM. (orig.)

  5. Torsion of a growing shaft

    Directory of Open Access Journals (Sweden)

    Alexander V. Manzhirov

    2017-12-01

    Full Text Available The torsion of a shaft by rigid disks is considered. The shaft has the form of circular cylinder. Two rigid disks are attached to its end faces. The process of continuous growth of such shaft under the influence of twisting torques applied to the disks is studied. Dual series equations which reflect the mathematical content of the problem at the different stages of the growing process are derived and solved. Results of the numerical analysis and singularities of the qualitative mechanical behaviour of the fundamental characteristics are discussed.

  6. Chemical shift-selective snapshot FLASH MR imaging in combination with inversion-recovery T1 contrast at different field strengths

    International Nuclear Information System (INIS)

    Matthaei, D.; Haase, A.; Henrich, D.; Duhmke, E.

    1991-01-01

    With fast MR imaging, chemical shift contract becomes available to the clinician in seconds. The purpose of this paper is to evaluate the combination of chemical shift selective (CHESS) MR imaging using the snapshot FLASH MR method with the inversion-recovery technique and to obtain information concerning the signal-to-noise and chemical shift with the presaturation method at different field strengths. Investigations with volunteers and experimental animals were done at 2 and 3 T (whole body) and in a 4.7-T animal image. For the inversion-recovery experiments, saturation was done before every snapshot FLASH image. With increasing field strength due to signal-to-noise and chemical shift advantages, the method performs better. Increasing T1 values are also important at high field strengths. The combined technique is useful only for T1 water images with fat saturation. It also allows fast quantification of T1 in water-containing organs and pathologic processes. At high field strengths, fast CHESS and T1 imaging promise fast quantitative information. This is a possible argument for clinical high-field-strength MR imagining along with MR spectroscopy

  7. Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions

    DEFF Research Database (Denmark)

    Svendsen, Casper Steinmann; Bratholm, L.A.; Olsen, Jógvan Magnus Haugaard

    2017-01-01

    that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we...

  8. High-Frequency H-1 NMR Chemical Shifts of Sn-II and Pb-II Hydrides Induced by Relativistic Effects: Quest for Pb-II Hydrides

    Czech Academy of Sciences Publication Activity Database

    Vícha, J.; Marek, R.; Straka, Michal

    2016-01-01

    Roč. 55, č. 20 (2016), s. 10302-10309 ISSN 0020-1669 Institutional support: RVO:61388963 Keywords : hydrides of TlI and PbII * high-frequency 1H chemical shifts * relativistic effects Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.857, year: 2016

  9. High-Frequency C-13 and Si-29 NMR Chemical Shifts in Diamagnetic Low-Valence Compounds of TII and Pb-II: Decisive Role of Relativistic Effects

    Czech Academy of Sciences Publication Activity Database

    Vícha, J.; Marek, R.; Straka, Michal

    2016-01-01

    Roč. 55, č. 4 (2016), s. 1770-1781 ISSN 0020-1669 R&D Projects: GA ČR(CZ) GA14-03564S Institutional support: RVO:61388963 Keywords : high-frequency NMR chemical shifts * HALA effect * relativistic DFT calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.857, year: 2016

  10. Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {l_brace}in-phase and out-of phase{r_brace} MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Ragab, Yasser [Radiology Department, Faculty of Medicine, Cairo University (Egypt); Radiology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yragab61@hotmail.com; Emad, Yasser [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt); Rheumatology and Rehabilitation Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yasseremad68@yahoo.com; Gheita, Tamer [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt)], E-mail: gheitamer@yahoo.com; Mansour, Maged [Oncology Department, Faculty of Medicine, Cairo University (Egypt); Oncology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: magedmansour@yahoo.com; Abou-Zeid, A. [Public Health Department, Faculty of Medicine, Cairo University, Cairo (Egypt)], E-mail: alaabouzeid@yahoo.com; Ferrari, Serge [Division of Bone Diseases, Department of Rehabilitation and Geriatrics, and WHO, Collaborating Center for Osteoporosis Prevention, Geneva University Hospital (Switzerland)], E-mail: serge.ferrari@medecine.unige.ch; Rasker, Johannes J. [Rheumatologist University of Twente, Enschede (Netherlands)], E-mail: j.j.rasker@utwente.nl

    2009-10-15

    Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

  11. Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C’ scalar couplings (3hbJNC’)

    NARCIS (Netherlands)

    Bonvin, A.M.J.J.; Houben, K.; Guenneugues, M.N.L.; Kaptein, R.; Boelens, R.

    2001-01-01

    The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small alpha/beta protein

  12. H-1 chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter

    NARCIS (Netherlands)

    Sijens, PE; Verbruggen, KT; Meiners, LC; Soorani-Lunsing, RJ; Rake, JP; Oudkerk, M

    MR spectroscopy results in a mild case of guanidinoacetate methyltransferase (GAMT) deficiency are presented. The approach differs from previous MRS studies in the acquisition of a chemical shift imaging spectral map showing gray and white matter with the corresponding spectra in one overview. MR

  13. A complete set of NMR chemical shifts and spin-spin coupling constants for L-Alanyl-L-Alanine zwitterion and analysis of its conformational behavior

    Czech Academy of Sciences Publication Activity Database

    Bouř, Petr; Buděšínský, Miloš; Špirko, Vladimír; Kapitán, Josef; Šebestík, Jaroslav; Sychrovský, Vladimír

    2005-01-01

    Roč. 127, - (2005), 17079-17089 ISSN 0002-7863 R&D Projects: GA AV ČR(CZ) IAA4055104; GA ČR(CZ) GA203/05/0388 Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR * chemical shifts * coupling constants Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.419, year: 2005

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

    Science.gov (United States)

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

    2018-05-10

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

  15. Teenage testicular torsion. | Onuigbo | International Journal of ...

    African Journals Online (AJOL)

    Aim: To study testicular torsion in teenagers in the Igbo community. Method: A retrospective study was carried out as regards requests for pathological examination of specimens received at a Regional Reference Laboratory based in Enugu. Results: Over a period of 30 years, 28 surgical specimens of testicular torsion in ...

  16. Right paratesticular abscess mimicking neonatal testicular torsion ...

    African Journals Online (AJOL)

    U.O. Ezomike

    Abstract. The clinical presentation of neonatal paratesticular abscess may closely resemble that of, neonatal testicular torsion and the use of scrotal ultrasonography to differentiate the two has low, sensitivity. We propose early operative treatment of suspected neonatal testicular torsion to salvage, the testicle in cases of ...

  17. Simultaneous acute appendicitis with right testicular torsion

    Directory of Open Access Journals (Sweden)

    Tanveer Akhtar

    2012-01-01

    Full Text Available We present a child with both acute appendicitis and torsion of the right testis presenting at the same time. Testicular torsion possibly occurring due to vomiting in acute appendicitis so far has not been reported in the literature.

  18. Appendicular Torsion | Dubhashi | Nigerian Journal of Surgery

    African Journals Online (AJOL)

    . It can be primary or secondary. This is a case report of 52-year-old female with 180° anti-clockwise rotation of the appendix. Torsion can further leads to strangulation and infarction of the organ. Appendicular torsion could be included in the ...

  19. Anomalous phase shift in a twisted quantum loop

    International Nuclear Information System (INIS)

    Taira, Hisao; Shima, Hiroyuki

    2010-01-01

    The coherent motion of electrons in a twisted quantum ring is considered to explore the effect of torsion inherent to the ring. Internal torsion of the ring composed of helical atomic configuration yields a non-trivial quantum phase shift in the electrons' eigenstates. This torsion-induced phase shift causes novel kinds of persistent current flow and an Aharonov-Bohm-like conductance oscillation. The two phenomena can occur even when no magnetic flux penetrates inside the twisted ring, thus being in complete contrast with the counterparts observed in untwisted rings.

  20. Optically probing torsional superelasticity in spider silks

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Bhupesh; Thakur, Ashish; Panda, Biswajit; Singh, Kamal P. [Department of Physical Sciences, IISER Mohali, Sector 81, Manauli, Mohali 140306 (India)

    2013-11-11

    We investigate torsion mechanics of various spider silks using a sensitive optical technique. We find that spider silks are torsionally superelastic in that they can reversibly withstand great torsion strains of over 10{sup 2−3} rotations per cm before failure. Among various silks from a spider, we find the failure twist-strain is greatest in the sticky capture silk followed by dragline and egg-case silk. Our in situ laser-diffraction measurements reveal that torsional strains on the silks induce a nano-scale transverse compression in its diameter that is linear and reversible. These unique torsional properties of the silks could find applications in silk-based materials and devices.

  1. Optically probing torsional superelasticity in spider silks

    International Nuclear Information System (INIS)

    Kumar, Bhupesh; Thakur, Ashish; Panda, Biswajit; Singh, Kamal P.

    2013-01-01

    We investigate torsion mechanics of various spider silks using a sensitive optical technique. We find that spider silks are torsionally superelastic in that they can reversibly withstand great torsion strains of over 10 2−3 rotations per cm before failure. Among various silks from a spider, we find the failure twist-strain is greatest in the sticky capture silk followed by dragline and egg-case silk. Our in situ laser-diffraction measurements reveal that torsional strains on the silks induce a nano-scale transverse compression in its diameter that is linear and reversible. These unique torsional properties of the silks could find applications in silk-based materials and devices

  2. Accuracy of chemical shift MR imaging in diagnosing indeterminate bone marrow lesions in the pelvis: review of a single institution's experience

    International Nuclear Information System (INIS)

    Kohl, Chad A.; Chivers, F.S.; Lorans, Roxanne; Roberts, Catherine C.; Kransdorf, Mark J.

    2014-01-01

    To re-assess the accuracy of chemical shift imaging in diagnosing indeterminate bone marrow lesions as benign or malignant. We retrospectively reviewed our experience with MR imaging of the pelvis to assess the accuracy of chemical shift imaging in distinguishing benign from malignant bone lesions. Two musculoskeletal radiologists retrospectively reviewed all osseous lesions biopsied since 2006, when chemical shift imaging was added to our routine pelvic imaging protocol. Study inclusion criteria required (1) MR imaging of an indeterminate bone marrow lesion about the pelvis and (2) subsequent histologic confirmation. The study group included 50 patients (29 male, 21 female) with an average age of 67 years (range, 41-89 years). MR imaging results were evaluated using biopsy results as the ''gold standard.'' There were 27 malignant and 23 benign lesions. Chemical shift imaging using an opposed-phase signal loss criteria of less than 20 % to indicate a malignant lesion, correctly diagnosed 27/27 malignant lesions and 14/23 benign lesions, yielding a 100 % sensitivity, 61 % specificity, 75 % PPV, 100 % NPV, and 82 % accuracy. The area under the receiver operator characteristic (ROC) curve was 0.88. The inter-rater and intra-rater agreement K values were both 1.0. Chemical shift imaging is a useful adjunct MR technique to characterize focal and diffuse marrow abnormalities on routine non-contrast pelvic imaging. It is highly sensitive in identifying malignant disease. Despite its lower specificity, the need for biopsy could be eliminated in more than 60 % of patients with benign disease. (orig.)

  3. Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

    International Nuclear Information System (INIS)

    Lehtivarjo, Juuso; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino; Peräkylä, Mikael

    2012-01-01

    While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1 H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6–17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for 1 Hα, 1 HN, 13 Cα, 13 Cβ, 13 CO and backbone 15 N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

  4. Diffusion-weighted imaging of the liver at 3 T using section-selection gradient reversal: emphasis on chemical shift artefacts and lesion conspicuity

    International Nuclear Information System (INIS)

    Lee, J.S.; Kim, Y.K.; Jeong, W.K.; Choi, D.; Lee, W.J.

    2015-01-01

    Aim: To assess the value of section-selection gradient reversal (SSGR) in liver diffusion-weighted imaging (DWI) by comparing it to conventional DWI with an emphasis on chemical shift artefacts and lesion conspicuity. Materials and methods: Forty-eight patients (29 men and 19 women; age range 33–80 years) with 48 liver lesions underwent two DWI examinations using spectral presaturation with inversion recovery fat suppression with and without SSGR at 3 T. Two reviewers evaluated each DWI (b = 100 and b = 800 image) with respect to chemical shift artefacts and liver lesion conspicuity using five-point scales and performed pairwise comparisons between the two DWIs. The signal-to-noise ratio (SNR) of the liver and the lesion and the lesion–liver contrast-to-noise ratio (CNR) were also calculated. Results: SSGR-DWI was significantly better than conventional DWI with respect to chemical shift artefacts and lesion conspicuity in both separate reviews and pairwise comparisons (p < 0.05). There were significant differences in the SNR of the liver (b = 100 and b = 800 images) and lesion (b = 800) between SSGR-DWI and conventional DWI (p < 0.05). Conclusion: Applying the SSGR method to DWI using SPIR fat suppression at 3 T could significantly reduce chemical shift artefacts without incurring additional acquisition time or SNR penalties, which leads to increased conspicuity of focal liver lesions. - Highlights: • Chemical shift artefact in liver DWI is markedly decreased by applying SSGR. • Liver lesion conspicuity is improved by applying SSGR to DWI. • In SNR of the liver, SSGR-DWI is better than conventional DWI

  5. Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

    Energy Technology Data Exchange (ETDEWEB)

    Lehtivarjo, Juuso, E-mail: juuso.lehtivarjo@uef.fi; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino [University of Eastern Finland, School of Pharmacy (Finland); Peraekylae, Mikael [University of Eastern Finland, Institute of Biomedicine (Finland)

    2012-03-15

    While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein {sup 1}H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6-17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for {sup 1}H{alpha}, {sup 1}HN, {sup 13}C{alpha}, {sup 13}C{beta}, {sup 13}CO and backbone {sup 15}N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

  6. Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E. [Stanford University, Stanford, California 94309 (United States)

    1997-08-01

    The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H{endash}Si bond on the H{endash}Si(111) surface, and (ii) replacement of Cl on the Cl{endash}Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C{endash}Si bond length of 1.85{plus_minus}0.05{Angstrom}. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. {copyright} {ital 1997 American Institute of Physics.}

  7. Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

    International Nuclear Information System (INIS)

    Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E.

    1997-01-01

    The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H endash Si bond on the H endash Si(111) surface, and (ii) replacement of Cl on the Cl endash Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C endash Si bond length of 1.85±0.05 Angstrom. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. copyright 1997 American Institute of Physics

  8. Chemical shift of U L3 edges in different uranium compounds obtained by X-ray absorption spectroscopy with synchrotron radiation

    International Nuclear Information System (INIS)

    Joseph, D.; Jha, S.N.; Nayak, C.; Bhattacharyya, D.; Babu, P. Venu

    2014-01-01

    Uranium L 3 X-ray absorption edge was measured in various compounds containing uranium in U 4+ , U 5+ and U 5+ oxidation states. The measurements have been carried out at the Energy Dispersive EXAFS beamline (BL-08) at INDUS-2 synchrotron radiation source at RRCAT, Indore. Energy shifts of ∼ 2-3 eV were observed for U L 3 edge in the U-compounds compared to their value in elemental U. The different chemical shifts observed for the compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on U cation in the above compounds. (author)

  9. Using chemical-shift MR imaging to quantify fatty degeneration within supraspinatus muscle due to supraspinatus tendon injuries

    Energy Technology Data Exchange (ETDEWEB)

    Gokalp, Gokhan; Yildirim, Nalan; Yazici, Zeynep [Uludag University Medical Faculty, Department of Radiology, Gorukle, Bursa (Turkey); Ercan, Ilker [Uludag University Medical Faculty, Department of Biostatistics, Gorukle, Bursa (Turkey)

    2010-12-15

    The objective of this study was to prospectively quantify the fatty degeneration of supraspinatus (SSP) muscle due to SSP tendon injuries by using chemical-shift magnetic resonance imaging (CS-MRI). Forty-one patients with suspected rotator cuff tear or impingement examined with MR arthrography were included in the study. The following images were obtained after injection of diluted gadolinium chelate into glenohumeral joint: fat-saturated T1-weighted spin echo in the coronal, axial, and sagittal-oblique plane; fat-saturated T2-weighted and intermediate-weighted fast spin-echo in the coronal-oblique plane; and T1-weighted spin echo in the sagittal-oblique plane. CS-MRI was performed in the coronal plane using a double-echo fast low-angle shot (FLASH) sequence. SSP tendon changes were classified as normal, tendinosis, and partial and complete tear according to MR arthrography findings. Fatty degeneration was quantified after measurement of signal intensity values within the region of interest (ROI) placed over SSP muscle. Signal intensity (SI) suppression ratio and SI index were calculated with the values obtained. Degrees of fatty degeneration depicted in normal subjects and subjects with rotator cuff injuries were compared. Median (min:max) was used as descriptive values. SI suppression ratio was -3.5% (-15.5:3.03) in normal subjects, whereas it was -13.5% (-28.55:-6.60), -30.7% (-41.5:-20.35), and -43.75% (-62:-24.90) in tendinosis, partial and complete tears, respectively. SI index was 0.75% (-6:11.5) in normal subjects. It was 10% (4.50:27), 26.5% (19.15:35.5), and 41% (23.9:57) in tendinosis, partial and complete tears, respectively. The increase in degree of fatty degeneration parallels the seriousness of tendon pathology. CS-MRI is a useful method for grading fat accumulation within SSP muscle. (orig.)

  10. High SNR Acquisitions Improve the Repeatability of Liver Fat Quantification Using Confounder-corrected Chemical Shift-encoded MR Imaging

    Science.gov (United States)

    Motosugi, Utaroh; Hernando, Diego; Wiens, Curtis; Bannas, Peter; Reeder, Scott. B

    2017-01-01

    Purpose: To determine whether high signal-to-noise ratio (SNR) acquisitions improve the repeatability of liver proton density fat fraction (PDFF) measurements using confounder-corrected chemical shift-encoded magnetic resonance (MR) imaging (CSE-MRI). Materials and Methods: Eleven fat-water phantoms were scanned with 8 different protocols with varying SNR. After repositioning the phantoms, the same scans were repeated to evaluate the test-retest repeatability. Next, an in vivo study was performed with 20 volunteers and 28 patients scheduled for liver magnetic resonance imaging (MRI). Two CSE-MRI protocols with standard- and high-SNR were repeated to assess test-retest repeatability. MR spectroscopy (MRS)-based PDFF was acquired as a standard of reference. The standard deviation (SD) of the difference (Δ) of PDFF measured in the two repeated scans was defined to ascertain repeatability. The correlation between PDFF of CSE-MRI and MRS was calculated to assess accuracy. The SD of Δ and correlation coefficients of the two protocols (standard- and high-SNR) were compared using F-test and t-test, respectively. Two reconstruction algorithms (complex-based and magnitude-based) were used for both the phantom and in vivo experiments. Results: The phantom study demonstrated that higher SNR improved the repeatability for both complex- and magnitude-based reconstruction. Similarly, the in vivo study demonstrated that the repeatability of the high-SNR protocol (SD of Δ = 0.53 for complex- and = 0.85 for magnitude-based fit) was significantly higher than using the standard-SNR protocol (0.77 for complex, P magnitude-based fit, P = 0.003). No significant difference was observed in the accuracy between standard- and high-SNR protocols. Conclusion: Higher SNR improves the repeatability of fat quantification using confounder-corrected CSE-MRI. PMID:28190853

  11. Dual-echo, chemical shift gradient-echo magnetic resonance imaging to quantify hepatic steatosis: Implications for living liver donation.

    Science.gov (United States)

    Rinella, Mary E; McCarthy, Richard; Thakrar, Kiran; Finn, John Paul; Rao, Sambasiva M; Koffron, Alan J; Abecassis, Michael; Blei, Andres T

    2003-08-01

    In living liver donation, a fatty liver poses risks for both recipient and donor. Currently, liver biopsy is the standard for assessing the presence and extent of steatosis. The goals of this study were to correlate a steatosis index derived from magnetic resonance imaging (MRI) to the histologic grade on biopsy as well as to determine the topographic distribution of steatosis within the liver. We examined the ability of dual-echo, chemical shift gradient-echo MRI to predict the degree of steatosis on liver biopsy. A total of 22 subjects received both a liver biopsy and detailed MRI evaluation. These individuals included 15 potential living donors and 7 patients with nonalcoholic fatty liver disease. MRI steatosis index was then compared with histologic grade on liver biopsy. The topographic distribution of hepatic steatosis was determined from those subjects in whom MRI detected hepatic steatosis. The steatosis index had a positive correlation with grade of steatosis on liver biopsy (correlation coefficient, 0.84). There was no significant variation in the degree of steatosis among segments. A steatosis index of >0.2 had good positive and negative predictive value for the presence of significant steatosis (>15%) on biopsy. Our quantitative MRI protocol can predict the degree of hepatic steatosis when it is minimal to moderate, and may obviate the need for liver biopsy for the purpose of quantification of steatosis in living donors. Fat saturation added to the MRI protocol may further improve diagnostic accuracy. This technique may be applicable to the larger population with hepatic steatosis.

  12. Using chemical-shift MR imaging to quantify fatty degeneration within supraspinatus muscle due to supraspinatus tendon injuries

    International Nuclear Information System (INIS)

    Gokalp, Gokhan; Yildirim, Nalan; Yazici, Zeynep; Ercan, Ilker

    2010-01-01

    The objective of this study was to prospectively quantify the fatty degeneration of supraspinatus (SSP) muscle due to SSP tendon injuries by using chemical-shift magnetic resonance imaging (CS-MRI). Forty-one patients with suspected rotator cuff tear or impingement examined with MR arthrography were included in the study. The following images were obtained after injection of diluted gadolinium chelate into glenohumeral joint: fat-saturated T1-weighted spin echo in the coronal, axial, and sagittal-oblique plane; fat-saturated T2-weighted and intermediate-weighted fast spin-echo in the coronal-oblique plane; and T1-weighted spin echo in the sagittal-oblique plane. CS-MRI was performed in the coronal plane using a double-echo fast low-angle shot (FLASH) sequence. SSP tendon changes were classified as normal, tendinosis, and partial and complete tear according to MR arthrography findings. Fatty degeneration was quantified after measurement of signal intensity values within the region of interest (ROI) placed over SSP muscle. Signal intensity (SI) suppression ratio and SI index were calculated with the values obtained. Degrees of fatty degeneration depicted in normal subjects and subjects with rotator cuff injuries were compared. Median (min:max) was used as descriptive values. SI suppression ratio was -3.5% (-15.5:3.03) in normal subjects, whereas it was -13.5% (-28.55:-6.60), -30.7% (-41.5:-20.35), and -43.75% (-62:-24.90) in tendinosis, partial and complete tears, respectively. SI index was 0.75% (-6:11.5) in normal subjects. It was 10% (4.50:27), 26.5% (19.15:35.5), and 41% (23.9:57) in tendinosis, partial and complete tears, respectively. The increase in degree of fatty degeneration parallels the seriousness of tendon pathology. CS-MRI is a useful method for grading fat accumulation within SSP muscle. (orig.)

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

    KAUST Repository

    Jang, Richard

    2011-01-01

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

  14. Modern MRI tools for the characterization of acute demyelinating lesions: value of chemical shift and diffusion-weighted imaging

    International Nuclear Information System (INIS)

    Kueker, W.; Mehnert, F.; Mader, I.; Naegele, T.; Ruff, J.; Gaertner, S.

    2004-01-01

    Acute demyelinating lesions occur in various inflammatory disorders of the CNS. Apart from multiple sclerosis, most cases can be attributed to an overshooting immunological response to infectious agents called acute disseminated encephalomyelitis (ADEM). ADEM, which is mostly characterized by a monophasic course, has a multiphasic variant (MDEM). The early application of corticosteroids has been shown to be beneficial for the outcome; thus, an early diagnosis is highly desirable. Furthermore, the differential diagnosis ruling out neoplastic disorders may be difficult using conventional MRI alone. The potential diagnostic value of advanced MR techniques such as chemical shift imaging (CSI) and diffusion-weighted imaging (DWI) was investigated in a patient with MDEM, who had a new lesion in continuity with the initial disease manifestation. CSI was performed at 1.5 T with a long echo time of 135 ms for the evaluation of N-acetyl-aspartate (NAA) and choline (Cho) and with short TE of 30 ms for macromolecules (mm) and myo-Inositol (mI). DWI was performed using a single-shot isotropic EPI sequence. Whereas acute and chronic areas of demyelination were neither distinguishable on T2- nor on contrast-enhanced T1-weigted images, CSI and DWI revealed different metabolite concentrations and diffusion characteristics within the composite lesion, clearly separating acute from chronic areas of demyelination. In conclusion, the addition of CSI and DWI may add to the diagnostic power of MRI in the setting of demyelinating disorders by identifying areas of acute and chronic demyelination, even in the absence of contrast enhancement. (orig.)

  15. Torsion of the vermiform appendix: A case report | Wani | Internet ...

    African Journals Online (AJOL)

    Torsion of the vermiform appendix is a rare condition with few cases reported in the literature. Various factors predispose to torsion. Various factors predispose to torsion. We report a case of primary torsion of the vermiform appendix. The clinical presentation was indistinguishable from acute appendicitis and the diagnosis ...

  16. Measurement of tibial torsion by computer tomography

    Energy Technology Data Exchange (ETDEWEB)

    Jend, H.H.; Heller, M.; Dallek, M.; Schoettle, H. (Hamburg Univ. (Germany, F.R.))

    1981-01-01

    A CT procedure for objective measurements of tibial torsion independent of axial rotation in the nearby joints is described. Transverse sections in defined planes of the tibia permit easy calculation of normal and abnormal congenital or posttraumatic angles of torsion. In 69 limbs normal tibial torsion was 40/sup 0/+-9/sup 0/. In a series of 42 limbs with complicated healing of a fracture of both bones of the leg it is shown that tibial maltorsion is a deformity which in most cases leads to arthrosis of the ankle joint.

  17. Torsion of wandering spleen and distal pancreas

    International Nuclear Information System (INIS)

    Sheflin, J.R.; Lee, C.M.; Kretchmar, K.A.

    1984-01-01

    Wandering spleen is the term applied to the condition in which a long pedicle allows the spleen to lie in an abnormal location. Torsion of a wandering spleen is an unusual cause of an acute abdomen and is rarely diagnosed preoperatively. Associated torsion of the distal pancreas is even more uncommon. The authors describe a patient with torsion of a wandering spleen and distal pancreas, who was correctly diagnosed, and define the merits of the imaging methods used. The initial examination should be 99 /sup m/Tc-sulfur colloid liner-spleen scanning

  18. Measurement of tibial torsion by computer tomography

    International Nuclear Information System (INIS)

    Jend, H.-H.; Heller, M.; Dallek, M.; Schoettle, H.

    1981-01-01

    A CT procedure for objective measurements of tibial torsion independent of axial rotation in the nearby joints is described. Transverse sections in defined planes of the tibia permit easy calculation of normal and abnormal congenital or posttraumatic angles of torsion. In 69 limbs normal tibial torsion was 40 0 +-9 0 . In a series of 42 limbs with complicated healing of a fracture of both bones of the leg it is shown that tibial maltorsion is a deformity which in most cases leads to arthrosis of the ankle joint. (Auth.)

  19. A retrospective cohort study of shift work and risk of cancer-specific mortality in German male chemical workers.

    Science.gov (United States)

    Yong, Mei; Nasterlack, Michael; Messerer, Peter; Oberlinner, Christoph; Lang, Stefan

    2014-02-01

    Human evidence of carcinogenicity concerning shift work is inconsistent. In a previous study, we observed no elevated risk of total mortality in shift workers followed up until the end of 2006. The present study aimed to investigate cancer-specific mortality, relative to shift work. The cohort consisted of male production workers (14,038 shift work and 17,105 day work), employed at BASF Ludwigshafen for at least 1 year between 1995 and 2005. Vital status was followed from 2000 to 2009. Cause-specific mortality was obtained from death certificates. Exposure to shift work was measured both as a dichotomous and continuous variable. While lifetime job history was not available, job duration in the company was derived from personal data, which was then categorized at the quartiles. Cox proportional hazard model was used to adjust for potential confounders, in which job duration was treated as a time-dependent covariate. Between 2000 and 2009, there were 513 and 549 deaths among rotating shift and day work employees, respectively. Risks of total and cancer-specific mortalities were marginally lower among shift workers when taking age at entry and job level into consideration and were statistically significantly lower when cigarette smoking, alcohol intake, job duration, and chronic disease prevalence at entry to follow-up were included as explanatory factors. With respect to mortality risks in relation to exposure duration, no increased risks were found in any of the exposure groups after full adjustment and there was no apparent trend suggesting an exposure-response relation with duration of shift work. The present analysis extends and confirms our previous finding of no excess risk of mortality associated with work in the shift system employed at BASF Ludwigshafen. More specifically, there is also no indication of an increased risk of mortality due to cancer.

  20. Effects of temperature and torsion speed on torsional properties of single-walled carbon nanotubes

    International Nuclear Information System (INIS)

    Khoei, A.R.; Ban, E.; Banihashemi, P.; Abdolhosseini Qomi, M.J.

    2011-01-01

    Carbon nanotubes (CNTs) are excellent candidates for torsional elements used in nanoelectro-mechanical systems (NEMS). Simulations show that after being twisted to a certain angle, they buckle and lose their mechanical strength. In this paper, classical molecular dynamics simulations are performed on single-walled carbon nanotubes (CNTs) to investigate the effects of torsion speed and temperature on CNT torsional properties. The AIREBO potential is employed to describe the bonded interactions between carbon atoms. The MD simulations clearly show that the buckling of CNTs in torsion is a reversible process, in which by unloading the buckled CNT in opposite direction, it returns to its original configuration. In addition, the numerical results reveal that the torsional shear modulus of CNTs increases by increasing the temperature and decreasing the torsion speed. Furthermore, the buckling torsion angle of CNTs increases by increasing the torsion speed and decreasing the temperature. Finally, it is observed that torsional properties of CNTs are highly affected by speed of twist and temperature of the nanotubes.

  1. Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

    International Nuclear Information System (INIS)

    Bellstedt, Peter; Herbst, Christian; Häfner, Sabine; Leppert, Jörg; Görlach, Matthias; Ramachandran, Ramadurai

    2012-01-01

    We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC′C and 3D C′NCA with sequential 13 C acquisitions, 3D NHH and 3D NC′H with sequential 1 H acquisitions and 3D CANH and 3D C’NH with broadband 13 C– 15 N mixing are demonstrated using microcrystalline samples of the β1 immunoglobulin binding domain of protein G (GB1) and the chicken α-spectrin SH3 domain.

  2. Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

    Energy Technology Data Exchange (ETDEWEB)

    Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)

    2012-12-15

    We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.

  3. NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

    Science.gov (United States)

    Wiedemann, Christoph; Ohlenschläger, Oliver; Mrestani-Klaus, Carmen; Bordusa, Frank

    2017-09-13

    NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual 1 H and 13 C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.

  4. CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

    International Nuclear Information System (INIS)

    Swain, Monalisa; Atreya, Hanudatta S.

    2009-01-01

    Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment

  5. Torsion sensing based on patterned piezoelectric beams

    Science.gov (United States)

    Cha, Youngsu; You, Hangil

    2018-03-01

    In this study, we investigated the sensing characteristics of piezoelectric beams under torsional loads. We used partially patterned piezoelectric beams to sense torsion. In particular, the piezoelectric patches are located symmetrically with respect to the line of the shear center of the beam. The patterned piezoelectric beam is modeled as a slender beam, and its electrical responses are obtained by piezoelectric electromechanical equations. To validate the modeling framework, experiments are performed using a setup that forces pure torsional deformation. Three different geometric configurations of the patterned piezoelectric layer are used for the experiments. The frequency and amplitude of the forced torsional load are systematically varied in order to study the behavior of the piezoelectric sensor. Experimental results demonstrate that two voltage outputs of the piezoelectric beam are approximately out of phase with identical amplitude. Moreover, the length of the piezoelectric layers has a significant influence on the sensing properties. Our theoretical predictions using the model support the experimental findings.

  6. Torsion, supersymmetry, and the heterotic string

    International Nuclear Information System (INIS)

    Curtright, T.

    1985-01-01

    The dynamical effects of torsion are summarized for bosonic and supersymmetric sigma models in two spacetime dimensions. Analogous structure for the heterotic superstring is discussed, including the presence of nonlinear realizations of supersymmetry on the world-sheet. 27 refs

  7. Isolated torsion of fallopian tube. Radiological findings

    International Nuclear Information System (INIS)

    Tomas Fanjul, L.; Aldea Martinez, J.; Fernandez Matia, G.; Rodrigo Verguizas, J.; Fernandez Alvarez, G.; Galindo Vicente, M.C.

    1993-01-01

    Isolated tubal torsion is a very uncommon disorder that is rarely diagnosed preoperatively. We present a case and review the literature, which only provides ultrasonographic findings in 5 cases reported to date. 11 refs

  8. Doubly graded sigma model with torsion

    International Nuclear Information System (INIS)

    Kowalski-Glikman, J.

    1986-08-01

    Using the Hull-Witten construction we show how to introduce torsion to the doubly graded sigma model. This construction enables us to find a link between this model and the ten-dimensional supergravity theory in superspace. (Auth.)

  9. Electrostatically actuated torsional resonant sensors and switches

    KAUST Repository

    Younis, Mohammad I.

    2016-01-01

    Embodiments in accordance of a torsional resonant sensor disclosure is configured to actuate a beam structure using electrostatic actuation with an AC harmonic load (e.g., AC and DC voltage sources) that is activated upon detecting a particular

  10. Evidence of chemical-potential shift with hole doping in Bi2Sr2CaCu2O8+δ

    International Nuclear Information System (INIS)

    Shen, Z.; Dessau, D.S.; Wells, B.O.; Olson, C.G.; Mitzi, D.B.; Lombado, L.; List, R.S.; Arko, A.J.

    1991-01-01

    We have performed photoemission studies on high-quality Bi 2 Sr 2 CaCu 2 O 8+δ samples with various δ. Our results show a clear chemical-potential shift (0.15--0.2 eV) as a function of doping. This result and the existing angle-resolved-photoemission data give a rather standard doping behavior of this compound in its highly doped regime

  11. Nonsuppressing normal thymus on chemical-shift MR imaging and anterior mediastinal lymphoma. Differentiation with diffusion-weighted MR imaging by using the apparent diffusion coefficient

    International Nuclear Information System (INIS)

    Priola, Adriano Massimiliano; Priola, Sandro Massimo; Gned, Dario; Veltri, Andrea; Giraudo, Maria Teresa

    2018-01-01

    To prospectively evaluate usefulness of the apparent diffusion coefficient (ADC) in differentiating anterior mediastinal lymphoma from nonsuppressing normal thymus on chemical-shift MR, and to look at the relationship between patient age and ADC. Seventy-three young subjects (25 men, 48 women; age range, 9-29 years), who underwent chemical-shift MR and diffusion-weighted MR were divided into a normal thymus group (group A, 40 subjects), and a lymphoma group (group B, 33 patients). For group A, all subjects had normal thymus with no suppression on opposed-phase chemical-shift MR. Two readers measured the signal intensity index (SII) and ADC. Differences in SII and ADC between groups were tested using t-test. ADC was correlated with age using Pearson correlation coefficient. Mean SII±standard deviation was 2.7±1.8% for group A and 2.2±2.4% for group B, with no significant difference between groups (P=.270). Mean ADC was 2.48±0.38 x 10 -3 mm 2 /s for group A and 1.24±0.23 x 10 -3 mm 2 /s for group B. A significant difference between groups was found (P<.001), with no overlap in range. Lastly, significant correlation was found between age and ADC (r=0.935, P<.001) in group A. ADC of diffusion-weighted MR is a noninvasive and accurate parameter for differentiating lymphoma from nonsuppressing thymus on chemical-shift MR in young subjects. (orig.)

  12. Backbone and sidechain methyl Ile (δ1), Leu and Val chemical shift assignments of RDE-4 (1-243), an RNA interference initiation protein in C. elegans.

    Science.gov (United States)

    Chiliveri, Sai Chaitanya; Kumar, Sonu; Marelli, Udaya Kiran; Deshmukh, Mandar V

    2012-10-01

    The RNAi pathway of several organisms requires presence of double stranded RNA binding proteins for functioning of Dicer in gene regulation. In C. elegans, a double stranded RNA binding protein, RDE-4 (385 aa, 44 kDa) recognizes long exogenous dsRNA and initiates the RNAi pathway. We have achieved complete backbone and stereospecific methyl sidechain Ile (δ1), Leu and Val chemical shifts of first 243 amino acids of RDE-4, namely RDE-4ΔC.

  13. Structure, solvent, and relativistic effects on the NMR chemical shifts in square-planar transition-metal complexes: assessment of DFT approaches

    Czech Academy of Sciences Publication Activity Database

    Vícha, J.; Novotný, J.; Straka, Michal; Repisky, M.; Ruud, K.; Komorovsky, S.; Marek, R.

    2015-01-01

    Roč. 17, č. 38 (2015), s. 24944-24955 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA14-03564S Institutional support: RVO:61388963 Keywords : NMR chemical shifts * transition metal complexes * relativistic effects * method calibration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.449, year: 2015 http://pubs.rsc.org/en/content/articlepdf/2015/cp/c5cp04214c

  14. Torsion and geometrostasis in covariant superstrings

    International Nuclear Information System (INIS)

    Zachos, C.

    1985-01-01

    The covariant action for freely propagating heterotic superstrings consists of a metric and a torsion term with a special relative strength. It is shown that the strength for which torsion flattens the underlying 10-dimensional superspace geometry is precisely that which yields free oscillators on the light cone. This is in complete analogy with the geometrostasis of two-dimensional sigma-models with Wess-Zumino interactions. 13 refs

  15. Torsion and geometrostasis in covariant superstrings

    Energy Technology Data Exchange (ETDEWEB)

    Zachos, C.

    1985-01-01

    The covariant action for freely propagating heterotic superstrings consists of a metric and a torsion term with a special relative strength. It is shown that the strength for which torsion flattens the underlying 10-dimensional superspace geometry is precisely that which yields free oscillators on the light cone. This is in complete analogy with the geometrostasis of two-dimensional sigma-models with Wess-Zumino interactions. 13 refs.

  16. Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers.

    Science.gov (United States)

    Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek; Faber, Rasmus; Lacerda, Evanildo G; Sauer, Stephan P A

    2016-02-05

    Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton, and xenon dimers and free atoms. Relativistic corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles with noniterative triple excitations [CCSD(T)] calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr, and the AQZP basis set for Xe. For the dimers also, zero-point vibrational (ZPV) corrections are obtained at the CCSD(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, ZPV, and relativistic corrections for the shieldings and chemical shifts is analyzed. © 2015 Wiley Periodicals, Inc.

  17. Spectral fitting for signal assignment and structural analysis of uniformly {sup 13}C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Matsuki, Yoh; Akutsu, Hideo; Fujiwara, Toshimichi [Osaka University, Institute for Protein Research (Japan)], E-mail: tfjwr@protein.osaka-u.ac.jp

    2007-08-15

    We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional {sup 13}C-{sup 13}C magic-angle-spinning solid-state NMR spectra of uniformly {sup 13}C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C', C{sup {alpha}} and C{sup {beta}} chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50 deg. from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 A.

  18. MR imaging of osteonecrosis using frequency selective chemical shift sequences; Neue Aspekte in der MR-Diagnostik der Osteonekrose: Selektive Fett/Wasser-Bildgebung

    Energy Technology Data Exchange (ETDEWEB)

    Duda, S H [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Laniado, M [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Schick, F [Inst. fuer Physik, Tuebingen Univ. (Germany)

    1994-12-31

    The MR appearance of osteonecrosis was assessed on selective fat- and water images to further evaluate the nature of double-line sign. Conventional T1- and T2-weighted SE and frequency selective chemical shift images of eight patients with avascular necrosis of the femoral head and three patients with bone infarcts were retrospectively reviewed. Eight of 11 patients showed a double-line sign on T2-weighted SE images. In these cases, correlation with selective water images revealed that a chemical shift artifact contributed to appearance and location of the hyperintense line. The authors conclude that chemical shift imaging improves our understanding of the nature of the double-line sign. (orig.) [Deutsch] Das MR-tomographische Erscheinungsbild der Osteonekrose auf selektiven Fett- und Wasserbildern wurde analysiert, um das in der Literatur beschriebene Doppellinienzeichen naeher zu untersuchen. Hierfuer wurden sowohl die herkoemmlichen T1- und T2-gewichteten Spin-Echo-Sequenzen herangezogen, als auch frequenzselektive Bilder, die aufgrund chemischer Verschiebung gewonnen wurden (1,5 T). Es wurden die Untersuchungen von acht Patienten mit avaskulaerer Hueftkopfnekrose und von drei Patienten mit Knocheninfarkten retrospektiv ausgewertet. Acht von 11 Patienten zeigten ein Doppellinienzeichen auf den T2-gewichteten Bildern. Die Korrelation mit den selektiven Wasserbildern ergab, dass durch chemische Verschiebung bedingte Artefakte das Erscheinungsbild und den Ort der hyperintensen Linie beeinflussten. Die Bildgebung mit Hilfe der chemischen Verschiebung verbessert unser Verstaendnis der MRT-Charakteristika der Osteonekrose. (orig.)

  19. Attentional Modulation of Eye Torsion Responses

    Science.gov (United States)

    Stevenson, Scott B.; Mahadevan, Madhumitha S.; Mulligan, Jeffrey B.

    2016-01-01

    Eye movements generally have both reflexive and voluntary aspects, but torsional eye movements are usually thought of as a reflexive response to image rotation around the line of sight (torsional OKN) or to head roll (torsional VOR). In this study we asked whether torsional responses could be modulated by attention in a case where two stimuli rotated independently, and whether attention would influence the latency of responses. The display consisted of rear-projected radial "pinwheel" gratings, with an inner annulus segment extending from the center to 22 degrees eccentricity, and an outer annulus segment extending from 22 degrees out to 45 degrees eccentricity. The two segments rotated around the center in independent random walks, stepping randomly 4 degrees clockwise or counterclockwise at 60 Hz. Subjects were asked to attend to one or the other while keeping fixation steady at the center of the display. To encourage attention on one or the other segment of the display, subjects were asked to move a joystick in synchrony with the back and forth rotations of one part of the image while ignoring the other. Eye torsion was recorded with the scleral search coil technique, sampled at 500 Hz. All four subjects showed roughly 50% stronger torsion responses to the attended compared to unattended segments. Latency varied from 100 to 150 msec across subjects and was unchanged by attention. These findings suggest that attention can influence eye movement responses that are not typically under voluntary control.

  20. Torsional Optomechanics of a Levitated Nonspherical Nanoparticle

    Science.gov (United States)

    Hoang, Thai M.; Ma, Yue; Ahn, Jonghoon; Bang, Jaehoon; Robicheaux, F.; Yin, Zhang-Qi; Li, Tongcang

    2016-09-01

    An optically levitated nanoparticle in vacuum is a paradigm optomechanical system for sensing and studying macroscopic quantum mechanics. While its center-of-mass motion has been investigated intensively, its torsional vibration has only been studied theoretically in limited cases. Here we report the first experimental observation of the torsional vibration of an optically levitated nonspherical nanoparticle in vacuum. We achieve this by utilizing the coupling between the spin angular momentum of photons and the torsional vibration of a nonspherical nanoparticle whose polarizability is a tensor. The torsional vibration frequency can be 1 order of magnitude higher than its center-of-mass motion frequency, which is promising for ground state cooling. We propose a simple yet novel scheme to achieve ground state cooling of its torsional vibration with a linearly polarized Gaussian cavity mode. A levitated nonspherical nanoparticle in vacuum will also be an ultrasensitive nanoscale torsion balance with a torque detection sensitivity on the order of 10-29 N m /√{Hz } under realistic conditions.

  1. Torsional oscillations of strange stars

    Directory of Open Access Journals (Sweden)

    Mannarelli Massimo

    2014-01-01

    Full Text Available Strange stars are one of the hypothetical compact stellar objects that can be formed after a supernova explosion. The existence of these objects relies on the absolute stability of strange collapsed quark matter with respect to standard nuclear matter. We discuss simple models of strange stars with a bare quark matter surface, thus standard nuclear matter is completely absent. In these models an electric dipole layer a few hundreds Fermi thick should exist close to the star surface. Studying the torsional oscillations of the electrically charged layer we estimate the emitted power, finding that it is of the order of 1045 erg/s, meaning that these objects would be among the brightest compact sources in the heavens. The associated relaxation times are very uncertain, with values ranging between microseconds and minutes, depending on the crust thickness. Although part of the radiated power should be absorbed by the electrosphere surrounding the strange star, a sizable fraction of photons should escape and be detectable.

  2. Reproducibility and influencing factors of 31P MR spectroscopy in rabbit liver with two-dimensional chemical shift imaging

    International Nuclear Information System (INIS)

    Yu Risheng; Sun Jianzhong; Ding Wenhong; Xu Xiufang; Wang Zhikang

    2009-01-01

    Objective: To investigate the reproducibility and influencing factors of relative quantification of phosphorus metabolites with two-dimensional chemical shift imaging (2D CSI) in rabbit liver. Methods: Using 2D CSI MRS, 500 ml phosphate (NaH 2 PO 4 ) solution phantom with 0.05 mol/L concentration and one healthy rabbit were scanned 30 times respectively in one day and rescanned 30 times in the next day, and the stability of MR scanner and reproducibility of within-run and between-days in the same individual were analyzed. Each of thirty rabbits was scanned and rescanned one time respectively in different days, and the reproducibility of between-days in one group was analyzed. The data were statistically analyzed with t tests. Results: (1) Phosphate solution phantom had a good reproducibility of within-run with the coefficient variation (CV) of 4.92% and 5.12% respectively in different two days. No significant change of phosphorus metabolites was detected in between-days, which was 16.68±0.82 and 16.56± 0.85 respectively (t=0.665, P>0.05). (2) The CV of metabolites in one healthy rabbit ranged from 8.04% to 34.13%. Among the metabolites, β-ATP had the best reproducibility with the CV less than 10%. PME was 0.88±0.28 and 0.88±0.30, PDE was 4.35±0.66 and 4.35±0.66, Pi was 0.95±0.30 and 0.97±0.28, α-ATP was 5.58±0.60 and 5.61±0.61, β-ATP was 2.70±0.22 and 2.71± 0.22, γ-ATP was 2.20±0.63 and 2.18±0.44 respectively, no significant changes of metabolites were detected in between-days (P>0.05). (3) The CV of metabolites in 30 healthy rabbits ranged from 8.48% to 36.21%. Among the metabolites, β-ATP had the best reproducibility with CV less than 10%. PME was 0.84±0.30 and 0.79±0.28, PDE was 4.29±0.72 and 3.94±0.84, Pi was 0.91±0.28 and 0.92± 0.31, α-ATP was 5.65±0.66 and 5.36±0.60, β-ATP was 2.71±0.23 and 2.66±0.25, γ-ATP was 2.07±0.29 and 1.99±0.37 respectively, no significant changes of metabolites were detected in between-days (P>0

  3. Hydroxyl free radical production during torsional phacoemulsification.

    Science.gov (United States)

    Aust, Steven D; Hebdon, Thomas; Humbert, Jordan; Dimalanta, Ramon

    2010-12-01

    To quantitate free radical generation during phacoemulsification using an ultrasonic phacoemulsification device that includes a torsional mode and evaluate tip designs specific to the torsional mode. Chemistry and Biochemistry Department, Utah State University, Logan, Utah, USA. Experimental study. Experiments were performed using the Infiniti Vision System and OZil handpiece. Hydroxyl radical concentrations in the aspirated irrigation solution during torsional phacoemulsification were quantitated as nanomolar malondialdehyde (nM MDA) and determined spectrophotometrically using the deoxyribose assay. The mean free radical production during phacoemulsification with torsional modality at 100% amplitude was 30.1 nM MDA ± 5.1 (SD) using a 0.9 mm 45-degree Kelman tapered ABS tip. With other tip designs intended for use with the torsional modality, free radical production was further reduced when fitted with the 0.9 mm 45-degree Kelman mini-flared ABS tip (13.2 ± 5.6 nM MDA) or the 0.9 mm 45-degree OZil-12 mini-flared ABS tip (14.3 ± 6.7 nM MDA). Although the measurements resulting from the use of the latter 2 tips were not statistically significantly different (P ≈ .25), they were different from those of the tapered tip (P<.0001). The MDA concentration in the aspirated irrigation solution using the torsional modality was approximately one half that reported for the handpiece's longitudinal modality in a previous study using the same bent-tip design (Kelman tapered, P<.0001). The level of MDA was further reduced approximately one half with torsional-specific tips. Copyright © 2010 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  4. Integrated ecological and chemical food web accumulation modeling explains PAH temporal trends during regime shifts in a shallow lake.

    Science.gov (United States)

    Kong, Xiangzhen; He, Wei; Qin, Ning; Liu, Wenxiu; Yang, Bin; Yang, Chen; Xu, Fuliu; Mooij, Wolf M; Koelmans, Albert A

    2017-08-01

    Shallow lakes can switch suddenly from a turbid situation with high concentrations of phytoplankton and other suspended solids to a vegetated state with clear water, and vice versa. These alternative stable states may have a substantial impact on the fate of hydrophobic organic compounds (HOCs). Models that are fit to simulate impacts from these complex interactions are scarce. We developed a contaminant fate model which is linked to an ecosystem model (PCLake) for shallow lakes. This integrated model was successful in simulating long-term dynamics (1953-2012) of representative polycyclic aromatic hydrocarbons (PAHs) in the main biotic and abiotic components in a large shallow lake (Chaohu in China), which has undergone regime shifts in this period. Historical records from sediment cores were used to evaluate the model. The model revealed that regime shifts in shallow lakes had a strong impact on the fate of less hydrophobic compounds due to the large storage capacity of macrophytes, which accumulated up to 55.6% of phenanthrene in the clear state. The abrupt disappearance of macrophytes after the regime shift resulted in a sudden change in phenanthrene distribution, as the sediment became the major sink. For more hydrophobic compounds such as benzo(a)pyrene, the modeled impact of the regime shift was negligible for the whole environment, yet large for biotic compartments. This study is the first to provide a full mechanistic analysis of the impact of regime shifts on the fate of PAHs in a real lake ecosystem. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Effects of irritant chemicals on Aedes aegypti resting behavior: is there a simple shift to untreated "safe sites"?

    Directory of Open Access Journals (Sweden)

    Hortance Manda

    2011-07-01

    Full Text Available BACKGROUND: Previous studies have identified the behavioral responses of Aedes aegypti to irritant and repellent chemicals that can be exploited to reduce man-vector contact. Maximum efficacy of interventions based on irritant chemical actions will, however, require full knowledge of variables that influence vector resting behavior and how untreated "safe sites" contribute to overall impact. METHODS: Using a laboratory box assay, resting patterns of two population strains of female Ae. aegypti (THAI and PERU were evaluated against two material types (cotton and polyester at various dark:light surface area coverage (SAC ratio and contrast configuration (horizontal and vertical under chemical-free and treated conditions. Chemicals evaluated were alphacypermethrin and DDT at varying concentrations. RESULTS: Under chemical-free conditions, dark material had significantly higher resting counts compared to light material at all SAC, and significantly increased when material was in horizontal configuration. Cotton elicited stronger response than polyester. Within the treatment assays, significantly higher resting counts were observed on chemical-treated dark material compared to untreated light fabric. However, compared to matched controls, significantly less resting observations were made on chemical-treated dark material overall. Most importantly, resting observations on untreated light material (or "safe sites" in the treatment assay did not significantly increase for many of the tests, even at 25% SAC. Knockdown rates were ≤5% for all assays. Significantly more observations of flying mosquitoes were made in test assays under chemical-treatment conditions as compared to controls. CONCLUSIONS/SIGNIFICANCE: When preferred Ae. aegypti resting sites are treated with chemicals, even at reduced treatment coverage area, mosquitoes do not simply move to safe sites (untreated areas following contact with the treated material. Instead, they become agitated

  6. Transport-induced shifts in condensate dew-point and composition in multicomponent systems with chemical reaction

    Science.gov (United States)

    Rosner, D. E.; Nagarajan, R.

    1985-01-01

    Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.

  7. Ultimate Strength of Ship Hulls under Torsion

    DEFF Research Database (Denmark)

    Paik, Jeom Kee; Thayamballi, Anil K.; Pedersen, Preben Terndrup

    2001-01-01

    For a ship hull with large deck openings such as container vessels and some large bulk carriers, the analysis of warping stresses and hatch opening deformations is an essential part of ship structural analyses. It is thus of importance to better understand the ultimate torsional strength characte......For a ship hull with large deck openings such as container vessels and some large bulk carriers, the analysis of warping stresses and hatch opening deformations is an essential part of ship structural analyses. It is thus of importance to better understand the ultimate torsional strength...... characteristics of ships with large hatch openings. The primary aim of the present study is to investigate the ultimate strength characteristics of ship hulls with large hatch openings under torsion. Axial (warping) as well as shear stresses are normally developed for thin-walled beams with open cross sections...... subjected to torsion. A procedure for calculating these stresses is briefly described. As an illustrative example, the distribution and magnitude of warping and shear stresses for a typical container vessel hull cross section under unit torsion is calculated by the procedure. By theoretical and numerical...

  8. Heat production: Longitudinal versus torsional phacoemulsification.

    Science.gov (United States)

    Han, Young Keun; Miller, Kevin M

    2009-10-01

    To compare the heat production of longitudinal versus torsional phacoemulsification under strict laboratory test conditions. Department of Ophthalmology, David Geffen School of Medicine at UCLA, and Jules Stein Eye Institute, Los Angeles, California, USA. Two Infiniti phacoemulsification handpieces were inserted into silicone test chambers filled with a balanced salt solution and imaged serially using a thermal camera. Incision compression was simulated by suspending 25.3 g weights from the silicone chambers. To simulate occlusion of the phacoemulsification tip, the aspiration line was clamped. Peak temperatures were measured 0, 10, 30, 60, and 120 seconds after the commencement of continuous ultrasound power. The 2 handpieces, operating exclusively in longitudinal or torsional modes, were compared 3 ways: (1) using the same power displayed on the instrument console, (2) using identical stroke lengths, and (3) using the same applied energy, a product of stroke length and frequency. For all 3 comparisons, torsional phacoemulsification resulted in lower temperatures at each time point. At the same displayed power setting, the scenario most familiar to cataract surgeons, longitudinal phacoemulsification elevated temperatures up to 41.5 degrees C more than torsional phacoemulsification. Torsional phacoemulsification generated less heat than longitudinal phacoemulsification in all 3 comparison tests. Lower operating temperatures indicate lower heat generation within the same volume of fluid, and this may provide additional thermal protection during cataract surgery.

  9. Prediction of microvascular invasion of hepatocellular carcinomas with gadoxetic acid-enhanced MR imaging: Impact of intra-tumoral fat detected on chemical-shift images

    Energy Technology Data Exchange (ETDEWEB)

    Min, Ji Hye [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Young Kon, E-mail: jmyr@dreamwiz.com [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Lim, Sanghyeok [Department of Radiology, Guri Hospital, Hanyang University College of Medicine, Guri (Korea, Republic of); Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)

    2015-06-15

    Highlights: • Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC. • Alfa-fetoprotein, tumor size, and fat component were associated with MVI of HCC. • Chemical shift MRI should be considered for the evaluation of HCC. - Abstract: Purpose: To investigate the impact of intra-tumoral fat detected by chemical-shift MR imaging in predicting the MVI of HCC. Materials and methods: Gadoxetic acid-enhanced MR imaging of 365 surgically proven HCCs from 365 patients (306 men, 59 women; mean age, 55.6 years) were evaluated. HCCs were classified into two groups, fat-containing and non-fat-containing, based on the presence of fat on chemical-shift images. Fat-containing HCCs were subdivided into diffuse or focal fatty change groups. Logistic regression analyses were used to identify clinical and MR findings associated with MVI. Results: Based on MR imaging, 66 tumors were classified as fat-containing HCCs and 299 as non-fat-containing HCCs. Among the 66 fat-containing HCCs, 38 (57.6%) showed diffuse fatty changes and 28 (42.4%) showed focal fatty changes. MVI was present in 18 (27.3%) fat-containing HCCs and in 117 (39.1%) non-fat-containing HCCs (P = 0.07). Univariate analysis revealed that serum alpha-fetoprotein (AFP) and tumor size were significantly associated with MVI (P < 0.001). A multiple logistic regression analysis showed that log AFP (odds ratio 1.178, P = 0.0016), tumor size (odds ratio 1.809, P < 0.001), and intra-tumoral fat (odds ratio 0.515, P = 0.0387) were independent variables associated with MVI. Conclusion: Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC and, therefore, a possibly more favorable prognosis, but the clinical value of this finding is uncertain.

  10. Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

    Science.gov (United States)

    Estes, Deven P; Gordon, Christopher P; Fedorov, Alexey; Liao, Wei-Chih; Ehrhorn, Henrike; Bittner, Celine; Zier, Manuel Luca; Bockfeld, Dirk; Chan, Ka Wing; Eisenstein, Odile; Raynaud, Christophe; Tamm, Matthias; Copéret, Christophe

    2017-12-06

    Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH 3 ) 3-x (CF 3 ) x } 3 ] (MoF 0 , x = 0; MoF 3 , x = 1; MoF 6 , x = 2; MoF 9 , x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The 13 C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF 0 molecular and supported species. Detailed solid-state NMR analysis of molecular and silica-supported metal alkylidyne catalysts coupled with DFT/ZORA calculations rationalize the NMR spectroscopic signatures and discernible activity trends at the frontier orbital level: (1) increasing the number of fluorine atoms lowers the energy of the π*(M≡C) orbital, explaining the more deshielded chemical shift values; it also leads to an increased electrophilicity and higher reactivity for catalysts up to MoF 6 , prior to a sharp decrease in reactivity for MoF 9 due to the formation of stable metallacyclobutadiene intermediates; (2) the silica-supported catalysts are less active than their molecular analogues because they are less electrophilic and dynamic, as revealed by their 13 C NMR chemical shift tensors.

  11. Prediction of microvascular invasion of hepatocellular carcinomas with gadoxetic acid-enhanced MR imaging: Impact of intra-tumoral fat detected on chemical-shift images

    International Nuclear Information System (INIS)

    Min, Ji Hye; Kim, Young Kon; Lim, Sanghyeok; Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae

    2015-01-01

    Highlights: • Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC. • Alfa-fetoprotein, tumor size, and fat component were associated with MVI of HCC. • Chemical shift MRI should be considered for the evaluation of HCC. - Abstract: Purpose: To investigate the impact of intra-tumoral fat detected by chemical-shift MR imaging in predicting the MVI of HCC. Materials and methods: Gadoxetic acid-enhanced MR imaging of 365 surgically proven HCCs from 365 patients (306 men, 59 women; mean age, 55.6 years) were evaluated. HCCs were classified into two groups, fat-containing and non-fat-containing, based on the presence of fat on chemical-shift images. Fat-containing HCCs were subdivided into diffuse or focal fatty change groups. Logistic regression analyses were used to identify clinical and MR findings associated with MVI. Results: Based on MR imaging, 66 tumors were classified as fat-containing HCCs and 299 as non-fat-containing HCCs. Among the 66 fat-containing HCCs, 38 (57.6%) showed diffuse fatty changes and 28 (42.4%) showed focal fatty changes. MVI was present in 18 (27.3%) fat-containing HCCs and in 117 (39.1%) non-fat-containing HCCs (P = 0.07). Univariate analysis revealed that serum alpha-fetoprotein (AFP) and tumor size were significantly associated with MVI (P < 0.001). A multiple logistic regression analysis showed that log AFP (odds ratio 1.178, P = 0.0016), tumor size (odds ratio 1.809, P < 0.001), and intra-tumoral fat (odds ratio 0.515, P = 0.0387) were independent variables associated with MVI. Conclusion: Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC and, therefore, a possibly more favorable prognosis, but the clinical value of this finding is uncertain

  12. 1H NMR spectra. Part 30(+): 1H chemical shifts in amides and the magnetic anisotropy, electric field and steric effects of the amide group.

    Science.gov (United States)

    Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

    2013-03-01

    The (1)H spectra of 37 amides in CDCl(3) solvent were analysed and the chemical shifts obtained. The molecular geometries and conformational analysis of these amides were considered in detail. The NMR spectral assignments are of interest, e.g. the assignments of the formamide NH(2) protons reverse in going from CDCl(3) to more polar solvents. The substituent chemical shifts of the amide group in both aliphatic and aromatic amides were analysed using an approach based on neural network data for near (≤3 bonds removed) protons and the electric field, magnetic anisotropy, steric and for aromatic systems π effects of the amide group for more distant protons. The electric field is calculated from the partial atomic charges on the N.C═O atoms of the amide group. The magnetic anisotropy of the carbonyl group was reproduced with the asymmetric magnetic anisotropy acting at the midpoint of the carbonyl bond. The values of the anisotropies Δχ(parl) and Δχ(perp) were for the aliphatic amides 10.53 and -23.67 (×10(-6) Å(3)/molecule) and for the aromatic amides 2.12 and -10.43 (×10(-6) Å(3)/molecule). The nitrogen anisotropy was 7.62 (×10(-6) Å(3)/molecule). These values are compared with previous literature values. The (1)H chemical shifts were calculated from the semi-empirical approach and also by gauge-independent atomic orbital calculations with the density functional theory method and B3LYP/6-31G(++) (d,p) basis set. The semi-empirical approach gave good agreement with root mean square error of 0.081 ppm for the data set of 280 entries. The gauge-independent atomic orbital approach was generally acceptable, but significant errors (ca. 1 ppm) were found for the NH and CHO protons and also for some other protons. Copyright © 2013 John Wiley & Sons, Ltd.

  13. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    Science.gov (United States)

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Detection of fat in focal liver lesions using chemical-shift MR imaging: its significance in patients with and without hepatic cirrhosis

    International Nuclear Information System (INIS)

    Martin, J.

    1999-01-01

    To determine the utility of the chemical shift technique in MRI for the detection of fact in focal hepatic lesions and to see its significance in patients with and without hepatic cirrhosis. 159 patients with 207 hepatic lesions were studied using MRI (IT). Two groups were established: a) patients with hepatic cirrhosis (n=63 with 69 lesions) and b) patients without cirrhosis (n=96 with 138 lesions). Images were obtained in phase (P) and in opposite phase (OP) with gradient echo sequences (RG). The parameter used to differentiate the lesions with fat from those without fat was the variation percentage of the intensity of the signal (VIS) between the images in P and in OP. The statistical valuation was carried out using Student's t tests and the area under the ROC curve. The chemical shift technique detected fat in 25 lesions (12%), 10 hepatocarcinomas in the patients with cirrhosis and two angiomyolipomas and 13 nodular fat infiltrations in the patients who did not have cirrhosis. The average VIS percentage in the 10 hepatocarcinomas was 174.77% (ranging from 88.64% to 369.33%) while in the remaining 59 hepatocarcinomas it was -4.03% (ranging from 12.79% to -19.10%) (p=0.003). In the patients who did not have cirrhosis the average VIS percentage of the lesions with fat was 161.23 (ranging from 19.82 to 605.78) while in the lesions without fat it was -0.41 (ranging from -18.96 to 19.52) (p=0.003). The area under the ROC curve was 1 for the VIS parameter. The chemical shift technique allowed for fat to be detected within hepatic lesions. Based on our study, a nodule with fat in a patient with hepatic cirrhosis is suspected to have hepatocarcinomas while in patients who do not suffer from cirrhosis the existence of fat in a nodule favours its bening nature. (Author) 39 refs

  15. On the relationship between tibia torsional deformation and regional muscle contractions in habitual human exercises in vivo.

    Science.gov (United States)

    Yang, Peng-Fei; Kriechbaumer, Andreas; Albracht, Kirsten; Sanno, Maximilian; Ganse, Bergita; Koy, Timmo; Shang, Peng; Brüggemann, Gert-Peter; Müller, Lars Peter; Rittweger, Jörn

    2015-02-05

    The mechanical relationship between bone and muscle has been long recognized. However, it still remains unclear how muscles exactly load on bone. In this study, utilizing an optical segment tracking technique, the in vivo tibia loading regimes in terms of tibia segment deformation in humans were investigated during walking, forefoot and rear foot stair ascent and running and isometric plantar flexion. Results suggested that the proximal tibia primarily bends to the posterior aspect and twists to the external aspect with respect to the distal tibia. During walking, peak posterior bending and peak torsion occurred in the first half (22%) and second half (76%) of the stance phase, respectively. During stair ascent, two noticeable peaks of torsion were found with forefoot strike (38% and 82% of stance phase), but only one peak of torsion was found with rear foot strike (78% of stance phase). The torsional deformation angle during both stair ascent and running was larger with forefoot strike than rear foot strike. During isometric plantar flexion, the tibia deformation regimes were characterized more by torsion (maximum 1.35°) than bending (maximum 0.52°). To conclude, bending and torsion predominated the tibia loading regimes during the investigated activities. Tibia torsional deformation is closely related to calf muscle contractions, which further confirm the notion of the muscle-bone mechanical link and shift the focus from loading magnitude to loading regimes in bone mechanobiology. It thus is speculated that torsion is another, yet under-rated factor, besides the compression and tension, to drive long bone mechano-adaptation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Ultrasonographic diagnosis of torsion of testicular appendages

    International Nuclear Information System (INIS)

    Esparza, J.; Gonzalez, A.; Cordero, J. L.

    2000-01-01

    To determine the efficacy of ultrasound in boys presenting torsion of a testicular appendage. A series of 30 boys with acute scrotal pain due to torsion of a testicular appendage was studied. Nine patients underwent surgery. The clinical findings and course in the remaining 21 suggested the presence of this abnormality. All of them underwent conventional and color Doppler ultrasound using a 7.5 MHz transducer. In 15 boys, ultrasound images depicted the affected appendage as a mass between the epididymal head and the testicle. In 13 cases, only signs of a inflammatory reaction, with enlargement of the epididymal head and tunicas presenting hyperflow and hydrocele, mimicking acute epididymities. In two cases, the images were normal. There is no definitive, distinguishing ultrasound image corresponding to testicular appendage torsion. Therefore, this diagnostic technique should be accompanied by clinical assessment. (Author) 14 refs

  17. Determination of the torsion angles of alanine and glycine residues of model compounds of spider silk (AGG){sub 10} using solid-state NMR methods

    Energy Technology Data Exchange (ETDEWEB)

    Ashida, Jun; Ohgo, Kosuke; Komatsu, Kohei; Kubota, Ayumi; Asakura, Tetsuo [Tokyo University of Agriculture and Technology, Department of Biotechnology (Japan)], E-mail: asakura@cc.tuat.ac.jp

    2003-02-15

    Spiders synthesize several kinds of silk fibers. In the primary structure of spider silk, one of the major ampullate (dragline, frame) silks, spidroin 1, and flagelliform silk (core fibers of adhesive spiral), there are common repeated X-Gly-Gly (X = Ala, Leu, Pro, Tyr, Glu, and Arg) sequences, which are considered to be related to the elastic character of these fibers. In this paper, two dimensional spin diffusion solid-state NMR under off magic angle spinning (OMAS), {sup 13}C chemical shift contour plots, and Rotational Echo DOuble Resonance (REDOR) were applied to determine the torsion angles of one Ala and two kinds of Gly residues in the Ala-Gly-Gly sequence of {sup 13}C=O isotope-labeled (Ala-Gly-Gly){sub 10}. The torsion angles were determined to be ({phi}, {psi}) = (-90 deg., 150 deg.) within an experimental error of {+-}10 deg. for each residue. This conformation is characterized as 3{sub 1} helix which is in agreement with the structure proposed from the X-ray powder diffraction pattern of poly(Ala-Gly-Gly). The 3{sub 1} helix of (Ala-Gly-Gly){sub 10} does not change by formic acid treatment although (Ala-Gly){sub 15} easily changes from the silk I conformation (the structure of Bombyx mori silk fibroin before spinning in the solid state) to silk II conformation (the structure of the silk fiber after spinning) by such treatment. Thus, the 3{sub 1} helix conformation of (Ala-Gly-Gly){sub 10} is considered very stable. Furthermore, the torsion angles of the 16th Leu residue of (Leu-Gly-Gly){sub 10} were also determined as ({phi}, {psi}) = (-90 deg., 150 deg.) and this peptide is also considered to take 3{sub 1} helix conformation.

  18. 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.

  19. Other compounds isolated from Simira glaziovii and the {sup 1}H and {sup 13}C NMR chemical shift assignments of new 1-epi-castanopsol

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Marcelo F. de; Vieira, Ivo J. Curcino [Universidade Federal Rural do Rio de Janeiro, Seropedica, RJ (Brazil). Dept. de Quimica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Centro de Ciencias Tecnologicas. Lab. de Ciencias Quimicas; Carvalho, Mario G. de, E-mail: mgeraldo@ufrrj.br [Universidade Federal do Rio de Janeiro (NPPN/UFRJ), RJ (Brazil). Centro de Ciencias da Saude. Nucleo de Pesquisa em Produtos Naturais

    2012-07-01

    A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D {sup 1}H, {sup 13}C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of {sup 1}H and {sup 13}C NMR chemical shift assignments. (author)

  20. Other compounds isolated from Simira glaziovii and the 1H and 13C NMR chemical shift assignments of new 1-epi-castanopsol

    International Nuclear Information System (INIS)

    Araujo, Marcelo F. de; Vieira, Ivo J. Curcino; Braz-Filho, Raimundo; Carvalho, Mario G. de

    2012-01-01

    A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D 1 H, 13 C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of 1 H and 13 C NMR chemical shift assignments. (author)

  1. Hydrogen exchange rate of tyrosine hydroxyl groups in proteins as studied by the deuterium isotope effect on C(zeta) chemical shifts.

    Science.gov (United States)

    Takeda, Mitsuhiro; Jee, Jungoo; Ono, Akira Mei; Terauchi, Tsutomu; Kainosho, Masatsune

    2009-12-30

    We describe a new NMR method for monitoring the individual hydrogen exchange rates of the hydroxyl groups of tyrosine (Tyr) residues in proteins. The method utilizes (2S,3R)-[beta(2),epsilon(1,2)-(2)H(3);0,alpha,beta,zeta-(13)C(4);(15)N]-Tyr, zeta-SAIL Tyr, to detect and assign the (13)C(zeta) signals of Tyr rings efficiently, either by indirect (1)H-detection through 7-8 Hz (1)H(delta)-(13)C(zeta) spin couplings or by direct (13)C(zeta) observation. A comparison of the (13)C(zeta) chemical shifts of three Tyr residues of an 18.2 kDa protein, EPPIb, dissolved in H(2)O and D(2)O, revealed that all three (13)C(zeta) signals in D(2)O appeared at approximately 0.13 ppm ( approximately 20 Hz at 150.9 MHz) higher than those in H(2)O. In a H(2)O/D(2)O (1:1) mixture, however, one of the three signals for (13)C(zeta) appeared as a single peak at the averaged chemical shifts, and the other two appeared as double peaks at exactly the same chemical shifts in H(2)O and D(2)O, in 50 mM phosphate buffer (pH 6.6) at 40 degrees C. These three peaks were assigned to Tyr-36, Tyr-120, and Tyr-30, from the lower to higher chemical shifts, respectively. The results indicate that the hydroxyl proton of Tyr-120 exchanges faster than a few milliseconds, whereas those of Tyr-30 and Tyr-36 exchange more slowly. The exchange rate of the Tyr-30 hydroxyl proton, k(ex), under these conditions was determined by (13)C NMR exchange spectroscopy (EXSY) to be 9.2 +/- 1.1 s(-1). The Tyr-36 hydroxyl proton, however, exchanges too slowly to be determined by EXSY. These profound differences among the hydroxyl proton exchange rates are closely related to their relative solvent accessibility and the hydrogen bonds associated with the Tyr hydroxyl groups in proteins.

  2. experimental and analytical comparison of torsion, bending moment

    African Journals Online (AJOL)

    HOD

    In structural analysis and design, the effects of torsion are usually neglected ... bending and torsion, using these codes and experimental work; and validates the ..... [7] Kharagpur, I. Structural Analysis: Civil Engineering. Course Material (Vol.

  3. Ozil IP torsional mode versus combined torsional/longitudinal microcoaxial phacoemulsification.

    Science.gov (United States)

    Helvacioglu, Firat; Tunc, Zeki; Yeter, Celal; Oguzhan, Hasan; Sencan, Sadik

    2012-01-01

    To compare the safety and efficacy of microcoaxial phacoemulsification surgeries performed with the Ozil Intelligent Phaco (IP) torsional mode and combined torsional/longitudinal ultrasound (US) mode using the Infiniti Vision System (Alcon Laboratories). In this prospective randomized comparative study, 60 eyes were assigned to 2.2-mm microcoaxial phacoemulsification using the Ozil IP torsional mode (group 1) or combined torsional/longitudinal US mode (group 2). The primary outcome measures were US time (UST), cumulative dissipated energy (CDE), longitudinal and torsional ultrasound amplitudes, mean operation time, mean volume of balanced salt solution (BSS) used, and surgical complications. Both groups included 30 eyes. Mean UST, CDE, and longitudinal and torsional ultrasound amplitudes in group 1 were 1 minute 15±34.33 seconds, 8.74±5.64, 0.43±0.74, and 25.56±8.56, respectively, and these parameters in group 2 were 1 minute 40±51.44 seconds, 9.28±5.99, 3.64±1.55, and 3.71±1.34, respectively. UST and longitudinal amplitudes were found to be significantly low in group 1 (p<0.001, p<0.001), whereas torsional amplitude was found to be significantly high in this group (p=0.001). Mean volumes of BSS used in groups 1 and 2 were 63.30±18.00 cc and 84.50±28.65 cc, respectively (p=0.001). The Ozil IP torsional mode may provide more effective lens removal than the combined torsional/longitudinal US mode with a lower UST and volume of BSS used.

  4. Quantum-chemical investigation of the 1,2-proton shift in protonated five-membered aromatic heterocycles

    International Nuclear Information System (INIS)

    Abronin, I.A.; Gorb, L.G.; Litvinov, V.P.

    1985-01-01

    Calculations of the energetics of the 1,2-proton shift in protonated five-membered aromatic heterocycles - pyrrole, furan, and thiophene - have been carried out by the SCF MO LCAO method in the MINDO/3 approximation and nonempirically on the OST-3GF (OST-3GF) basis. The general features of this process, and also the influence of solvation and of taking into account the vacant d-AOs of the sulfur atom in the protonated form of thiophene on the results of the calculation are considered. The results obtained have been used for a discussion of the activity and selectivity of the heterocycles considered in aromatic electrophilic substitution reactions

  5. On the geometrization of electromagnetism by torsion

    International Nuclear Information System (INIS)

    Fonseca Neto, J.B. da.

    1984-01-01

    The possibility of electromagnetism geometrization using an four dimension Cartan geometry is investigated. The Lagrangian density which presents dual invariance for dyons electrodynamics formulated in term of two potentials is constructed. This theory by association of two potentials with track and with torsion pseudo-track and of the field with torsion covariant divergent is described. The minimum coupling of particle gravitational field of scalar and spinorial fields with dyon geometry theory by the minimum coupling of these fields with Cartan geometry was obtained. (author)

  6. Comparison of the solution and crystal structures of staphylococcal nuclease with 13C and 15N chemical shifts used as structural fingerprints

    International Nuclear Information System (INIS)

    Cole, H.B.R.; Sparks, S.W.; Torchia, D.A.

    1988-01-01

    The authors report high-resolution 13 C and 15 N NMR spectra of crystalline staphylococcal nuclease (Nase) complexed to thymidine 3',5'-diphosphate and Ca 2+ . High sensitivity and resolution are obtained by applying solid-state NMR techniques-high power proton decoupling and cross-polarization magic angle sample spinning (CPMASS)-to protein samples that have been efficiently synthesized and labeled by an overproducing strain of Escherichia coli. A comparison of CPMASS and solution spectra of Nase labeled with either [methyl- 13 C]methionine or [ 15 ]valine shows that the chemical shifts in the crystalline and solution states are virtually identical. This result is strong evidence that the protein conformations in the solution and crystalline states are nearly the same. Because of the close correspondence of the crystal and solution chemical shifts, sequential assignments obtained in solution apply to the crystal spectra. It should therefore be possible to study the molecular structure and dynamics of many sequentially assigned atomic sites in Nase crystals. Similar experiments are applicable to the growing number of proteins that can be obtained from efficient expression systems

  7. Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C' scalar couplings (3hbJNC')

    Energy Technology Data Exchange (ETDEWEB)

    Bonvin, Alexandre M.J.J.; Houben, Klaartje; Guenneugues, Marc; Kaptein, Robert; Boelens, Rolf [Utrecht University, Bijvoet Center for Biomolecular Research, NMR Spectroscopy (Netherlands)

    2001-11-15

    The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small {alpha}/{beta} protein chymotrypsin inhibitor 2. Dihedral angle restraints for the {phi} and {psi} angles of 32 out of 64 residues could be obtained from secondary chemical shift analysis with the TALOS program (Corneliscu et al., 1999a). This information was supplemented by 18 hydrogen-bond restraints derived from experimentally measured cross-hydrogen bond {sup 3hb}J{sub NC'} coupling constants. These experimental data were sufficient to generate structures that are as close as 1.0 A backbone rmsd from the crystal structure. The fold is, however, not uniquely defined and several solutions are generated that cannot be distinguished on the basis of violations or energetic considerations. Correct folds could be identified by combining clustering methods with knowledge-based potentials derived from structural databases.

  8. Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori

    Energy Technology Data Exchange (ETDEWEB)

    Gardiennet, Carole [Université de Lorraine, CNRS, CRM2, UMR 7036 (France); Wiegand, Thomas [ETH Zurich, Physical Chemistry (Switzerland); Bazin, Alexandre [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Cadalbert, Riccardo [ETH Zurich, Physical Chemistry (Switzerland); Kunert, Britta; Lacabanne, Denis [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Gutsche, Irina [Université Grenoble Alpes, Institut de Biologie Structurale (IBS), CNRS, IBS, CEA, IBS (France); Terradot, Laurent, E-mail: l.terradot@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France)

    2016-03-15

    We here investigate the interactions between the DnaB helicase and the C-terminal domain of the corresponding DnaG primase of Helicobacter pylori using solid-state NMR. The difficult crystallization of this 387 kDa complex, where the two proteins interact in a six to three ratio, is circumvented by simple co-sedimentation of the two proteins directly into the MAS-NMR rotor. While the amount of information that can be extracted from such a large protein is still limited, we can assign a number of amino-acid residues experiencing significant chemical-shift perturbations upon helicase-primase complex formation. The location of these residues is used as a guide to model the interaction interface between the two proteins in the complex. Chemical-shift perturbations also reveal changes at the interaction interfaces of the hexameric HpDnaB assembly on HpDnaG binding. A structural model of the complex that explains the experimental findings is obtained.

  9. Benchmarking of density functionals for a soft but accurate prediction and assignment of (1) H and (13)C NMR chemical shifts in organic and biological molecules.

    Science.gov (United States)

    Benassi, Enrico

    2017-01-15

    A number of programs and tools that simulate 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts using empirical approaches are available. These tools are user-friendly, but they provide a very rough (and sometimes misleading) estimation of the NMR properties, especially for complex systems. Rigorous and reliable ways to predict and interpret NMR properties of simple and complex systems are available in many popular computational program packages. Nevertheless, experimentalists keep relying on these "unreliable" tools in their daily work because, to have a sufficiently high accuracy, these rigorous quantum mechanical methods need high levels of theory. An alternative, efficient, semi-empirical approach has been proposed by Bally, Rablen, Tantillo, and coworkers. This idea consists of creating linear calibrations models, on the basis of the application of different combinations of functionals and basis sets. Following this approach, the predictive capability of a wider range of popular functionals was systematically investigated and tested. The NMR chemical shifts were computed in solvated phase at density functional theory level, using 30 different functionals coupled with three different triple-ζ basis sets. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

    Science.gov (United States)

    Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

    2010-03-17

    Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

  11. Fractional enrichment of proteins using [2-{sup 13}C]-glycerol as the carbon source facilitates measurement of excited state {sup 13}Cα chemical shifts with improved sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Ahlner, Alexandra; Andresen, Cecilia; Khan, Shahid N. [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden); Kay, Lewis E. [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry, One King’s College Circle (Canada); Lundström, Patrik, E-mail: patlu@ifm.liu.se [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden)

    2015-07-15

    A selective isotope labeling scheme based on the utilization of [2-{sup 13}C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state {sup 13}Cα chemical shifts using Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-{sup 13}C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state {sup 13}Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s{sup −1}, despite the small fraction of {sup 13}Cα–{sup 13}Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using {sup 13}Cα spin probes.

  12. 13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

    DEFF Research Database (Denmark)

    Nyrop Albers, Christian; Hansen, Poul Erik

    2010-01-01

    Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical...... side missing structural elements in the models can be suggested. A number of proposed structures for humic and fulvic acids are discussed based on the above analysis....

  13. Torsional Oscillations of the Earths's Core

    Science.gov (United States)

    Hide, Raymond; Boggs, Dale H.; Dickey, Jean O.

    1997-01-01

    Torsional oscillations of the Earth's liquid metallic outer core are investigated by diving the core into twenty imaginary e1qui-volume annuli coaxial with the axis of ratation of the Earth and determining temproal fluctuations in the axial component of angular memonetum of each annulus under the assumption of iso-rotation on cylindrical surfaces.

  14. Torsion of the gallbladder: a case report

    Directory of Open Access Journals (Sweden)

    Ijaz Samia

    2008-07-01

    Full Text Available Abstract Introduction Torsion of the gallbladder is a rare condition that most commonly affects the elderly. Pre-operative diagnosis is the exception rather than the rule. Any delay in treatment can be fatal as the gallbladder may rupture, leading to biliary peritonitis. Case presentation We present the case of an 80-year-old woman who was admitted with right upper quadrant pain initially thought to be secondary to acute cholecystitis. Subsequent ultrasound and computed tomography scans of the abdomen revealed signs suggestive of acute cholecystitis but neither modality detected any gallstones. As the patient's symptoms failed to resolve on conservative management, she was taken to theatre for an open cholecystectomy. Intra-operatively, the gallbladder had undergone complete torsion and appeared gangrenous. A routine cholecystectomy followed and she recovered from the operation without incident. Conclusion It is rare to diagnose torsion of the gallbladder pre-operatively despite advances in diagnostic imaging. However, this differential diagnosis should be borne in mind particularly in the elderly patient, without proven gallstones, who fails to improve on conservative management. An emergency cholecystectomy is indicated in the event of diagnosing torsion of the gallbladder to avert the potentially lethal sequelae of biliary peritonitis.

  15. The spectrum of axisymmetric torsional Alfven waves

    International Nuclear Information System (INIS)

    Sy, W.N.

    1977-03-01

    The spectrum of axisymmetric torsional Alfven waves propagating in a cylindrical, non-uniform, resistive plasma waveguide has been analysed by a method of singular perturbations. A simple condition has been derived which predicts whether the spectrum is continuous or discrete under given physical conditions. Application of this result to resolve an apparent discrepancy in experimental observations is briefly discussed. (Author)

  16. Conformal deformation of Riemann space and torsion

    International Nuclear Information System (INIS)

    Pyzh, V.M.

    1981-01-01

    Method for investigating conformal deformations of Riemann spaces using torsion tensor, which permits to reduce the second ' order equations for Killing vectors to the system of the first order equations, is presented. The method is illustrated using conformal deformations of dimer sphere as an example. A possibility of its use when studying more complex deformations is discussed [ru

  17. Adnexal torsion in 6 years old girl

    International Nuclear Information System (INIS)

    Plachkov, I.; Tzvetankov, K.; Dimova, M.; Dobreva, Tz.; Hadjidekov, G.

    2012-01-01

    MRI and US findings in Ovarian torsion in a premenarcheal girl are described. Adnexal torsion is an uncommon cause of severe lower abdominal pain in young women (mean age is 10-11), and in 50% of cases such symptoms are observed in pre-menarchal females. However, adnexal torsion should be considered in all premenarcheal girls admitted with acute abdominal pain and evidence of an ovarian mass. Accurate imaging is crucial after onset of early clinical symptoms to confirm the diagnosis and to preserve the viability of the affected ovary. A pelvic ovoid mass was visualised on ultrasound, suggesting several hypothesis -cystic mass, ovarian torsion, dermoid. Magnetic resonance imaging visualized edematous ovary enlargement and the presence of multiple follicules at the periphery due to congestion from the twisted vascular pedicule. Smooth wail thickening of the partially necrotic. Twisted ovary was seen in the subacute phase, which has been confirmed during laparoscopy. CT was not considered in this 6 years old girl due to ionizing radiation. (authors)

  18. Torsional Performance of Wind Turbine Blades

    DEFF Research Database (Denmark)

    Branner, Kim; Berring, Peter; Berggreen, Christian

    2007-01-01

    The present work investigates how well different finite element modeling techniques can predict bending and torsion behavior of a wind turbine blade. Two shell models are investigated. One model has element offsets and the other has the elements at the mid-thickness surfaces of the model. The las...

  19. Plant-based torsional actuator with memory

    Science.gov (United States)

    Nayomi Plaza; Samuel L. Zelinka; Don S. Stone; Joseph E. Jakes

    2013-01-01

    A bundle of a few loblolly pine (Pinus taeda) cells are moisture-activated torsional actuators that twist multiple revolutions per cm length in direct proportion to moisture content. The bundles generate 10 N m kg􀀀1 specific torque during both twisting and untwisting, which is higher than an electric motor. Additionally, the bundles exhibit a moisture-...

  20. Pseudotopological quasilocal energy of torsion gravity

    Science.gov (United States)

    Ko, Sheng-Lan; Lin, Feng-Li; Ning, Bo

    2017-08-01

    Torsion gravity is a natural extension to Einstein gravity in the presence of fermion matter sources. In this paper we adopt Wald's covariant method of calculating the Noether charge to construct the quasilocal energy of the Einstein-Cartan-fermion system, and find that its explicit expression is formally independent of the coupling constant between the torsion and axial current. This seemingly topological nature is unexpected and is reminiscent of the quantum Hall effect and topological insulators. However, a coupling dependence does arise when evaluating it on shell, and thus the situation is pseudotopological. Based on the expression for the quasilocal energy, we evaluate it for a particular solution on the entanglement wedge and find agreement with the holographic relative entropy obtained before. This shows the equivalence of these two quantities in the Einstein-Cartan-fermion system. Moreover, the quasilocal energy in this case is not always positive definite, and thus it provides an example of a swampland in torsion gravity. Based on the covariant Noether charge, we also derive the nonzero fermion effect on the Komar angular momentum. The implications of our results for future tests of torsion gravity in gravitational-wave astronomy are also discussed.

  1. Torsional ultrasound mode versus combined torsional and conventional ultrasound mode phacoemulsification for eyes with hard cataract.

    Science.gov (United States)

    Fakhry, Mohamed A; El Shazly, Malak I

    2011-01-01

    To compare torsional versus combined torsional and conventional ultrasound modes in hard cataract surgery regarding ultrasound energy and time and effect on corneal endothelium. Kasr El Aini hospital, Cairo University, and International Eye Hospital, Cairo, Egypt. Ninety-eight eyes of 63 patients were enrolled in this prospective comparative randomized masked clinical study. All eyes had nuclear cataracts of grades III and IV using the Lens Opacities Classification System III (LOCS III). Two groups were included, each having an equal number of eyes (49). The treatment for group A was combined torsional and conventional US mode phacoemulsification, and for group B torsional US mode phacoemulsification only. Pre- and post-operative assessments included best corrected visual acuity (BCVA), intraocular pressure (IOP), slit-lamp evaluation, and fundoscopic evaluation. Endothelial cell density (ECD) and central corneal thickness (CCT) were measured preoperatively, 1 day, 7 days, and 1 month postoperatively. All eyes were operated on using the Alcon Infiniti System (Alcon, Fort Worth, TX) with the quick chop technique. All eyes were implanted with AcrySof SA60AT (Alcon) intraocular lens (IOL). The main phaco outcome parameters included the mean ultrasound time (UST), the mean cumulative dissipated energy (CDE), and the percent of average torsional amplitude in position 3 (%TUSiP3). Improvement in BCVA was statistically significant in both groups (P < 0.001). Comparing UST and CDE for both groups revealed results favoring the pure torsional group (P = 0.002 and P < 0.001 for UST; P = 0.058 and P = 0.009 for CDE). As for %TUSiP3, readings were higher for the pure torsional group (P = 0.03 and P = 0.01). All changes of CCT, and ECD over time were found statistically significant using one-way ANOVA testing (P < 0.001). Both modes are safe in hard cataract surgery, however the pure torsional mode showed less US energy used.

  2. Shift Colors

    Science.gov (United States)

    Publications & News Shift Colors Pages default Sign In NPC Logo Banner : Shift Colors Search Navy Personnel Command > Reference Library > Publications & News > Shift Colors Top Link Bar Navy Personnel Library Expand Reference Library Quick Launch Shift Colors Shift Colors Archives Mailing Address How to

  3. Endocrine Disrupting Chemical Induced "Pollution of Metabolic Pathways": A Case of Shifting Paradigms With Implications for Vascular Diseases.

    Science.gov (United States)

    Janardhanan, Rajiv

    2018-05-14

    The latter half of the twentieth century has witnessed a humongous spurt in the use of synthetic chemicals in a wide variety of industrial and agricultural applications are leading to niche specific perturbations affecting every trophic level of the ecosystems due to unmitigated environmental contamination. Despite the incremental usefulness of endocrine disrupting chemicals (EDCs) such as pesticides and plasticizers, their statutory impact on environmental health is assuming worrisome proportions. The EDCs can disrupt physiological homeostasis resulting in developmental and reproductive abnormalities. Both preclinical animal experiments, as well as epidemiological studies, have correlated EDC exposure with metabolic disorders such as metabolic syndrome, type 2 diabetes as well as cardiovascular health. Here we briefly review the statutory impact of EDCs on metabolic disruption as well as their impact on environmental health. Finally, difficulties pertaining to the categorization of EDC induced metabolic diseases as risk factors for global disease burden have been addressed taking into account the complexity of such interactions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  4. Isotopic shifts in chemical exchange systems. 1. Large isotope effects in the complexation of Na+ isotopes by macrocyclic polyethers

    International Nuclear Information System (INIS)

    Knoechel, A.; Wilken, R.D.

    1981-01-01

    The complexation of 24 Na + and 22 Na + by 18 of the most widely used macrocyclic polyethers (crown ethers and monocyclic and bicyclic aminopolyethers) has been investigated in view of possible equilibrium isotope shifts. Solvated salts and polyether complexes were distributed differently into two phases and isotope ratios determined in both phases. Chloroform/water systems were shown to be particularly suitable to the investigations allowing favorable distribution for Na + and 13 of the 18 polyethers employed. With crown ethers 24 Na + enrichment varied from nonsignficant values (for large crown ethers) up to 3.1 +- 0.4% (18-crown-6). In the case of bicyclic aminopolyethers, ligands with cages of optimum size to accommodate Na + showed 24 Na + enrichment between O (nonsignificant) (2.2/sub B/2./sub B/) and 5.2 +- 1.8% (2.2.1). In contrast, for 2.2.2. and its derivatives, being too large for Na + , 22 Na + enrichment varying from O (nonsignificant) (2.2.2.p) up to 5.4 +- 0.5% (2.2.2.) has been observed. These values are remarkably high. They are explained by different bonding in solvate structure and polyether complex by using the theoretical approach of Bigeleisen

  5. Torsion limits from t t macr production at the LHC

    Science.gov (United States)

    de Almeida, F. M. L.; de Andrade, F. R.; do Vale, M. A. B.; Nepomuceno, A. A.

    2018-04-01

    Torsion models constitute a well-known class of extended quantum gravity models. In this work, one investigates the phenomenological consequences of a torsion field interacting with top quarks at the LHC. A torsion field could appear as a new heavy state characterized by its mass and couplings to fermions. This new state would form a resonance decaying into a top antitop pair. The latest ATLAS t t ¯ production results from LHC 13 TeV data are used to set limits on torsion parameters. The integrated luminosity needed to observe torsion resonance at the next LHC upgrades are also evaluated, considering different values for the torsion mass and its couplings to Standard Model fermions. Finally, prospects for torsion exclusion at the future LHC phases II and III are obtained using fast detector simulations.

  6. Calculation of 125Te NMR Chemical Shifts at the Full Four-Component Relativistic Level with Taking into Account Solvent and Vibrational Corrections: A Gateway to Better Agreement with Experiment.

    Science.gov (United States)

    Rusakova, Irina L; Rusakov, Yuriy Yu; Krivdin, Leonid B

    2017-06-29

    Four-component relativistic calculations of 125 Te NMR chemical shifts were performed in the series of 13 organotellurium compounds, potential precursors of the biologically active species, at the density functional theory level under the nonrelativistic and four-component fully relativistic conditions using locally dense basis set scheme derived from relativistic Dyall's basis sets. The relativistic effects in tellurium chemical shifts were found to be of as much as 20-25% of the total calculated values. The vibrational and solvent corrections to 125 Te NMR chemical shifts are about, accordingly, 6 and 8% of their total values. The PBE0 exchange-correlation functional turned out to give the best agreement of calculated tellurium shifts with their experimental values giving the mean absolute percentage error of 4% in the range of ∼1000 ppm, provided all corrections are taken into account.

  7. In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

    Science.gov (United States)

    Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

    2016-10-24

    The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Comparison of CT and chemical-shift MRI for differentiating thymoma from non-thymomatous conditions in myasthenia gravis: value of qualitative and quantitative assessment

    International Nuclear Information System (INIS)

    Priola, A.M.; Priola, S.M.; Gned, D.; Giraudo, M.T.; Fornari, A.; Veltri, A.

    2016-01-01

    Aim: To evaluate the usefulness of computed tomography (CT) and chemical-shift magnetic resonance imaging (MRI) in patients with myasthenia gravis (MG) for differentiating thymoma (THY) from thymic lymphoid hyperplasia (TLH) and normal thymus (NT), and to determine which technique is more accurate. Materials and methods: Eighty-three patients with generalised MG who underwent surgery were divided into the TLH/NT group (A; 65 patients) and THY group (B; 24 patients). Differences in qualitative characteristics and quantitative data (CT: radiodensity in Hounsfield units; MRI: signal intensity index [SII]) between groups were tested using Fisher's exact test and Student's t-test. Logistic regression models were estimated for both qualitative and quantitative analyses. At quantitative analysis, discrimination abilities were determined according to the area under the receiver operating characteristic (ROC) curve (AUROC) with computation of optimal cut-off points. The diagnostic accuracies of CT and MRI were compared using McNemar's test. Results: At qualitative assessment, MRI had higher accuracy than CT (96.4%, 80/83 and 86.7%, 72/83, respectively). At quantitative analysis, both the radiodensity and SII were significantly different between groups (p<0.0001). For CT, at quantitative assessment, the AUROC of the radiodensity in discriminating between groups was 0.904 (optimal cut-off point, 20 HU) with an accuracy of 77.1% (64/83). For MRI, the AUROC of the SII was 0.989 (optimal cut-off point, 7.766%) with an accuracy of 96.4% (80/83), which was significantly higher than CT (p<0.0001). By using optimal cut-off points for cases with an erroneous diagnosis at qualitative assessment, accuracy improved both for CT (89.2%, 74/83) and MRI (97.6%, 81/83). Conclusion: Quantitative analysis is useful in evaluating patients with MG and improves the diagnostic accuracy of CT and MRI based on qualitative assessment. Chemical-shift MRI is more reliable than CT in differentiating

  9. Design of high-power, broadband 180o pulses and mixing sequences for fast MAS solid state chemical shift correlation NMR spectroscopy

    International Nuclear Information System (INIS)

    Herbst, Christian; Herbst, Jirada; Kirschstein, Anika; Leppert, Joerg; Ohlenschlaeger, Oliver; Goerlach, Matthias; Ramachandran, Ramadurai

    2009-01-01

    An approach for the design of high-power, broadband 180 o pulses and mixing sequences for generating dipolar and scalar coupling mediated 13 C- 13 C chemical shift correlation spectra of isotopically labelled biological systems at fast magic-angle spinning frequencies without 1 H decoupling during mixing is presented. Considering RF field strengths in the range of 100-120 kHz, as typically available in MAS probes employed at high spinning speeds, and limited B 1 field inhomogeneities, the Fourier coefficients defining the phase modulation profile of the RF pulses were optimised numerically to obtain broadband inversion and refocussing pulses and mixing sequences. Experimental measurements were carried out to assess the performance characteristics of the mixing sequences reported here

  10. Stereochemistry of Complex Marine Natural Products by Quantum Mechanical Calculations of NMR Chemical Shifts: Solvent and Conformational Effects on Okadaic Acid

    Directory of Open Access Journals (Sweden)

    Humberto J. Domínguez

    2014-01-01

    Full Text Available Marine organisms are an increasingly important source of novel metabolites, some of which have already inspired or become new drugs. In addition, many of these molecules show a high degree of novelty from a structural and/or pharmacological point of view. Structure determination is generally achieved by the use of a variety of spectroscopic methods, among which NMR (nuclear magnetic resonance plays a major role and determination of the stereochemical relationships within every new molecule is generally the most challenging part in structural determination. In this communication, we have chosen okadaic acid as a model compound to perform a computational chemistry study to predict 1H and 13C NMR chemical shifts. The effect of two different solvents and conformation on the ability of DFT (density functional theory calculations to predict the correct stereoisomer has been studied.

  11. Evaluation of the Aromaticity of a Non-Planar Carbon Nano-Structure by Nucleus-Independent Chemical Shift Criterion: Aromaticity of the Nitrogen- Doped Corannulene

    Directory of Open Access Journals (Sweden)

    A. Reisi-Vanani

    2014-04-01

    Full Text Available Substitution of two or four carbon atoms by nitrogen in the corannulene molecule as a carbon nanostructure was done and the obtained structures were optimized at MP2/6-31G(d level of theory. Calculations of the nucleus-independent chemical shift (NICS were performed to analyze the aromaticity of the corannulene rings and its derivatives upon doping with N at B3LYP/6-31G(d level of theory. Results showed NICS values in six-membered and five-membered rings of two and four N atoms doped corannulene are different and very dependent to number and position of the N atoms. The values of the mean NICS of all N-doped structures are more positive than intact corannulene that show insertion of N atom to the structures causes to decreasing aromaticity of them.

  12. Stopping powers from the inverted doppler shift attenuation method: Z-oscillations; Bragg's rule or chemical effects; solid and liquid state effects

    International Nuclear Information System (INIS)

    Pietsch, W.; Hauser, U.; Neuwirth, W.

    1976-01-01

    With the 'Inverted Doppler Shift Attenuation (IDSA)' method stopping cross sections for swift ions can be measured with an accuracy of about 1%. Here results are reported with lithium and carbon projectiles in very different stopping materials. It turns out that the stopping cross section around Bohr's velocity is linearly dependent on the velocity. Stopping cross sections of elements show the expected Z 2 -oscillations. With compound targets strong deviations from Bragg's rule were found which means that the stopping cross section is influenced by the chemical bonding. In electrolytic solutions effects due to ion-dipole interactions can be observed. These phenomena demonstrate the strong sensitivity of electronic stopping cross sections on the specific distribution of the outer electrons of the target atoms. Further Lindhard's formula has been modified which gives a good description of this influence. (Auth.)

  13. A simple method for measuring signs of {sup 1}H{sup N} chemical shift differences between ground and excited protein states

    Energy Technology Data Exchange (ETDEWEB)

    Bouvignies, Guillaume; Korzhnev, Dmitry M.; Neudecker, Philipp; Hansen, D. Flemming [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada); Cordes, Matthew H. J. [University of Arizona, Department of Chemistry and Biochemistry (United States); Kay, Lewis E., E-mail: kay@pound.med.utoronto.c [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

    2010-06-15

    NMR relaxation dispersion spectroscopy is a powerful method for studying protein conformational dynamics whereby visible, ground and invisible, excited conformers interconvert on the millisecond time-scale. In addition to providing kinetics and thermodynamics parameters of the exchange process, the CPMG dispersion experiment also allows extraction of the absolute values of the chemical shift differences between interconverting states, |{Delta}{omega}-tilde|, opening the way for structure determination of excited state conformers. Central to the goal of structural analysis is the availability of the chemical shifts of the excited state that can only be obtained once the signs of {Delta}{omega}-tilde are known. Herein we describe a very simple method for determining the signs of {sup 1}H{sup N} {Delta}{omega}-tilde values based on a comparison of peak positions in the directly detected dimensions of a pair of {sup 1}H{sup N}-{sup 15}N correlation maps recorded at different static magnetic fields. The utility of the approach is demonstrated for three proteins that undergo millisecond time-scale conformational rearrangements. Although the method provides fewer signs than previously published techniques it does have a number of strengths: (1) Data sets needed for analysis are typically available from other experiments, such as those required for measuring signs of {sup 15}N {Delta}{omega}-tilde values, thus requiring no additional experimental time, (2) acquisition times in the critical detection dimension can be as long as necessary and (3) the signs obtained can be used to cross-validate those from other approaches.

  14. 31P-MR spectroscopy of all regions of the human heart at 1.5 T with acquisition-weighted chemical shift imaging

    International Nuclear Information System (INIS)

    Koestler, H.; Beer, M.; Buchner, S.; Sandstede, J.; Pabst, T.; Kenn, W.; Hahn, D.

    2001-01-01

    Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac 31 P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders 31 P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.) [de

  15. NUMERICAL INVESTIGATION OF CURVATURE AND TORSION EFFECTS ON WATER FLOW FIELD IN HELICAL RECTANGULAR CHANNELS

    Directory of Open Access Journals (Sweden)

    A. H. ELBATRAN

    2015-07-01

    Full Text Available Helical channels have a wide range of applications in petroleum engineering, nuclear, heat exchanger, chemical, mineral and polymer industries. They are used in the separation processes for fluids of different densities. The centrifugal force, free surface and geometrical effects of the helical channel make the flow pattern more complicated; hence it is very difficult to perform physical experiment to predict channel performance. Computational Fluid Dynamics (CFD can be suitable alternative for studying the flow pattern characteristics in helical channels. The different ranges of dimensional parameters, such as curvature and torsion, often cause various flow regimes in the helical channels. In this study, the effects of physical parameters such as curvature, torsion, Reynolds number, Froude number and Dean Number on the characteristics of the turbulent flow in helical rectangular channels have been investigated numerically, using a finite volume RANSE code Fluent of Ansys workbench 10.1 UTM licensed. The physical parameters were reported for range of curvature (δ of 0.16 to 0.51 and torsion (λ of 0.032 to 0.1 .The numerical results of this study showed that the decrease in the channel curvature and the increase in the channel torsion numbers led to the increase of the flow velocity inside the channel and the change in the shape of water free surface at given Dean, Reynolds and Froude numbers.

  16. Torsional ultrasound mode versus combined torsional and conventional ultrasound mode phacoemulsification for eyes with hard cataract

    Directory of Open Access Journals (Sweden)

    Fakhry MA

    2011-07-01

    Full Text Available Mohamed A Fakhry1,2, Malak I El Shazly11Department of Ophthalmology, Kasr El Aini Hospital, Cairo University, Cairo, Egypt; 2Cataract and Refractive Consultant, International Eye Hospital, Cairo, EgyptPurpose: To compare torsional versus combined torsional and conventional ultrasound modes in hard cataract surgery regarding ultrasound energy and time and effect on corneal endothelium.Settings: Kasr El Aini hospital, Cairo University, and International Eye Hospital, Cairo, Egypt.Methodology: Ninety-eight eyes of 63 patients were enrolled in this prospective comparative randomized masked clinical study. All eyes had nuclear cataracts of grades III and IV using the Lens Opacities Classification System III (LOCS III. Two groups were included, each having an equal number of eyes (49. The treatment for group A was combined torsional and conventional US mode phacoemulsification, and for group B torsional US mode phacoemulsification only. Pre- and post-operative assessments included best corrected visual acuity (BCVA, intraocular pressure (IOP, slit-lamp evaluation, and fundoscopic evaluation. Endothelial cell density (ECD and central corneal thickness (CCT were measured preoperatively, 1 day, 7 days, and 1 month postoperatively. All eyes were operated on using the Alcon Infiniti System (Alcon, Fort Worth, TX with the quick chop technique. All eyes were implanted with AcrySof SA60AT (Alcon intraocular lens (IOL. The main phaco outcome parameters included the mean ultrasound time (UST, the mean cumulative dissipated energy (CDE, and the percent of average torsional amplitude in position 3 (%TUSiP3.Results: Improvement in BCVA was statistically significant in both groups (P < 0.001. Comparing UST and CDE for both groups revealed results favoring the pure torsional group (P = 0.002 and P < 0.001 for UST; P = 0.058 and P = 0.009 for CDE. As for %TUSiP3, readings were higher for the pure torsional group (P = 0.03 and P = 0.01. All changes of CCT, and ECD

  17. Biothermal sensing of a torsional artificial muscle.

    Science.gov (United States)

    Lee, Sung-Ho; Kim, Tae Hyeob; Lima, Márcio D; Baughman, Ray H; Kim, Seon Jeong

    2016-02-14

    Biomolecule responsive materials have been studied intensively for use in biomedical applications as smart systems because of their unique property of responding to specific biomolecules under mild conditions. However, these materials have some challenging drawbacks that limit further practical application, including their speed of response and mechanical properties, because most are based on hydrogels. Here, we present a fast, mechanically robust biscrolled twist-spun carbon nanotube yarn as a torsional artificial muscle through entrapping an enzyme linked to a thermally sensitive hydrogel, poly(N-isopropylacrylamide), utilizing the exothermic catalytic reaction of the enzyme. The induced rotation reached an equilibrated angle in less than 2 min under mild temperature conditions (25-37 °C) while maintaining the mechanical properties originating from the carbon nanotubes. This biothermal sensing of a torsional artificial muscle offers a versatile platform for the recognition of various types of biomolecules by replacing the enzyme, because an exothermic reaction is a general property accompanying a biochemical transformation.

  18. Electronic transport in torsional strained Weyl semimetals

    Science.gov (United States)

    Soto-Garrido, Rodrigo; Muñoz, Enrique

    2018-05-01

    In a recent paper (Muñoz and Soto-Garrido 2017 J. Phys.: Condens. Matter 29 445302) we have studied the effects of mechanical strain and magnetic field on the electronic transport properties in graphene. In this article we extended our work to Weyl semimetals (WSM). We show that although the WSM are 3D materials, most of the analysis done for graphene (2D material) can be carried out. In particular, we studied the electronic transport through a cylindrical region submitted to torsional strain and external magnetic field. We provide exact analytical expressions for the scattering cross section and the transmitted electronic current. In addition, we show the node-polarization effect on the current and propose a recipe to measure the torsion angle from transmission experiments.

  19. High-pressure torsion of hafnium

    International Nuclear Information System (INIS)

    Edalati, Kaveh; Horita, Zenji; Mine, Yoji

    2010-01-01

    Pure Hf (99.99%) is processed by high-pressure torsion (HPT) under pressures of 4 and 30 GPa to form an ultrafine-grained structure with a gain size of ∼180 nm. X-ray diffraction analysis shows that, unlike Ti and Zr, no ω phase formation is detected after HPT processing even under a pressure of 30 GPa. A hydride formation is detected after straining at the pressure of 4 GPa. The hydride phase decomposes either by application of a higher pressure as 30 GPa or by unloading for prolong time after HPT processing. Microhardness, tensile and bending tests show that a high hardness (360 Hv) and an appreciable ductility (8%) as well as high tensile and bending strength (1.15 and 2.75 GPa, respectively) are achieved following the high-pressure torsion.

  20. Torsional Tribological Behavior and Torsional Friction Model of Polytetrafluoroethylene against 1045 Steel

    Science.gov (United States)

    Wang, Shibo; Niu, Chengchao

    2016-01-01

    In this work, the plane-on-plane torsional fretting tribological behavior of polytetrafluoroethylene (PTFE) was studied. A model of a rigid, flat-ended punch acting on an elastic half-space was built according to the experimental conditions. The results indicate that the shape of T–θ curves was influenced by both the torsional angle and the normal load. The torsion friction torque and wear rate of PTFE exponentially decreased when the torsion angle rose. The torsional torque increased from 0.025 N·m under a normal load of 43 N to 0.082 N·m under a normal load of 123 N. With sequentially increasing normal load, the value of torque was maintained. With rising normal load, the wear mass loss of PTFE disks was increased and the wear rate was decreased. Good agreement was found with the calculated torque according to the model and the experimental torque except for that under a normal load of 163 N. The difference under a normal load of 163 N was caused by the coefficient of friction. Usually the coefficient of friction of a polymer decreases with increasing normal load, whereas a constant coefficient of friction was applied in the model. PMID:26799324

  1. Torsional oscillator studies of rotating 3He-A in a slab

    International Nuclear Information System (INIS)

    Walmsley, P.M.Paul M.; Cousins, D.J.Derek J.; Hall, H.E.Henry E.; Golov, A.I.Andrei I.

    2003-01-01

    Using a rotating cryostat we have manipulated l-textures of 3 He-A in a 0.26 mm-thick slab contained in a torsional oscillator. Application of a magnetic field or a counterflow due to rotation lead to a sudden distortion of a uniform texture. The uniformity of the initial texture can be characterized by the resulting shift in frequency and bandwidth of the torsional resonance. With a certain density of vortices induced by rotation a uniform texture can be stabilized even in presence of magnetic. The optimal speed of rotation to prepare a uniform texture while cooling through T c was found. The critical velocities for the flow-induced textural transition and vortex nucleation are determined

  2. Torsion method for measuring piezooptic coefficients

    Energy Technology Data Exchange (ETDEWEB)

    Skab, I.; Smaga, I.; Savaryn, V.; Vasylkiv, Yu.; Vlokh, R. [Institute of Physical Optics, Lviv (Ukraine)

    2011-01-15

    We develop and describe analytically a torsion method for measuring piezooptic coefficients associated with shear stresses. It is shown that the method enables to increase significantly the accuracy of determination of piezooptic coefficients. The method and the appropriate apparatus are verified experimentally on the example of LiNbO{sub 3} crystals. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  3. Torsional asymmetry in suspension bridge systems

    Czech Academy of Sciences Publication Activity Database

    Malík, Josef

    2015-01-01

    Roč. 60, č. 6 (2015), s. 677-701 ISSN 0862-7940 R&D Projects: GA MŠk ED2.1.00/03.0082 Institutional support: RVO:68145535 Keywords : suspension bridge * Hamilton principle * vertical and torsional oscillation * uniqueness * existence Subject RIV: BA - General Mathematics Impact factor: 0.507, year: 2015 http://link.springer.com/article/10.1007%2Fs10492-015-0117-3

  4. Electrostatically actuated torsional resonant sensors and switches

    KAUST Repository

    Younis, Mohammad I.

    2016-12-29

    Embodiments in accordance of a torsional resonant sensor disclosure is configured to actuate a beam structure using electrostatic actuation with an AC harmonic load (e.g., AC and DC voltage sources) that is activated upon detecting a particular agent having a mass above a predefined level. In various embodiments, the beam structure may be different types of resonant structures that is at least partially coated or layered with a selective material.

  5. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

    International Nuclear Information System (INIS)

    Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L.; Markley, John L.; Akutsu, Hideo; Fujiwara, Toshimichi

    2012-01-01

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1 H, 13 C and 15 N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001–2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

  6. Ab initio/GIAO-CCSD(T) study of structures, energies, and 13C NMR chemical shifts of C4H7(+) and C5H9(+) ions: relative stability and dynamic aspects of the cyclopropylcarbinyl vs bicyclobutonium ions.

    Science.gov (United States)

    Olah, George A; Surya Prakash, G K; Rasul, Golam

    2008-07-16

    The structures and energies of the carbocations C 4H 7 (+) and C 5H 9 (+) were calculated using the ab initio method. The (13)C NMR chemical shifts of the carbocations were calculated using the GIAO-CCSD(T) method. The pisigma-delocalized bisected cyclopropylcarbinyl cation, 1 and nonclassical bicyclobutonium ion, 2 were found to be the minima for C 4H 7 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level the structure 2 is 0.4 kcal/mol more stable than the structure 1. The (13)C NMR chemical shifts of 1 and 2 were calculated by the GIAO-CCSD(T) method. Based on relative energies and (13)C NMR chemical shift calculations, an equilibrium involving the 1 and 2 in superacid solutions is most likely responsible for the experimentally observed (13)C NMR chemical shifts, with the latter as the predominant equilibrating species. The alpha-methylcyclopropylcarbinyl cation, 4, and nonclassical bicyclobutonium ion, 5, were found to be the minima for C 5H 9 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level ion 5 is 5.9 kcal/mol more stable than the structure 4. The calculated (13)C NMR chemical shifts of 5 agree rather well with the experimental values of C 5H 9 (+).

  7. Spacetime thermodynamics in the presence of torsion

    Science.gov (United States)

    Dey, Ramit; Liberati, Stefano; Pranzetti, Daniele

    2017-12-01

    It was shown by Jacobson in 1995 that the Einstein equation can be derived as a local constitutive equation for an equilibrium spacetime thermodynamics. With the aim to understand if such thermodynamical description is an intrinsic property of gravitation, many attempts have been made so far to generalize this treatment to a broader class of gravitational theories. Here we consider the case of the Einstein-Cartan theory as a prototype of theories with nonpropagating torsion. In doing so, we study the properties of Killing horizons in the presence of torsion, establish the notion of local causal horizon in Riemann-Cartan spacetimes, and derive the generalized Raychaudhuri equation for these kinds of geometries. Then, starting with the entropy that can be associated to these local causal horizons, we derive the Einstein-Cartan equation by implementing the Clausius equation. We outline two ways of proceeding with the derivation depending on whether we take torsion as a geometric field or as a matter field. In both cases we need to add internal entropy production terms to the Clausius equation as the shear and twist cannot be taken to be 0 a priori for our setup. This fact implies the necessity of a nonequilibrium thermodynamics treatment for the local causal horizon. Furthermore, it implies that a nonzero twist at the horizon in general contributes to the Hartle-Hawking tidal heating for black holes with possible implications for future observations.

  8. Isolated Fallopian Tube Torsion in Adolescents

    Directory of Open Access Journals (Sweden)

    S. Rajaram

    2013-01-01

    Full Text Available Background. Fallopian tube torsion is a rare cause of acute abdomen, occurring commonly in females of reproductive age. It lacks pathognomonic symptoms, signs, or imaging features, thus causing delay in surgical intervention. Case. We report two cases of isolated fallopian tube torsion in adolescent girls. In the first case a 19-year-old patient presented with acute pain in the left iliac region associated with episodes of vomiting for one day and mild tenderness on examination. Laparoscopy revealed left sided twisted fallopian tube associated with hemorrhagic cyst of ovary. The tube was untwisted and salvaged. In another case an 18-year-old virgin girl presented with similar complaints since one week, associated with mild tenderness in the lower abdomen and tender cystic mass on per rectal examination. On laparoscopy right twisted fallopian tube associated with a paratubal cyst was found. Salpingectomy was done as the tube was gangrenous. Conclusion. Fallopian tube torsion, though rare, should be considered in women of reproductive age with unilateral pelvic pain. Early diagnostic laparoscopy is important for an accurate diagnosis and could salvage the tube.

  9. Gauge fields in a torsion field

    International Nuclear Information System (INIS)

    Rosu, Ion

    2004-01-01

    In this paper we analyse the motion and the field equations in a non-null curvature and torsion space. In this 4-n dimensional space, the connection coefficients are γ bc a = 1/2S bc a + 1/2T bc a, where S bc a is the symmetrical part and T bc a are the components of the torsion tensor. We will consider that all the fields depend on x = x α , α = 1,2,3,4 and do not depend on y = y k , k=1,2,...,n. The factor S bc a depends on the components of the metric tensor g αβ (x) and on the gauge fields A ν s 0 (x) and the components of the torsion depend only on the gauge fields A ν s 0 (x). We take into consideration the particular case for which the geodesic equations coincide with the motion equations in the presence of the gravitational and the gauge fields. In this case the field equations are Einstein equations in a 4-n dimensional space. We show that both the geodesic equations and the field equations can be obtained from a variational principle. (author)

  10. Design of a nonlinear torsional vibration absorber

    Science.gov (United States)

    Tahir, Ammaar Bin

    Tuned mass dampers (TMD) utilizing linear spring mechanisms to mitigate destructive vibrations are commonly used in practice. A TMD is usually tuned for a specific resonant frequency or an operating frequency of a system. Recently, nonlinear vibration absorbers attracted attention of researchers due to some potential advantages they possess over the TMDs. The nonlinear vibration absorber, or the nonlinear energy sink (NES), has an advantage of being effective over a broad range of excitation frequencies, which makes it more suitable for systems with several resonant frequencies, or for a system with varying excitation frequency. Vibration dissipation mechanism in an NES is passive and ensures that there is no energy backflow to the primary system. In this study, an experimental setup of a rotational system has been designed for validation of the concept of nonlinear torsional vibration absorber with geometrically induced cubic stiffness nonlinearity. Dimensions of the primary system have been optimized so as to get the first natural frequency of the system to be fairly low. This was done in order to excite the dynamic system for torsional vibration response by the available motor. Experiments have been performed to obtain the modal parameters of the system. Based on the obtained modal parameters, the design optimization of the nonlinear torsional vibration absorber was carried out using an equivalent 2-DOF modal model. The optimality criterion was chosen to be maximization of energy dissipation in the nonlinear absorber attached to the equivalent 2-DOF system. The optimized design parameters of the nonlinear absorber were tested on the original 5-DOF system numerically. A comparison was made between the performance of linear and nonlinear absorbers using the numerical models. The comparison showed the superiority of the nonlinear absorber over its linear counterpart for the given set of primary system parameters as the vibration energy dissipation in the former is

  11. Fast Torsional Artificial Muscles from NiTi Twisted Yarns.

    Science.gov (United States)

    Mirvakili, Seyed M; Hunter, Ian W

    2017-05-17

    Torsional artificial muscles made of multiwalled carbon nanotube/niobium nanowire yarns have shown remarkable torsional speed and gravimetric torque. The muscle structure consists of a twisted yarn with half of its length infiltrated with a stimuli-responsive guest material such as paraffin wax. The volumetric expansion of the guest material creates the torsional actuation in the yarn. In the present work, we show that this type of actuation is not unique to wax-infiltrated carbon multiwalled nanotube (MWCNT) or niobium nanowire yarns and that twisted yarn of NiTi alloy fibers also produces fast torsional actuation. By gold-plating half the length of a NiTi twisted yarn and Joule heating it, we achieved a fully reversible torsional actuation of up to 16°/mm with peak torsional speed of 10 500 rpm and gravimetric torque of 8 N·m/kg. These results favorably compare to those of MWCNTs and niobium nanowire yarns.

  12. Isolated Penile Torsion in Brothers: A Case Report

    Directory of Open Access Journals (Sweden)

    Metin Gunduz

    2012-04-01

    Full Text Available Penile torsion can be congenital and associated with hypospadias and chordee, or can be acquired after circumcision. The incidence of isolated neonatal penile torsion was 1.7 to 27% in the literature. The majority were between 10 and deg; and 20 and deg;. Generally, torsion was to the left in cases. The techniques for correction of penile torsion described in the literature are penile de-gloving and reattaching of skin, resection of Buck's fascia incising the base of the penis and removing angular ellipses of corporeal tissue with subsequent plication of tunica, and dorsal dartos flap rotation in severe cases. In conclusion, penile torsion may be familial. Therefore, brothers should be examined carefully. The degloving and realignment technique is successful in isolated penile torsion. [Arch Clin Exp Surg 2012; 1(2.000: 122-124

  13. Development of a simple computerized torsion test to quantify subjective ocular torsion.

    Science.gov (United States)

    Kim, Y D; Yang, H K; Hwang, J-M

    2017-11-01

    PurposeThe double Maddox-rod test (DMRT) and Lancaster red-green test (LRGT) are the most widely used tests worldwide to assess subjective ocular torsion. However, these tests require equipment and the quantified results of ocular torsion are only provided in rough values. Here we developed a novel computerized torsion test (CTT) for individual assessment of subjective ocular torsion and validated the reliability and accuracy of the test compared with those of the DMRT and LRGT.MethodsA total of 30 patients with cyclovertical strabismus and 30 controls were recruited. The CTT was designed using Microsoft Office PowerPoint. Subjects wore red-green filter spectacles and viewed gradually tilted red and cyan lines on an LCD monitor and pressed the keyboard to go through the slides, until both lines seemed parallel. All subjects underwent the CTT, DMRT, and LRGT. Intraclass correlation coefficients and Bland-Altman plots were analyzed to assess the acceptability of the CTT compared with that of the DMRT.ResultsBoth the DMRT and CTT showed no significant test-retest differences in the strabismus and control groups. The DMRT and CTT results demonstrated an acceptable agreement. The reliability of the CTT was better than that of the DMRT. The LRGT showed low sensitivity for the detection of ocular torsion compared with the DMRT (40.0%) and CTT (39.1%).ConclusionOur results suggest that the assessment of subjective ocular torsion using the CTT based on PowerPoint software is simple, reproducible, and accurate and can be applied in clinical practice.

  14. Determination of the Tautomeric Equilibria of Pyridoyl Benzoyl -Diketones in the Liquid and Solid State through the use of Deuterium Isotope Effects on 1H and 13C NMR Chemical Shifts and Spin Coupling Constants

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Borisov, Eugeny V.; Lindon, John C.

    2015-01-01

    The tautomeric equilibria for 2-pyridoyl-, 3-pyridoyl-, and 4-pyridoyl-benzoyl methane have been investigated using deuterium isotope effects on 1H and 13C chemical shifts both in the liquid and the solid state. Equilibria are established both in the liquid and the solid state. In addition......, in the solution state the 2-bond and 3-bond J(1H–13C) coupling constants have been used to confirm the equilibrium positions. The isotope effects due to deuteriation at the OH position are shown to be superior to chemical shift in determination of equilibrium positions of these almost symmetrical -pyridoyl......-benzoyl methanes. The assignments of the NMR spectra are supported by calculations of the chemical shifts at the DFT level. The equilibrium positions are shown to be different in the liquid and the solid state. In the liquid state the 4-pyridoyl derivative is at the B-form (C-1 is OH), whereas the 2-and 3-pyridoyl...

  15. Characterization of mu s-ms dynamics of proteins using a combined analysis of N-15 NMR relaxation and chemical shift: Conformational exchange in plastocyanin induced by histidine protonations

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Thuesen, Marianne Hallberg; Christensen, Hans Erik Mølager

    2004-01-01

    of the exchanging species can be determined independently of the relaxation rates. The applicability of the approach is demonstrated by a detailed analysis of the conformational exchange processes previously observed in the reduced form of the blue copper protein, plastocyanin from the cyanobacteria Anabaena......An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the mus-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift...... quantitatively by the correlation between the R-ex terms and the corresponding chemical shift differences of the exchanging species. By this approach, the R-ex terms of N-15 nuclei belonging to contiguous regions in the protein could be assigned to the same exchange process. Furthermore, the analysis...

  16. Painless inter epididymal testicular torsion of the spermatic cord

    Directory of Open Access Journals (Sweden)

    Salomon V. Romano

    2007-02-01

    Full Text Available Inter epididymal testicular torsion of the spermatic cord is extremely rare and usually diagnosed at surgery. We present an unusual case of spermatic cord torsion in a 14-year-old male patient. It is important to highlight that the torsion occurred only on the distal half of the epididymis leaving the head untwisted and edematous. In addition, the fact that this condition was painless made this case extremely rare and motivated our presentation.

  17. Painless inter epididymal testicular torsion of the spermatic cord

    OpenAIRE

    Salomon V. Romano; Haime S. Hernan; Norberto Fredotovich

    2007-01-01

    Inter epididymal testicular torsion of the spermatic cord is extremely rare and usually diagnosed at surgery. We present an unusual case of spermatic cord torsion in a 14-year-old male patient. It is important to highlight that the torsion occurred only on the distal half of the epididymis leaving the head untwisted and edematous. In addition, the fact that this condition was painless made this case extremely rare and motivated our presentation.

  18. Saturated amine oxides: Part 8. Hydroacridines: Part 27. Effects of N-oxidation and of N-quaternization on the 15N NMR chemical shifts of N-methylpiperidine-derived mono-, bi-, and tricycloaliphatic tertiary amines.

    Science.gov (United States)

    Potmischil, Francisc; Duddeck, Helmut; Nicolescu, Alina; Deleanu, Calin

    2007-03-01

    The (15)N chemical shifts of 13 N-methylpiperidine-derived mono-, bi- and tricycloaliphatic tertiary amines, their methiodides and their N-epimeric pairs of N-oxides were measured, and the contributions of specific structural parameters to the chemical shifts were determined by multilinear regression analysis. Within the examined compounds, the effects of N-oxidation upon the (15)N chemical shifts of the amines vary from +56 ppm to +90 ppm (deshielding), of which approx. +67.7 ppm is due to the inductive effect of the incoming N(+)--O(-) oxygen atom, whereas the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The effects of quaternization vary from -3.1 ppm to +29.3 ppm, of which approx. +8.9 ppm is due to the inductive effect of the incoming N(+)--CH(3) methyl group, and the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The shift effects of the C-alkyl substituents in the amines, the N-oxides and the methiodides are discussed. Copyright (c) 2007 John Wiley & Sons, Ltd.

  19. Ultrasonographic features of prenatal testicular torsion: Case report

    Directory of Open Access Journals (Sweden)

    Elif Ağaçayak

    2013-01-01

    Full Text Available Although prenatal testicular torsion (PNTT is rarely observed,it is an important condition that can cause bilateralvanishing testis. Generally, PNTT cases observed asextravaginal torsion and treatment is emergency surgicalop-eration. In this article, 39 week presented a case diagnosedin the prenatal testicular torsion. PNTT diagnosiswas confirmed by Doppler ultrasonography and emergencysurgery was performed. Extravaginal left testiculartorsion gangrene and necrosis of the testis was observedin the operation. Left orchiectomy was performed andintrauter-ine ultrasonographic diagnosis was found to becorrect.Key words: Testicular torsion, prenatal diagnosis, features,ultrasonography

  20. Association of Torsion With Testicular Cancer: A Retrospective Study.

    Science.gov (United States)

    Uguz, Sami; Yilmaz, Sercan; Guragac, Ali; Topuz, Bahadır; Aydur, Emin

    2016-02-01

    Testicular torsion is a medical emergency that usually requires surgical exploration. However, testicular malignancy has been anecdotally reported with the association of torsion in surgical specimens, and the published data remain scant on the association of torsion with testicular tumors. By retrospective medical record review, we identified 32 patients who had been diagnosed with testicular torsion, 20 of whom had undergone orchiectomy. Of these 20 patients, 2 were diagnosed with a malignancy. Our study, the largest case series to date, has shown an association between testicular torsion and testicular cancer of 6.4%. Testicular torsion is a medical emergency that usually requires surgical exploration. However, testicular malignancy has been anecdotally reported in association with torsion in surgical specimens. However, the published data remain scant on the association between torsion and the presence of testicular tumors. The present retrospective study explored the association between torsion and testicular cancer in patients with testicular torsion undergoing orchiectomy during scrotal exploration. A medical record review was performed of patients who had had a diagnosis of testicular torsion from January 2003 to February 2015. The clinicopathologic characteristics of the patients were recorded. A total of 32 patients were identified. Their mean age was 21.1 years (range, 7-39 years). All the patients had unilateral testicular torsion, which affected the left side in 17 and the right side in 15. Manual detorsion was successful in 6 patients, and 26 patients underwent emergency surgery with testicular detorsion (6 fixation surgery and 20 orchiectomy). The type of incision was scrotal in 6, inguinal in 10, and unspecified in 4. Pathologic examination of the orchiectomy specimens showed malignancy in 2 cases (seminoma and malign mixed germ cell tumor). To the best of our knowledge, the present single-center case series is the largest case series to date of

  1. Secondary Torsion of Vermiform Appendix with Mucinous Cystadenoma

    Directory of Open Access Journals (Sweden)

    Maki Kitagawa

    2007-06-01

    Full Text Available Torsion of the vermiform appendix is a rare disorder, which causes abdominal symptoms indistinguishable from acute appendicitis. We report a case (a 34-year-old male of secondary torsion of the vermiform appendix with mucinous cystadenoma. This case was characterized by mild inflammatory responses, pentazocine-resistant abdominal pain, and appendiceal tumor, which was not enhanced by the contrast medium on computed tomography presumably because of reduced blood flow by the torsion. These findings may be helpful for the preoperative diagnosis of secondary appendiceal torsion.

  2. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts.

    Science.gov (United States)

    Doyle, Colleen M; Rumfeldt, Jessica A; Broom, Helen R; Sekhar, Ashok; Kay, Lewis E; Meiering, Elizabeth M

    2016-03-08

    The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.

  3. A lanthanide complex with dual biosensing properties: CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts) with europium DOTA-tetraglycinate.

    Science.gov (United States)

    Coman, Daniel; Kiefer, Garry E; Rothman, Douglas L; Sherry, A Dean; Hyder, Fahmeed

    2011-12-01

    Responsive contrast agents (RCAs) composed of lanthanide(III) ion (Ln3R) complexes with a variety of1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (DOTA4S) derivatives have shown great potential as molecular imaging agents for MR. A variety of LnDOTA–tetraamide complexes have been demonstrated as RCAs for molecular imaging using chemical exchange saturation transfer (CEST). The CEST method detects proton exchange between bulk water and any exchangeable sites on the ligand itself or an inner sphere of bound water that is shifted by a paramagnetic Ln3R ion bound in the core of the macrocycle. It has also been shown that molecular imaging is possible when the RCA itself is observed (i.e. not its effect on bulk water) using a method called biosensor imaging of redundant deviation in shifts (BIRDS). The BIRDS method utilizes redundant information stored in the nonexchangeable proton resonances emanating from the paramagnetic RCA for ambient factors such as temperature and/or pH.Thus, CEST and BIRDS rely on exchangeable and nonexchangeable protons, respectively, for biosensing. We posited that it would be feasible to combine these two biosensing features into the same RCA (i.e. dual CEST and BIRDS properties). A complex between europium(III) ion (Eu3R) and DOTA–tetraglycinate [DOTA–(gly)S4] was used to demonstrate that its CEST characteristics are preserved, while its BIRDS properties are also detectable. The in vitro temperature sensitivity of EuDOTA–(gly)S4 was used to show that qualitative MR contrast with CEST can be calibrated using quantitative MR mapping with BIRDS, thereby enabling quantitative molecular imaging at high spatial resolution.

  4. Comparison of qualitative and quantitative evaluation of diffusion-weighted MRI and chemical-shift imaging in the differentiation of benign and malignant vertebral body fractures.

    Science.gov (United States)

    Geith, Tobias; Schmidt, Gerwin; Biffar, Andreas; Dietrich, Olaf; Dürr, Hans Roland; Reiser, Maximilian; Baur-Melnyk, Andrea

    2012-11-01

    The objective of our study was to compare the diagnostic value of qualitative diffusion-weighted imaging (DWI), quantitative DWI, and chemical-shift imaging in a single prospective cohort of patients with acute osteoporotic and malignant vertebral fractures. The study group was composed of patients with 26 osteoporotic vertebral fractures (18 women, eight men; mean age, 69 years; age range, 31 years 6 months to 86 years 2 months) and 20 malignant vertebral fractures (nine women, 11 men; mean age, 63.4 years; age range, 24 years 8 months to 86 years 4 months). T1-weighted, STIR, and T2-weighted sequences were acquired at 1.5 T. A DW reverse fast imaging with steady-state free precession (PSIF) sequence at different delta values was evaluated qualitatively. A DW echo-planar imaging (EPI) sequence and a DW single-shot turbo spin-echo (TSE) sequence at different b values were evaluated qualitatively and quantitatively using the apparent diffusion coefficient. Opposed-phase sequences were used to assess signal intensity qualitatively. The signal loss between in- and opposed-phase images was determined quantitatively. Two-tailed Fisher exact test, Mann-Whitney test, and receiver operating characteristic analysis were performed. Sensitivities, specificities, and accuracies were determined. Qualitative DW-PSIF imaging (delta = 3 ms) showed the best performance for distinguishing between benign and malignant fractures (sensitivity, 100%; specificity, 88.5%; accuracy, 93.5%). Qualitative DW-EPI (b = 50 s/mm(2) [p = 1.00]; b = 250 s/mm(2) [p = 0.50]) and DW single-shot TSE imaging (b = 100 s/mm(2) [p = 1.00]; b = 250 s/mm(2) [p = 0.18]; b = 400 s/mm(2) [p = 0.18]; b = 600 s/mm(2) [p = 0.39]) did not indicate significant differences between benign and malignant fractures. DW-EPI using a b value of 500 s/mm(2) (p = 0.01) indicated significant differences between benign and malignant vertebral fractures. Quantitative DW-EPI (p = 0.09) and qualitative opposed-phase imaging (p = 0

  5. Creatinine and creatininium cation in water solution. Tautomerism and quantitative interpretation of the solution acidity effect on 1H, 13C and 1:4N NMR chemical shifts

    International Nuclear Information System (INIS)

    Kotsyubynskyy, D.; Molchanov, S.; Gryff-Keller, A.

    2004-01-01

    1 H, 13 C and 1 :4N NMR chemical shifts for creatinine in water solution of various acidity have been measured. Analysis of these data enabled determination of the acidity constant of creatininium cation and the chemical shifts of the neutral and protonated forms of creatinine. Molecular energies and carbon and nitrogen magnetic shielding constants for various tautomeric structures of the investigated species have been calculated using the quantum chemistry method GIAO DFT B3LYP/6-311++G(2d,p). Compilation of the available experimental and theoretical results has provided additional information on the problem of tautomerism of this important biological molecule. (author)

  6. The torsional barriers of two equivalent methyl internal rotations in 2,5-dimethylfuran investigated by microwave spectroscopy

    Science.gov (United States)

    Van, Vinh; Bruckhuisen, Jonas; Stahl, Wolfgang; Ilyushin, Vadim; Nguyen, Ha Vinh Lam

    2018-01-01

    The microwave spectrum of 2,5-dimethylfuran was recorded using two pulsed molecular jet Fourier transform microwave spectrometers which cover the frequency range from 2 to 40 GHz. The internal rotations of two equivalent methyl tops with a barrier height of approximately 439.15 cm-1 introduce torsional splittings of all rotational transitions in the spectrum. For the spectral analysis, two different computer programs were applied and compared, the PAM-C2v-2tops code based on the principal axis method which treats several torsional states simultaneously, and the XIAM code based on the combined axis method, yielding accurate molecular parameters. The experimental work was supplemented by quantum chemical calculations. Two-dimensional potential energy surfaces depending on the torsional angles of both methyl groups were calculated and parametrized.

  7. Structural Modifications for Torsional Vibration Control of Shafting Systems Based on Torsional Receptances

    Directory of Open Access Journals (Sweden)

    Zihao Liu

    2016-01-01

    Full Text Available Torsional vibration of shafts is a very important problem in engineering, in particular in ship engines and aeroengines. Due to their high levels of integration and complexity, it is hard to get their accurate structural data or accurate modal data. This lack of data is unhelpful to vibration control in the form of structural modifications. Besides, many parts in shaft systems are not allowed to be modified such as rotary inertia of a pump or an engine, which is designed for achieving certain functions. This paper presents a strategy for torsional vibration control of shaft systems in the form of structural modifications based on receptances, which does not need analytical or modal models of the systems under investigation. It only needs the torsional receptances of the system, which can be obtained by testing simple auxiliary structure attached to relevant locations of the shaft system and using the finite element model (FEM of the simple structure. An optimization problem is constructed to determine the required structural modifications, based on the actual requirements of modal frequencies and mode shapes. A numerical experiment is set up and the influence of several system parameters is analysed. Several scenarios of constraints in practice are considered. The numerical simulation results demonstrate the effectiveness of this method and its feasibility in solving torsional vibration problems in practice.

  8. Toward laboratory torsional spine magnetic reconnection

    Science.gov (United States)

    Chesny, David L.; Orange, N. Brice; Oluseyi, Hakeem M.; Valletta, David R.

    2017-12-01

    Magnetic reconnection is a fundamental energy conversion mechanism in nature. Major attempts to study this process in controlled settings on Earth have largely been limited to reproducing approximately two-dimensional (2-D) reconnection dynamics. Other experiments describing reconnection near three-dimensional null points are non-driven, and do not induce any of the 3-D modes of spine fan, torsional fan or torsional spine reconnection. In order to study these important 3-D modes observed in astrophysical plasmas (e.g. the solar atmosphere), laboratory set-ups must be designed to induce driven reconnection about an isolated magnetic null point. As such, we consider the limited range of fundamental resistive magnetohydrodynamic (MHD) and kinetic parameters of dynamic laboratory plasmas that are necessary to induce the torsional spine reconnection (TSR) mode characterized by a driven rotational slippage of field lines - a feature that has yet to be achieved in operational laboratory magnetic reconnection experiments. Leveraging existing reconnection models, we show that within a 3$ apparatus, TSR can be achieved in dense plasma regimes ( 24~\\text{m}-3$ ) in magnetic fields of -1~\\text{T}$ . We find that MHD and kinetic parameters predict reconnection in thin current sheets on time scales of . While these plasma regimes may not explicitly replicate the plasma parameters of observed astrophysical phenomena, studying the dynamics of the TSR mode within achievable set-ups signifies an important step in understanding the fundamentals of driven 3-D magnetic reconnection and the self-organization of current sheets. Explicit control of this reconnection mode may have implications for understanding particle acceleration in astrophysical environments, and may even have practical applications to fields such as spacecraft propulsion.

  9. Transverse posterior element fractures associated with torsion

    International Nuclear Information System (INIS)

    Abel, M.S.

    1989-01-01

    Six examples of a previously undescribed class of transverse vertebral element fractures are presented. These fractures differ from Chance and Smith fractures and their variants in the following respects: (1) the etiology is torsion and not flexion; (2) there is neither distraction of posterior ring fragments nor posterior ligament tears; (3) in contrast to Chance and Smith fractures, extension of the fracture into the vertebral body is absent or minimal; (4) the transverse process of the lumbar vertebra is avulsed at its base with a vertical fracture, not split horizontally. These fractures occur in cervical, lumbar, and sacral vertebrae in normal or compromised areas of the spine. (orig.)

  10. Possible role of torsion in gravitational theories

    International Nuclear Information System (INIS)

    Nieh, H.T.

    1983-01-01

    Torsion is of interest in an indirect way, in that it has the potential of being an important ingredient in a future successful quantum theory of gravitation. Einstein's theory of gravitation, despite its simplicity and elegance, and its successes in large-scale gravitational phenomena, can only be regarded as a macroscopic classical theory. It is a non-renormalizable quantum field theory, and, therefore, lacks the status of a good microscopic theory. It is the search for a successful quantum field theory of gravitation that poses as one of the great challenges to theoretical physics today. (Auth.)

  11. Torsion of the normal fallopian tube.

    Science.gov (United States)

    Provost, M W

    1972-01-01

    From 1961 to 1970 a number of cases of torsion of the Fallopian tube were seen at the Kaiser Foundation Hospital in San Francisco of which 3 cases are reported. Of the many theories of causation, pelvic congestion seemed the most likely. The only universal symptom is pain, located in the quadrant of the affected tube and sometimes radiating to the thigh or flank. Nausea and vomiting are frequent; temperature and white cell count are only slightly elevated or normal. A mass is often felt, depending on the amount of hemorrhage. Correct diagnosis is almost never made preoperatively. The only treatment is laparotomy and surgical correction.

  12. Deuterium isotope effects on 13C and 15N chemical shifts of intramolecularly hydrogen-bonded enaminocarbonyl derivatives of Meldrum’s and Tetronic acid

    Science.gov (United States)

    Ullah, Saif; Zhang, Wei; Hansen, Poul Erik

    2010-07-01

    Secondary deuterium isotope effects on 13C and 15N nuclear shieldings in a series of cyclic enamino-diesters and enamino-esters and acyclic enaminones and enamino-esters have been examined and analysed using NMR and DFT (B3LYP/6-31G(d,p)) methods. One-dimensional and two-dimensional NMR spectra of enaminocarbonyl and their deuterated analogues were recorded in CDCl 3 and CD 2Cl 2 at variable temperatures and assigned. 1JNH coupling constants for the derivatives of Meldrum's and tetronic acids reveal that they exist at the NH-form. It was demonstrated that deuterium isotope effects, for the hydrogen bonded compounds, due to the deuterium substitution at the nitrogen nucleus lead to large one-bond isotope effects at nitrogen, 1Δ 15N(D), and two-bond isotope effects on carbon nuclei, 2ΔC(ND), respectively. A linear correlations exist between 2ΔC(ND) and 1Δ 15N(D) whereas the correlation with δNH is divided into two. A good agreement between the experimentally observed 2ΔC(ND) and calculated dσ 13C/dR NH was obtained. A very good correlation between calculated NH bond lengths and observed NH chemical shifts is found. The observed isotope effects are shown to depend strongly on Resonance Assisted Hydrogen bonding.

  13. Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.

    Science.gov (United States)

    Kobayashi, Ayaho; Kanaba, Teppei; Satoh, Ryosuke; Ito, Yutaka; Sugiura, Reiko; Mishima, Masaki

    2017-10-01

    Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1. Phosphorylation significantly reduces RNA-binding activity and likely modulates Nrd1 function. To reveal the relationship between the structure and function of Nrd1 and how phosphorylation affects structure, we used heteronuclear NMR techniques to investigate the three-dimensional structure of Nrd1. Here we report the 1 H, 13 C, and 15 N resonance assignments of RRM1-RRM2 (residues 108-284) comprising the first and second RRMs obtained using heteronuclear NMR techniques. Secondary structures derived from the chemical shifts are reported. These data should contribute to the understanding of the three-dimensional structure of the RRM1-RRM2 region of Nrd1 and the perturbation caused by phosphorylation.

  14. Chemical shift effect predicting lymph node status in rectal cancer using high-resolution MR imaging with node-for-node matched histopathological validation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hongmei; Zhang, Chongda; Ye, Feng; Liu, Yuan; Zhou, Chunwu [Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, ChaoYang District, Beijing (China); Zheng, Zhaoxu [Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Colorectal Oncology, National Cancer Center/Cancer Hospital, ChaoYang District, Beijing (China); Zou, Shuangmei [Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Pathology, National Cancer Center/Cancer Hospital, ChaoYang District, Beijing (China)

    2017-09-15

    To evaluate the value of the chemical shift effect (CSE) as well as other criteria for the prediction of lymph node status. Twenty-nine patients who underwent radical surgery of rectal cancers were studied with pre- and postoperative specimen MRI. Lymph nodes were harvested from transverse whole-mount specimens and compared with in vivo and ex vivo images to obtain a precise slice-for-section match. Preoperative MR characteristics including CSE, as well as other predictors, were evaluated by two readers independently between benign and metastatic nodes. A total of 255 benign and 35 metastatic nodes were obtained; 71.4% and 69.4% of benign nodes were detected with regular CSE for two readers, whereas 80.0% and 74.3% of metastatic nodes with absence of CSE. The CSE rendered areas under the ROC curve (AUC) of 0.879 and 0.845 for predicting nodal status for two readers. The criteria of nodal location, border, signal intensity and minimum distance to the rectal wall were also useful but with AUCs (0.629-0.743) lower than those of CSE. CSE is a reliable predictor for differentiating benign from metastatic nodes. Additional criteria should be taken into account when it is difficult to determine the nodal status by using only a single predictor. (orig.)

  15. Comparison of diffusion-weighted images using short inversion time inversion recovery or chemical shift selective pulse as fat suppression in patients with breast cancer

    International Nuclear Information System (INIS)

    Kazama, Toshiki; Nasu, Katsuhiro; Kuroki, Yoshifumi; Nawano, Shigeru; Ito, Hisao

    2009-01-01

    Fat suppression is essential for diffusion-weighted imaging (DWI) in the body. However, the chemical shift selective (CHESS) pulse often fails to suppress fat signals in the breast. The purpose of this study was to compare DWI using CHESS and DWI using short inversion time inversion recovery (STIR) in terms of fat suppression and the apparent diffusion coefficient (ADC) value. DWI using STIR, DWI using CHESS, and contrast-enhanced T1-weighted images were obtained in 32 patients with breast carcinoma. Uniformity of fat suppression, ADC, signal intensity, and visualization of the breast tumors were evaluated. In 44% (14/32) of patients there was insufficient fat suppression in the breasts on DWI using CHESS, whereas 0% was observed on DWI using STIR (P<0.0001). The ADCs obtained for DWI using STIR were 4.3% lower than those obtained for DWI using CHESS (P<0.02); there was a strong correlation of the ADC measurement (r=0.93, P<0.001). DWI using STIR may be excellent for fat suppression; and the ADC obtained in this sequence was well correlated with that obtained with DWI using CHESS. DWI using STIR may be useful when the fat suppression technique in DWI using CHESS does not work well. (author)

  16. Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder.

    Science.gov (United States)

    Thurber, Kent R; Tycko, Robert

    2009-01-01

    Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of (79)Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determination of internal sample temperatures. Advantages of this method include high signal-to-noise, proximity of the (79)Br NMR frequency to that of (13)C, applicability from 20 K to 320 K or higher, and simultaneity with adjustment of the MAS axis direction. We show that spin-lattice relaxation in KBr is driven by a quadrupolar mechanism. We demonstrate a simple approach to including KBr powder in hydrated samples, such as biological membrane samples, hydrated amyloid fibrils, and hydrated microcrystalline proteins, that allows direct assessment of the effects of frictional and radio-frequency heating under experimentally relevant conditions.

  17. "1H and "1"3C NMR Data on Hydroxy/methoxy Flavonoids and the Effects of Substituents on Chemical Shifts

    International Nuclear Information System (INIS)

    Yoon, Hyuk; Eom, Sung Lock; Hyun, Ji Ye; Jo, Geun Hyeong; Hwang, Do Seok; Lee, Sun Hee; Yong, Yeon Joong; Lee, Young Han; Lim, Yoong Ho; Park, Jun Cheol

    2011-01-01

    Polyphenols have recently been examined for such applications, and they are classified based on their carbon skeletons: phenolic acids with C6-C1 skeleton, hydrocinammates with C6-C_3 skeleton, stilbenes with C6-C2-C6 skeleton, and flavonoids with C6-C_3-C6 skeleton.2 Of these compounds, flavonoids are ubiquitously found in most plants. Since flavonoids belong to polyphenols, they have many hydroxy groups. From a bioavailability point of view, hydroxy groups prevent cell membrane transport, and hydroxyflavonoids can be metabolized by O-methyltransferases. However, methoxylated flavonoids may not have these problems. Hydroxylated or methoxylated flavonoids are found from natural sources. Nuclear magnetic resonance (NMR) spectroscopy is widely used to identify different compounds including hydroxylated or methoxylated flavonoids. Because the position and the number of substituted hydroxy or/and methoxy groups will change the "1H and "1"3C chemical shifts, it is important to understand these changes so that the structures of newly isolated hydroxy/methoxy-flavonoids can be easily identified

  18. VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C.; Nesbitt, Anna E.; Hallock, Michael J. [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Rupasinghe, Sanjeewa G. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Tang Ming [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Harris, Jason; Baudry, Jerome [University of Tennessee, Department of Biochemistry, Cellular and Molecular Biology (United States); Schuler, Mary A. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Rienstra, Chad M., E-mail: rienstra@illinois.edu [University of Illinois at Urbana-Champaign, Department of Chemistry (United States)

    2012-01-15

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., {sup 13}C-{sup 13}C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  19. VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C [University of Illinois, Urbana-Champaign; Nesbitt, Anna E [University of Illinois, Urbana-Champaign; Hallock, Michael J [University of Illinois, Urbana-Champaign; Rupasinghe, Sanjeewa [University of Illinois, Urbana-Champaign; Tang, Ming [University of Illinois, Urbana-Champaign; Harris, Jason B [ORNL; Baudry, Jerome Y [ORNL; Schuler, Mary A [University of Illinois, Urbana-Champaign; Rienstra, Chad M [University of Illinois, Urbana-Champaign

    2011-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  20. Repeatability of two-dimensional chemical shift imaging multivoxel proton magnetic resonance spectroscopy for measuring human cerebral choline-containing compounds.

    Science.gov (United States)

    Puri, Basant K; Egan, Mary; Wallis, Fintan; Jakeman, Philip

    2018-03-22

    To investigate the repeatability of proton magnetic resonance spectroscopy in the in vivo measurement of human cerebral levels of choline-containing compounds (Cho). Two consecutive scans were carried out in six healthy resting subjects at a magnetic field strength of 1.5 T. On each occasion, neurospectroscopy data were collected from 64 voxels using the same 2D chemical shift imaging (CSI) sequence. The data were analyzed in the same way, using the same software, to obtain the values for each voxel of the ratio of Cho to creatine. The Wilcoxon related-samples signed-rank test, coefficient of variation (CV), repeatability coefficient (RC), and intraclass correlation coefficient (ICC) were used to assess the repeatability. The CV ranged from 2.75% to 33.99%, while the minimum RC was 5.68%. There was excellent reproducibility, as judged by significant ICC values, in 26 voxels. Just three voxels showed significant differences according to the Wilcoxon related-samples signed-rank test. It is therefore concluded that when CSI multivoxel proton neurospectroscopy is used to measure cerebral choline-containing compounds at 1.5 T, the reproducibility is highly acceptable.

  1. Hepatic steatosis assessment with {sup 1}H-spectroscopy and chemical shift imaging at 3.0 T before hepatic surgery: Reliable enough for making clinical decisions?

    Energy Technology Data Exchange (ETDEWEB)

    Koelblinger, Claus, E-mail: claus.koelblinger@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Krssak, Martin, E-mail: martin.krssak@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Maresch, Judith, E-mail: judith.maresch@meduniwien.ac.at [Department of Pathology, Medical University of Vienna (Austria); Wrba, Fritz, E-mail: fritz.wrba@meduniwien.ac.at [Department of Pathology, Medical University of Vienna (Austria); Kaczirek, Klaus, E-mail: klaus.kaczirek@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Gruenberger, Thomas, E-mail: thomas.gruenberger@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Tamandl, Dietmar, E-mail: dietmar.tamandl@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Ba-Ssalamah, Ahmed, E-mail: ahmed.ba-ssalamah@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Berger-Kulemann, Vanessa, E-mail: vanessa.berger-kulemann@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Weber, Michael, E-mail: michael.weber@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Schima, Wolfgang, E-mail: wolfgang.schima@khgh.at [Department of Radiology, KH Goettlicher Heiland and Herz-Jesu Krankenhaus, Dornbacher Strasse 20-28, 1170 Vienna (Austria)

    2012-11-15

    Purpose: To compare the accuracy of liver fat quantification using chemical shift imaging (CSI) and H1 MR-spectroscopy (MRS) at 3.0 T in patients undergoing liver resection. Methods: Totally 35 patients were included in this prospective IRB approved study. The histopathologically assessed liver fat was compared to the hepatic fat fractions calculated with CSI (with and without spleen correction) and MRS. Spearman's rank correlation and Fisher z-test were used for correlation analysis. Sensitivity and specificity regarding the detection of marked steatosis were calculated for the different modalities and compared using the McNemar test. Results: MRS (r = .85) and CSI with spleen correction (r = .85) showed a significantly better correlation (p = .03) with histology compared to CSI without spleen correction (r = .67). Sensitivity and specificity for the detection of marked steatosis was 100% (12/12) and 87% (20/23) for MRS and 92% (11/12) and 83% (19/23) for CSI with spleen correction (p > .12). Conclusion: For the assessment of hepatic steatosis both CSI with spleen correction and MRS at 3.0 T, show a good correlation with histology. CSI without spleen correction should not be used. Sensitivity and specificity for the detection of marked steatosis are high with both modalities. However, results that are scattered around the cut-off values are not reliable enough for clinical decisions.

  2. Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

    Science.gov (United States)

    Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.

    2005-01-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221

  3. Scan time reduction in {sup 23}Na-Magnetic Resonance Imaging using the chemical shift imaging sequence. Evaluation of an iterative reconstruction method

    Energy Technology Data Exchange (ETDEWEB)

    Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology

    2015-07-01

    To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.

  4. Investigation method of torsional properties and damages of glass/epoxy composite pipes

    Directory of Open Access Journals (Sweden)

    Putić Slaviša S.

    2006-01-01

    Full Text Available Pipes made of composites glass fiber/epoxy resin are predominantly used in the chemical industry, construction, infrastructure and war technique. The pipes made for this purpose are in their use exposed to static and dynamic loading. Depending on the purpose, the pipes, especially those in complex structures, can be loaded by torsion. In that case, exceeding allowed tensions can cause damages such as cracking the fibers and matrix delamination. These damages can lead to the appearance of cracks on the pipes and in many cases to complete breakage of the pipe. Because of this, it is very important to evaluate composite pipes exposed to torsion and find out in which way the construction is weakened, what actually is the main goal of this paper.

  5. Dismal salvage of testicular torsion: A call to action! | Maranya ...

    African Journals Online (AJOL)

    ... were not subjected to orchidopexy. There was no occurrence of torsion after orchidopexy. Conclusion: Testicular torsions were associated with low salvage rates. Increased public awareness coupled with clinician, parental, teacher, teenage and adult male education with respect to the consequences of acute scrotal pain ...

  6. Quantum gravity effect in torsion driven inflation and CP violation

    Energy Technology Data Exchange (ETDEWEB)

    Choudhury, Sayantan [Department of Theoretical Physics, Tata Institute of Fundamental Research,Colaba, 1, Homi Bhabha Road, Mumbai 400005 (India); Pal, Barun Kumar [Inter-University Centre for Astronomy and Astrophysics,Ganeshkhind, Pune 411007 (India); Netaji Nagar College for Women,Regent Estate, Kolkata 700092 (India); Basu, Banasri; Bandyopadhyay, Pratul [Physics and Applied Mathematics Unit, Indian Statistical Institute,203 B.T. Road, Kolkata 700 108 (India)

    2015-10-28

    We have derived an effective potential for inflationary scenario from torsion and quantum gravity correction in terms of the scalar field hidden in torsion. A strict bound on the CP violating θ parameter, O(10{sup −10})<θ

  7. Torsion of the Spermatic Cord: Is Bilateral Orchidopexy Really ...

    African Journals Online (AJOL)

    Aim: To evaluate the rationale for bilateral orchidopexy as treatment for unilateral torsion of the testis, by determining how frequently the contralateral testis shows an abnormal pathology in unilateral testicular torsion. Patients and Methods:This is a retrospective study using adult urology patients treated for both acute and ...

  8. Comparison of torsional and longitudinal modes using phacoemulsification parameters.

    Science.gov (United States)

    Rekas, Marek; Montés-Micó, Robert; Krix-Jachym, Karolina; Kluś, Adam; Stankiewicz, Andrzej; Ferrer-Blasco, Teresa

    2009-10-01

    To compare phacoemulsification parameters of torsional and longitudinal ultrasound modes. Ophthalmology Department, Military Health Service Institute, Warsaw, Poland. This prospective study evaluated eyes 1, 7, and 30 days after phacoemulsification with an Infiniti Vision System using the torsional or longitudinal ultrasound (US) mode. Cataract classification was according to the Lens Opacities Classification System II. Nucleus fragmentation was by the phaco-chop and quick-chop methods. Primary outcome measures were phaco time, mean phaco power, mean torsional amplitude, and aspiration time. Total energy, defined as cumulative dissipated energy (CDE) x aspiration time, and the effective coefficient, defined as aspiration time/phaco time, were also calculated. Four hundred eyes were evaluated. The CDE was statistically significantly lower in the torsional mode for nucleus grades I, II, and III (P.05). Aspiration time was statistically significantly shorter in the torsional mode than in the longitudinal mode for nucleus grades III and IV (P<.05). Total energy was significantly lower in the torsional mode for all nucleus densities (P<.05). The effective coefficient was significantly lower in the longitudinal mode except for nucleus grade I (P<.05). Torsional phacoemulsification was more effective than longitudinal phacoemulsification in the amount of applied fluid and the quantity of US energy expended. With the torsional method, it was possible to maintain a constant ratio of amount of fluid flow to quantity of US energy used, regardless of nucleus density.

  9. Additivity for parametrized topological Euler characteristic and Reidemeister torsion

    OpenAIRE

    Badzioch, Bernard; Dorabiala, Wojciech

    2005-01-01

    Dwyer, Weiss, and Williams have recently defined the notions of parametrized topological Euler characteristic and parametrized topological Reidemeister torsion which are invariants of bundles of compact topological manifolds. We show that these invariants satisfy additivity formulas paralleling the additive properties of the classical Euler characteristic and Reidemeister torsion of finite CW-complexes.

  10. Perinatal testicular torsion: literature review and local experience ...

    African Journals Online (AJOL)

    The prognosis in TUDT is guarded and contralateral fixation was not practiced, except in a 5-week-old infant. Early orchiopexy at 3–6 months is recommended. Cooperation between surgeons, neonatologists, and parents is mandatory to avoid time delay. Keywords: intrauterine testicular torsion, postnatal testicular torsion, ...

  11. Mechanical origins of rightward torsion in early chick brain development

    Science.gov (United States)

    Chen, Zi; Guo, Qiaohang; Dai, Eric; Taber, Larry

    2015-03-01

    During early development, the neural tube of the chick embryo undergoes a combination of progressive ventral bending and rightward torsion. This torsional deformation is one of the major organ-level left-right asymmetry events in development. Previous studies suggested that bending is mainly due to differential growth, however, the mechanism for torsion remains poorly understood. Since the heart almost always loops rightwards that the brain twists, researchers have speculated that heart looping affects the direction of brain torsion. However, direct evidence is lacking, nor is the mechanical origin of such torsion understood. In our study, experimental perturbations show that the bending and torsional deformations in the brain are coupled and that the vitelline membrane applies an external load necessary for torsion to occur. Moreover, the asymmetry of the looping heart gives rise to the chirality of the twisted brain. A computational model and a 3D printed physical model are employed to help interpret these findings. Our work clarifies the mechanical origins of brain torsion and the associated left-right asymmetry, and further reveals that the asymmetric development in one organ can induce the asymmetry of another developing organ through mechanics, reminiscent of D'Arcy Thompson's view of biological form as ``diagram of forces''. Z.C. is supported by the Society in Science - Branco Weiss fellowship, administered by ETH Zurich. L.A.T acknowledges the support from NIH Grants R01 GM075200 and R01 NS070918.

  12. Torsional structural response from free-field ground motion

    International Nuclear Information System (INIS)

    Lam, P.C.; Scavuzzo, R.J.

    1979-01-01

    Torsional response of structures subjected to the action of both the free-field torsional inputs and external torque is investigated. By expanding the work of Scanlan, both lateral and torsional foundation inputs due to a travelling shear wave are derived from the free-field point motion. These free-field torsional motions are used as the basis of numerical studies. Response for different soil stiffness and structural characteristics are studied, as well as different dynamic models. In one dynamic model the structure is coupled to the soil using a compliance spring matrix and in the second model the structure coupled to an elastic half-space. Results of these two basic models are compared and found to be in good agreement. Finally, torsional structural response caused by torsional inputs is compared with lateral response caused by modified lateral inputs to determine the significance of torsional excitation on the seismic response of building structures. Numerical results show that these torsional seismic loads are as large or larger than those from modified lateral inputs. (orig.)

  13. Quantum gravity effect in torsion driven inflation and CP violation

    International Nuclear Information System (INIS)

    Choudhury, Sayantan; Pal, Barun Kumar; Basu, Banasri; Bandyopadhyay, Pratul

    2015-01-01

    We have derived an effective potential for inflationary scenario from torsion and quantum gravity correction in terms of the scalar field hidden in torsion. A strict bound on the CP violating θ parameter, O(10"−"1"0)<θ< O(10"−"9) has been obtained, using Planck+WMAP9 best fit cosmological parameters.

  14. Torsional stresses in the transverse fillet weld tubular joints

    NARCIS (Netherlands)

    Gunay, D.; Aydemir, A.; Özer, H.

    1996-01-01

    Torsional stresses, 'tre and tel , in tbe transverse fillet tubular weld joint subjected to torsional load have been analyzed by the finite element method using triangular and quadrilateral izoparametric axisymmetric fourier type torus finite elements. There is an axisymmetry with respect to

  15. Severe congenital penile torsion with anterior urethral diverticulum ...

    African Journals Online (AJOL)

    On examination, he was found to be a case of severe congenital penile torsion with diversion and rotation of median raphae in a counterclockwise fashion upto the midline dorsally confirming 180◦ torsion. During voiding, there was appearance of a swelling in distal penile region with passage of urinary drops while ...

  16. A Patient Presenting with Concurrent Testis Torsion and Epididymal Leiomyoma

    Directory of Open Access Journals (Sweden)

    E. Arpali

    2013-01-01

    Full Text Available Leiomyomas are the second most common tumors of epididymis. Patients with leiomyomas are sometimes misdiagnosed with testicular tumors. A Case of a patient with a scrotal mass presenting with testicular torsion is reported. Concurrent occurrence of testicular torsion and epididymal leiomyoma is an extremely rare condition.

  17. Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel β-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.

    Science.gov (United States)

    Yazawa, Koji; Suzuki, Furitsu; Nishiyama, Yusuke; Ohata, Takuya; Aoki, Akihiro; Nishimura, Katsuyuki; Kaji, Hironori; Shimizu, Tadashi; Asakura, Tetsuo

    2012-11-25

    The accurate (1)H positions of alanine tripeptide, A(3), with anti-parallel and parallel β-sheet structures could be determined by highly resolved (1)H DQMAS solid-state NMR spectra and (1)H chemical shift calculation with gauge-including projector augmented wave calculations.

  18. The Reidemeister torsion of 3-manifolds

    CERN Document Server

    Nicolaescu, Liviu I

    2003-01-01

    This is a state-of-the-art introduction to the work of Franz Reidemeister, Meng Taubes, Turaev, and the author on the concept of torsion and its generalizations. Torsion is the oldest topological (but not with respect to homotopy) invariant that in its almost eight decades of existence has been at the center of many important and surprising discoveries. During the past decade, in the work of Vladimir Turaev, new points of view have emerged, which turned out to be the "right ones" as far as gauge theory is concerned. The book features mostly the new aspects of this venerable concept. The theoretical foundations of this subject are presented in a style accessible to those, who wish to learn and understand the main ideas of the theory. Particular emphasis is upon the many and rather diverse concrete examples and techniques which capture the subleties of the theory better than any abstract general result. Many of these examples and techniques never appeared in print before, and their choice is often justified by ...

  19. Curvature and torsion in growing actin networks

    International Nuclear Information System (INIS)

    Shaevitz, Joshua W; Fletcher, Daniel A

    2008-01-01

    Intracellular pathogens such as Listeria monocytogenes and Rickettsia rickettsii move within a host cell by polymerizing a comet-tail of actin fibers that ultimately pushes the cell forward. This dense network of cross-linked actin polymers typically exhibits a striking curvature that causes bacteria to move in gently looping paths. Theoretically, tail curvature has been linked to details of motility by considering force and torque balances from a finite number of polymerizing filaments. Here we track beads coated with a prokaryotic activator of actin polymerization in three dimensions to directly quantify the curvature and torsion of bead motility paths. We find that bead paths are more likely to have low rather than high curvature at any given time. Furthermore, path curvature changes very slowly in time, with an autocorrelation decay time of 200 s. Paths with a small radius of curvature, therefore, remain so for an extended period resulting in loops when confined to two dimensions. When allowed to explore a three-dimensional (3D) space, path loops are less evident. Finally, we quantify the torsion in the bead paths and show that beads do not exhibit a significant left- or right-handed bias to their motion in 3D. These results suggest that paths of actin-propelled objects may be attributed to slow changes in curvature, possibly associated with filament debranching, rather than a fixed torque

  20. Physics of detecting torsion and placing limits on its effects

    International Nuclear Information System (INIS)

    Stoeger, W.R.

    1985-01-01

    The essential principles of torsion-detection physics are presented, and an evaluation is conducted of several conceivable types of experiments and observations for actually detecting torsion fields, reemphasizing also the evident impossibility of successfully searching for its manifestations among cosmological relics. In particular, a polarized body, with net intrinsic (fundamental-particle) spin, is essential for detecting a torsion field. One which possesses only orbital angular momentum - rotation - or an unpolarized intrinsic spin density will not feel torsion. The fundamental problem in searching for such fields is the extremely small basic unit of the coupling or interaction energy between the torsion field and spin. The best way of maximizing the total interaction energy is to increase the spin density of the source sigma-s and at the same time the spin number SD of the detector. 15 references

  1. Krukenberg Tumor: A Rare Cause of Ovarian Torsion

    Directory of Open Access Journals (Sweden)

    Sameer Sandhu

    2012-01-01

    Full Text Available Ovarian torsion is the fifth most common gynecological surgical emergency. Ovarian torsion is usually associated with a cyst or a tumor, which is typically benign. The most common is mature cystic teratoma. We report the case of a 43-year-old woman who came to the Emergency Department with rare acute presentation of bilateral Krukenberg tumors, due to unilateral ovarian torsion. In this case report, we highlight the specific computed tomography (CT features of ovarian torsion and demonstrate the unique radiological findings on CT imaging. Metastasis to the ovary is not rare and 5 to 10% of all ovarian malignancies are metastatic. The stomach is the common primary site in most Krukenberg tumors (70%; an acute presentation of metastatic Krukenberg tumors with ovarian torsion is rare and not previously reported in radiology literature.

  2. Peculiar torsion dynamical response of spider dragline silk

    Science.gov (United States)

    Liu, Dabiao; Yu, Longteng; He, Yuming; Peng, Kai; Liu, Jie; Guan, Juan; Dunstan, D. J.

    2017-07-01

    The torsional properties of spider dragline silks from Nephila edulis and Nephila pilipes spiders are investigated by using a torsion pendulum technique. A permanent torsional deformation is observed after even small torsional strain. This behaviour is quite different from that of the other materials tested here, i.e., carbon fiber, thin metallic wires, Kevlar fiber, and human hair. The spider dragline thus displays a strong energy dissipation upon the initial excitation (around 75% for small strains and more for a larger strain), which correspondingly reduces the amplitude of subsequent oscillations around the new equilibrium position. The variation of torsional stiffness in relaxation dynamics of spider draglines for different excitations is also determined. The experimental result is interpreted in the light of the hierarchical structure of dragline silk.

  3. {sup 31}P-MR spectroscopy of all regions of the human heart at 1.5 T with acquisition-weighted chemical shift imaging; P-MR-Spektroskopie aller Wandabschnitte des menschlichen Herzens bei 1,5 T mit akquisitionsgewichteter Chemical-shift-Bildgebung

    Energy Technology Data Exchange (ETDEWEB)

    Koestler, H.; Beer, M.; Buchner, S.; Sandstede, J.; Pabst, T.; Kenn, W.; Hahn, D. [Wuerzburg Univ. (Germany). Abt. fuer Roentgendiagnostik; Landschuetz, W.; Kienlin, M. von [Wuerzburg Univ. (Germany). Physikalisches Inst.; Neubauer, S. [Dept. of Cardiovascular Medicine, John Radcliffe Hospital, Oxford (United Kingdom)

    2001-12-01

    Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac {sup 31}P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders {sup 31}P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.) [German] Ziel: Ziel der Arbeit war es zu untersuchen, ob die akquisitionsgewichtete Chemical-shift-Bildgebung (AW-CSI) die Bestimmung von PCr und ATP in der Seiten- und Hinterwand des menschlichen Herzens an einem klinischen 1,5 T MR-Tomographen erlaubt. Methoden: 12 gesunde Probanden wurden jeweils mit einer chemical shift imaging (CSI) und einer AW-CSI-Sequenz untersucht. Die Sequenzen unterschieden sich lediglich in der Anzahl der Wiederholungen der einzelnen

  4. Thigh muscle segmentation of chemical shift encoding-based water-fat magnetic resonance images: The reference database MyoSegmenTUM.

    Directory of Open Access Journals (Sweden)

    Sarah Schlaeger

    Full Text Available Magnetic resonance imaging (MRI can non-invasively assess muscle anatomy, exercise effects and pathologies with different underlying causes such as neuromuscular diseases (NMD. Quantitative MRI including fat fraction mapping using chemical shift encoding-based water-fat MRI has emerged for reliable determination of muscle volume and fat composition. The data analysis of water-fat images requires segmentation of the different muscles which has been mainly performed manually in the past and is a very time consuming process, currently limiting the clinical applicability. An automatization of the segmentation process would lead to a more time-efficient analysis. In the present work, the manually segmented thigh magnetic resonance imaging database MyoSegmenTUM is presented. It hosts water-fat MR images of both thighs of 15 healthy subjects and 4 patients with NMD with a voxel size of 3.2x2x4 mm3 with the corresponding segmentation masks for four functional muscle groups: quadriceps femoris, sartorius, gracilis, hamstrings. The database is freely accessible online at https://osf.io/svwa7/?view_only=c2c980c17b3a40fca35d088a3cdd83e2. The database is mainly meant as ground truth which can be used as training and test dataset for automatic muscle segmentation algorithms. The segmentation allows extraction of muscle cross sectional area (CSA and volume. Proton density fat fraction (PDFF of the defined muscle groups from the corresponding images and quadriceps muscle strength measurements/neurological muscle strength rating can be used for benchmarking purposes.

  5. Aromaticity of graphene nanoflakes in a new way: fragment analysis by combination of the nucleus-independent chemical shifts and the anisotropy of current induced density.

    Science.gov (United States)

    Li, Qing; Li, Chun-Min; Xu, Hong-Liang; Su, Zhong-Min

    2017-08-01

    A graphene nanoflake (GNF) is a polycyclic aromatic hydrocarbon (PAH) with a huge two-dimensional π-conjugated carbon material in which a central benzene ring is surrounded by identical benzene-type rings through infinite alternant method. In this paper, we explore the structure-aromaticity relationship of the GNFs and the GNFs with hollow sites (GNFHs) by combining the nucleus-independent chemical shifts (NICS) with the anisotropy of the current induced density (ACID). Firstly, the benzene is a typical aromatic molecule (NICS = -9.671 ppm), GNFs 1-6 is darned with benzene and the corresponding GNFHs 1'-6'. Secondly, the NICS values of GNFs 1-6 alternately vary: -1.214 (1) > -13.847 (2)  -14.530 (4)  -13.978 (6) ppm, the GNFs (2, 4, 6) with even fragments of annulene have larger aromaticity than that of GNFs (1, 3, 5) with odd fragments of annulene. Significantly, the NICS values of GNFs 1-6 can also be fragment analyzed by the NICS values and ACID of benzene and corresponding GNFHs 1'-6'. The NICS values for GNFs (2, 4, 6) can be roughly estimated by the NICS value of benzene minus the NICS value of the GNFHs (2', 4', 6'), respectively. The NICS values for GNFs (1, 3, 5) can be roughly estimated by the NICS value of the GNFHs (1', 3', 5') minus the NICS value of benzene, respectively. We hope that the present work can provide a simple and reliable method for the rational design of the GNF with aromaticity, which may be used to understand the origin of the graphene nanoflake aromatic properties.

  6. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  7. Shifting Attention

    Science.gov (United States)

    Ingram, Jenni

    2014-01-01

    This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…

  8. Torsional actuation with extension-torsion composite coupling and a magnetostrictive actuator

    Science.gov (United States)

    Bothwell, Christopher M.; Chandra, Ramesh; Chopra, Inderjit

    1995-04-01

    An analytical-experimental study of using magnetostrictive actuators in conjunction with an extension-torsion coupled composite tube to actuate a rotor blade trailing-edge flap to actively control helicopter vibration is presented. Thin walled beam analysis based on Vlasov theory was used to predict the induced twist and extension in a composite tube with magnetostrictive actuation. The study achieved good correlation between theory and experiment. The Kevlar-epoxy systems showed good correlation between measured and predicted twist values.

  9. Online Identification and Verification of the Elastic Coupling Torsional Stiffness

    Directory of Open Access Journals (Sweden)

    Wanyou Li

    2016-01-01

    Full Text Available To analyze the torsional vibration of a diesel engine shaft, the torsional stiffness of the flexible coupling is a key kinetic parameter. Since the material properties of the elastic element of the coupling might change after a long-time operation due to the severe working environment or improper use and the variation of such properties will change dynamic feature of the coupling, it will cause a relative large calculation error of torsional vibration to the shaft system. Moreover, the torsional stiffness of the elastic coupling is difficult to be determined, and it is inappropriate to measure this parameter by disassembling the power unit while it is under normal operation. To solve these problems, this paper comes up with a method which combines the torsional vibration test with the calculation of the diesel shafting and uses the inherent characteristics of shaft torsional vibration to identify the dynamic stiffness of the elastic coupling without disassembling the unit. Analysis results show that it is reasonable and feasible to identify the elastic coupling dynamic torsional stiffness with this method and the identified stiffness is accurate. Besides, this method provides a convenient and practical approach to examine the dynamic behavior of the long running elastic coupling.

  10. Dynamic Bending and Torsion Stiffness Derivation from Modal Curvatures and Torsion Rates

    Science.gov (United States)

    MAECK, J.; DE ROECK, G.

    1999-08-01

    In order to maintain the reliability of civil engineering structures, considerable effort is currently spent on developing a non-destructive vibration testing method for monitoring the structural integrity of constructions. The technique must be able to observe damage, secondly to localize the damage; and finally to give an idea of the severity of the damage. Within the framework of relating changes of measured modal parameters to changes in the integrity of the structure, it is important to be able to determine the dynamic stiffness in each section of the structure from measured modal characteristics.A damaged structure results in a dynamic stiffness reduction of the cracked sections. The dynamic stiffnesses provide directly an indication of the extension of the cracked zones in the structure. The dynamic stiffness reduction can also be associated with a degree of cracking in a particular zone.In an experimental programme, a concrete beam of 6 m length is subjected to an increasing static load to produce cracks. After each static perload, the beam is tested dynamically in a free-free set-up. The change in modal parameters is then related to damage in the beam.The technique that will be presented in the paper to predict the damage location and intensity is a direct stiffness derivation from measured modal displacement derivatives. Using the bending modes, the dynamic bending stiffness can be derived from modal curvatures. Using the torsional modes, the dynamic torsion stiffness can be derived from modal torsion rates.

  11. Experimental study on pure titanium during the positive-torsion and positive-negative-torsion

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Han; Li, Fuguo, E-mail: fuguolx@nwpu.edu.cn; Li, Jinghui; Zhao, Zhen; Zhou, Shunshun; Wan, Qiong

    2016-09-30

    The results of the mechanical properties, microstructure and fracture analysis of the pure titanium deformed by positive-torsion (PT) and positive-negative-torsion (PNT) are investigated by uniaxial tensile (UT) test, micro-indentation (MI) test, optical microscope (OM), transmission electron microscope (TEM) and scanning electron microscope (SEM). The UT test indicates that the strength increases obviously with the increase of torsion radian during PT. However, the strength firstly increases quickly, and then tends to steady with the increase of deformation during PNT. The similar phenomena are also shown through MI hardness analysis. The results from geometrically necessary dislocations (GNDs) and statistically stored dislocations (SSDs) indicate that the dislocation density varies differently with the increase of deformation during PT and PNT. OM observation shows the grains are elongated and large numbers of deformation twins are observed during PT while the equiaxial grains are always presented during PNT. The variations of dislocation density during PT and PNT are verified by TEM. Besides, quantities of subgrains (SGs) are observed owing to the accumulated larger plastic strain during PNT while large numbers of deformation twins intersect with each other during PT. The fracture analysis indicates that large numbers of micro-voids distribute non-uniformly on fracture surface of sample twisted by PNT. However, the characteristics of ductile and brittle fracture are observed on fracture surface of sample twisted by PT.

  12. Torsion based universal MEMS logic device

    KAUST Repository

    Ilyas, Saad; Carreno, Armando Arpys Arevalo; Bayes, Ernesto; Foulds, Ian G.; Younis, Mohammad I.

    2015-01-01

    In this work we demonstrate torsion based complementary MEMS logic device, which is capable, of performing INVERTER, AND, NAND, NOR, and OR gates using one physical structure within an operating range of 0-10 volts. It can also perform XOR and XNOR with one access inverter using the same structure with different electrical interconnects. The paper presents modeling, fabrication and experimental calculations of various performance features of the device including lifetime, power consumption and resonance frequency. The fabricated device is 535 μm by 150 μm with a gap of 1.92 μm and a resonant frequency of 6.51 kHz. The device is capable of performing the switching operation with a frequency of 1 kHz.

  13. ZNxZM orbifolds and discrete torsion

    International Nuclear Information System (INIS)

    Font, A.; Quevedo, F.

    1989-01-01

    We extend previous work on Z N -orbifolds to the general Z N xZ M abelian case for both (2, 2) and (0, 2) models. We classify the corresponding (2, 2) compactifications and show that a number of models obtained by tensoring minimal N = 2 superconformal theories can be constructed as Z N xZ M -orbifolds. Furthermore, Z N xZ M -orbifolds allow the addition of discrete torsion which leads to new (2, 2) compactifications not considered previously. Some of the latter have negative Euler characteristics and Betti numbers equal to those of some complete intersection Calabi-Yau (CICY) manifolds. This suggests the existence of a previously overlooked connection between CICY models and orbifolds. (orig.)

  14. Torsion based universal MEMS logic device

    KAUST Repository

    Ilyas, Saad

    2015-10-28

    In this work we demonstrate torsion based complementary MEMS logic device, which is capable, of performing INVERTER, AND, NAND, NOR, and OR gates using one physical structure within an operating range of 0-10 volts. It can also perform XOR and XNOR with one access inverter using the same structure with different electrical interconnects. The paper presents modeling, fabrication and experimental calculations of various performance features of the device including lifetime, power consumption and resonance frequency. The fabricated device is 535 μm by 150 μm with a gap of 1.92 μm and a resonant frequency of 6.51 kHz. The device is capable of performing the switching operation with a frequency of 1 kHz.

  15. Covariant formulation of scalar-torsion gravity

    Science.gov (United States)

    Hohmann, Manuel; Järv, Laur; Ualikhanova, Ulbossyn

    2018-05-01

    We consider a generalized teleparallel theory of gravitation, where the action contains an arbitrary function of the torsion scalar and a scalar field, f (T ,ϕ ) , thus encompassing the cases of f (T ) gravity and a nonminimally coupled scalar field as subclasses. The action is manifestly Lorentz invariant when besides the tetrad one allows for a flat but nontrivial spin connection. We derive the field equations and demonstrate how the antisymmetric part of the tetrad equations is automatically satisfied when the spin connection equation holds. The spin connection equation is a vital part of the covariant formulation, since it determines the spin connection associated with a given tetrad. We discuss how the spin connection equation can be solved in general and provide the cosmological and spherically symmetric examples. Finally, we generalize the theory to an arbitrary number of scalar fields.

  16. Origin of the chemical shift in X-ray absorption near-edge spectroscopy at the Mn K-Edge in manganese oxide compounds

    NARCIS (Netherlands)

    de Vries, AH; Hozoi, L.; Broer, R.

    2003-01-01

    The absorption edge in Mn K-edge X-ray absorption spectra of manganese oxide compounds shows a shift of several electronvolts in going from MnO through LaMnO3 to CaMnO3. On the other hand, in X-ray photoelectron spectra much smaller shifts are observed. To identify the mechanisms that cause the

  17. Torsional malalignment, how much significant in the trochanteric fractures?

    Science.gov (United States)

    Kim, Tae Young; Lee, Yong Beom; Chang, Jun Dong; Lee, Sang Soo; Yoo, Jae Hyun; Chung, Kook Jin; Hwang, Ji Hyo

    2015-11-01

    The rotational alignment is definitely important in the long bones such as tibias and femurs. We also predict the importance of rotational alignment in the trochanteric fractures. So we measured torsional malalignment in trochanteric fracture and anlaysed their risk factors and their clinical significance. A total of 109 inpatients who had undergone internal fixation following trochanteric fracture and a postoperative pelvic CT scan between 2008 and 2013, with at least one year follow-up, were selected. Factors that affect torsional malalignment, such as age, gender, fracture stability, injured area, operative time, time of surgery after admission, and ASA status, were investigated. Factors that affect the patients' clinical results in malrotation, including ambulation time after surgery, postoperative complication rates, pain assessment of VAS one year postoperatively and Koval score, were also investigated. Of the 109 subjects, torsional malalignment was observed in 28 (25.7%) subjects with a mean torsional malalignment angle of 20.7° (range: -31.2° to 27.1°). Torsional malalignment risk factors were fracture stability (p=0.021) and operative time (p=0.043). In terms of the time to ambulation after surgery, the postoperative complication rates, and the VAS and Koval scores at one year postoperatively, no statistically significant difference was observed between the torsional malalignment patients and the non-deformity patients. In this study, 25.7% of the patients who had undergone internal fixation following trochanteric fracture experienced torsional malalignment. Major factors of the torsional malalignment were an unstable fracture and the consequent delay in the operative time. But the torsional malalignment was deemed to have no effect on clinical results. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Torsion as a dynamic degree of freedom of quantum gravity

    International Nuclear Information System (INIS)

    Kim, Sang-Woo; Pak, D G

    2008-01-01

    The gauge approach to gravity based on the local Lorentz group with a general independent affine connection A μcd is developed. We consider SO(1, 3) gauge theory with a Lagrangian quadratic in curvature as a simple model of quantum gravity. The torsion is proposed to represent a dynamic degree of freedom of quantum gravity at scales above the Planckian energy. The Einstein-Hilbert theory is induced as an effective theory due to quantum corrections of torsion via generating a stable gravito-magnetic condensate. We conjecture that torsion possesses an intrinsic quantum nature and can be confined

  19. Dynamics of continuous medium in space with torsion

    International Nuclear Information System (INIS)

    Krechet, V.G.

    1985-01-01

    In frames of Einstein-Cartan gravitation theory general properties of continuous media dynamics using description formalism of continuous medium steam-line congruence geometry are investigated. Raichaudhuri type equations in space with torsion applied to study the problem of singularities in gravitation theory are derived. It is shown that space-time torsion tensor trace may immediately affect volumetric autoparallel divergence and torsion pseudo trace - rotation of continuous medium steam-line congruences. Using formalism considered metrics of homogeneous rotation nonstationary cosmological model is determined and investigated

  20. Generalised discrete torsion and mirror symmetry for G2 manifolds

    International Nuclear Information System (INIS)

    Gaberdiel, Matthias R.; Kaste, Peter

    2004-01-01

    A generalisation of discrete torsion is introduced in which different discrete torsion phases are considered for the different fixed points or twist fields of a twisted sector. The constraints that arise from modular invariance are analysed carefully. As an application we show how all the different resolutions of the T 7 /Z 2 3 orbifold of Joyce have an interpretation in terms of such generalised discrete torsion orbifolds. Furthermore, we show that these manifolds are pairwise identified under G 2 mirror symmetry. From a conformal field theory point of view, this mirror symmetry arises from an automorphism of the extended chiral algebra of the G 2 compactification. (author)

  1. Ultrafine grained Cu processed by compression with oscillatory torsion

    OpenAIRE

    K. Rodak

    2007-01-01

    Purpose: The aim of this work is a study of Cu microstructure after severe plastic deformation process by usingcompression with oscillatory torsion test.Design/methodology/approach: Cu samples were deformed at torsion frequency (f) changed from 0 Hz(compression) to 1.8 Hz under a constant torsion angle (α) ≈8° and compression speed (v)=0.1mm/s. Structuralinvestigations were conducted by using light microscopy (LM) and transmission electron microscopy (TEM).Findings: The structural analysis ma...

  2. Gastric dilatation-volvulus after splenic torsion in two dogs.

    Science.gov (United States)

    Millis, D L; Nemzek, J; Riggs, C; Walshaw, R

    1995-08-01

    Two dogs developed gastric dilatation-volvulus 2 and 17 months, respectively, after splenectomy for treatment of splenic torsion. Splenic displacement and torsion may stretch the gastric ligaments, allowing increased mobility of the stomach. After splenectomy, an anatomic void may be created in the cranioventral part of the abdomen, contributing to the mobility of the stomach. Veterinarians treating dogs with isolated splenic torsion may wish to consider prophylactic gastropexy at splenectomy, to reduce the chance of future gastric dilatation-volvulus. Prophylactic gastropexy should be done only if the dog's hemodynamic status is stable enough to allow for performance of the additional surgery.

  3. 5D Lovelock gravity: New exact solutions with torsion

    Science.gov (United States)

    Cvetković, B.; Simić, D.

    2016-10-01

    Five-dimensional Lovelock gravity is investigated in the first order formalism. A new class of exact solutions is constructed: the Bañados, Teitelboim, Zanelli black rings with and without torsion. We show that our solution with torsion exists in a different sector of the Lovelock gravity, as compared to the Lovelock Chern-Simons sector or the one investigated by Canfora et al. The conserved charges of the solutions are found using Nester's formula, and the results are confirmed by the canonical method. We show that the theory linearized around the background with torsion possesses two additional degrees of freedom with respect to general relativity.

  4. Hepatic fat quantification using chemical shift MR imaging and MR spectroscopy in the presence of hepatic iron deposition: validation in phantoms and in patients with chronic liver disease.

    Science.gov (United States)

    Lee, Seung Soo; Lee, Youngjoo; Kim, Namkug; Kim, Seong Who; Byun, Jae Ho; Park, Seong Ho; Lee, Moon-Gyu; Ha, Hyun Kwon

    2011-06-01

    To compare the accuracy of four chemical shift magnetic resonance imaging (MRI) (CS-MRI) analysis methods and MR spectroscopy (MRS) with and without T2-correction in fat quantification in the presence of excess iron. CS-MRI with six opposed- and in-phase acquisitions and MRS with five-echo acquisitions (TEs of 20, 30, 40, 50, 60 msec) were performed at 1.5 T on phantoms containing various fat fractions (FFs), on phantoms containing various iron concentrations, and in 18 patients with chronic liver disease. For CS-MRI, FFs were estimated with the dual-echo method, with two T2*-correction methods (triple- and multiecho), and with multiinterference methods that corrected for both T2* and spectral interference effects. For MRS, FF was estimated without T2-correction (single-echo MRS) and with T2-correction (multiecho MRS). In the phantoms, T2*- or T2-correction methods for CS-MRI and MRS provided unbiased estimations of FFs (mean bias, -1.1% to 0.5%) regardless of iron concentration, whereas the dual-echo method (-5.5% to -8.4%) and single-echo MRS (12.1% to 37.3%) resulted in large biases in FFs. In patients, the FFs estimated with triple-echo (R = 0.98), multiecho (R = 0.99), and multiinterference (R = 0.99) methods had stronger correlations with multiecho MRS FFs than with the dual-echo method (R = 0.86; P ≤ 0.011). The FFs estimated with multiinterference method showed the closest agreement with multiecho MRS FFs (the 95% limit-of-agreement, -0.2 ± 1.1). T2*- or T2-correction methods are effective in correcting the confounding effects of iron, enabling an accurate fat quantification throughout a wide range of iron concentrations. Spectral modeling of fat may further improve the accuracy of CS-MRI in fat quantification. Copyright © 2011 Wiley-Liss, Inc.

  5. Transitional Failure of Carbon Nanotube Systems under a Combination of Tension and Torsion

    OpenAIRE

    Jeong, Byeong-Woo

    2012-01-01

    Transitional failure envelopes of single- and double-walled carbon nanotubes under combined tension-torsion are predicted using classical molecular dynamics simulations. The observations reveal that while the tensile failure load decreases with combined torsion, the torsional buckling moment increases with combined tension. As a result, the failure envelopes under combined tension-torsion are definitely different from those under pure tension or torsion. In such combined loading, there is a m...

  6. Wet-Spun Biofiber for Torsional Artificial Muscles.

    Science.gov (United States)

    Mirabedini, Azadeh; Aziz, Shazed; Spinks, Geoffrey M; Foroughi, Javad

    2017-12-01

    The demands for new types of artificial muscles continue to grow and novel approaches are being enabled by the advent of new materials and novel fabrication strategies. Self-powered actuators have attracted significant attention due to their ability to be driven by elements in the ambient environment such as moisture. In this study, we demonstrate the use of twisted and coiled wet-spun hygroscopic chitosan fibers to achieve a novel torsional artificial muscle. The coiled fibers exhibited significant torsional actuation where the free end of the coiled fiber rotated up to 1155 degrees per mm of coil length when hydrated. This value is 96%, 362%, and 2210% higher than twisted graphene fiber, carbon nanotube torsional actuators, and coiled nylon muscles, respectively. A model based on a single helix was used to evaluate the torsional actuation behavior of these coiled chitosan fibers.

  7. Isolated adnexal torsion in a 20-week spontaneous twin pregnancy

    Directory of Open Access Journals (Sweden)

    Ilker Kahramanoglu

    2016-01-01

    Discussion: Adnexal torsion as a cause of acute abdomen may be kept in mind in pregnants, even if there is no predisposing factor. Laparoscopy may be performed safely in 2nd trimester for acute abdomen.

  8. Incidence and predictive factors of isolated neonatal penile glanular torsion.

    Science.gov (United States)

    Sarkis, Pierrot E; Sadasivam, Muthurajan

    2007-12-01

    To determine the incidence of isolated neonatal penile glanular torsion, describe the basic characteristics, and explore the relationship between foreskin and glans torsion. A prospective survey was conducted of all male newborns admitted to nursery after delivery, or neonates less than 3 months presenting for circumcision. Cases with associated genital malformations were excluded. The incidence of isolated neonatal penile torsion was 27% (95% CI: 22.2%-31.84%), to the left in 99% of cases. In 3.5% of cases, the penis had an angle 20 degrees. Using Spearman's correlational coefficient, deviation of penile raphe from the midline at the foreskin tip had a better correlation with glans torsion than deviation of raphe at the coronal sulcus (0.727 vs 0.570; both significant at pscope of the study.

  9. Torsional Newton–Cartan geometry from Galilean gauge theory

    International Nuclear Information System (INIS)

    Banerjee, Rabin; Mukherjee, Pradip

    2016-01-01

    Using the recently advanced Galilean gauge theory (GGT) we give a comprehensive construction of torsional Newton–Cartan (NC) geometry. The coupling of a Galilean symmetric model with background NC geometry following GGT is illustrated by a free nonrelativistic scalar field theory. The issue of spatial diffeomorphism (Son and Wingate 2006 Ann. Phys. 321 197–224; Banerjee et al 2015 Phys. Rev. D 91 084021) is focussed from a new angle. The expression of the torsionful connection is worked out, which is in complete parallel with the relativistic theory. Also, smooth transition of the connection to its well known torsionless expression is demonstrated. A complete (implicit) expression of the torsion tensor for the NC spacetime is provided where the first-order variables occur in a suggestive way. The well known result for the temporal part of torsion is reproduced from our expression. (paper)

  10. Timoshenko-Wagner-Kappus Torsion Bending Theory and Wind ...

    Indian Academy of Sciences (India)

    Theory and Wind Tunnel Balance Design. S P Govinda ... The study of torsion and bending has always been a favourite ... Since it was difficult to work quietlyin Petersburg, .... should be stiff and strong to endure shocks and ensure long life.

  11. Spin-torsion effects in the hyperfine structure of methanol

    International Nuclear Information System (INIS)

    Coudert, L. H.; Gutlé, C.; Huet, T. R.; Grabow, J.-U.; Levshakov, S. A.

    2015-01-01

    The magnetic hyperfine structure of the non-rigid methanol molecule is investigated experimentally and theoretically. 12 hyperfine patterns are recorded using molecular beam microwave spectrometers. These patterns, along with previously recorded ones, are analyzed in an attempt to evidence the effects of the magnetic spin-torsion coupling due to the large amplitude internal rotation of the methyl group [J. E. M. Heuvel and A. Dymanus, J. Mol. Spectrosc. 47, 363 (1973)]. The theoretical approach setup to analyze the observed data accounts for this spin-torsion in addition to the familiar magnetic spin-rotation and spin-spin interactions. The theoretical approach relies on symmetry considerations to build a hyperfine coupling Hamiltonian and spin-rotation-torsion wavefunctions compatible with the Pauli exclusion principle. Although all experimental hyperfine patterns are not fully resolved, the line position analysis yields values for several parameters including one describing the spin-torsion coupling

  12. Outcomes of Surgery for Posterior Polar Cataract Using Torsional Ultrasound

    Directory of Open Access Journals (Sweden)

    Selçuk Sızmaz

    2013-10-01

    Full Text Available Purpose: The aim of this study is to report outcomes of surgery for posterior polar cataract using torsional ultrasound. Material and Method: Medical records of 26 eyes of 21 consecutive patients with posterior polar cataract who had cataract surgery using the torsional phacoemulsification were evaluated retrospectively. The surgical procedure used, phacoemulsification parameters, intraoperative complications, and postoperative visual outcome were recorded. Results: Of the 26 eyes, 24 (92.3% had small to medium posterior polar opacity. Two eyes had large opacity. All surgeries were performed using the torsional handpiece. Posterior capsule rupture occurred in 4 (15.3% eyes. The mean visual acuity improved significantly after surgery (p<0.001. The postoperative visual acuity was worse than 20/20 in 5 eyes. The cause of the low acuity was amblyopia. Discussion: Successful surgical results and good visual outcome can be achieved with phacoemulsification using the torsional handpiece. (Turk J Ophthalmol 2013; 43: 345-7

  13. Torsional Dynamics of Steerable Needles: Modeling and Fluoroscopic Guidance

    Science.gov (United States)

    Swensen, John P.; Lin, MingDe; Okamura, Allison M.; Cowan, Noah J.

    2017-01-01

    Needle insertions underlie a diversity of medical interventions. Steerable needles provide a means by which to enhance existing needle-based interventions and facilitate new ones. Tip-steerable needles follow a curved path and can be steered by twisting the needle base during insertion, but this twisting excites torsional dynamics that introduce a discrepancy between the base and tip twist angles. Here, we model the torsional dynamics of a flexible rod—such as a tip-steerable needle—during subsurface insertion and develop a new controller based on the model. The torsional model incorporates time-varying mode shapes to capture the changing boundary conditions inherent during insertion. Numerical simulations and physical experiments using two distinct setups—stereo camera feedback in semi-transparent artificial tissue and feedback control with real-time X-ray imaging in optically opaque artificial tissue— demonstrate the need to account for torsional dynamics in control of the needle tip. PMID:24860026

  14. Torsion effect on fully developed flow in a helical pipe

    Science.gov (United States)

    Kao, Hsiao C.

    1987-01-01

    Two techniques, a series expansion method of perturbed Poiseuille flow valid for low Dean numbers and a solution of the complete Navier-Stokes equation applicable to intermediate Dean values, are used to investigate the torsion effect on the fully developed laminar flow in a helical pipe of constant circular cross section. For the secondary flow patterns, the results show that the presence of torsion can produce a significant effect if the ratio of the curvature to the torsion is of order unity. The secondary flow is distorted in these cases. It is noted that the torsion effect is, however, usually small, and that the secondary flow has the usual pattern of a pair of counter-rotating vortices of nearly equal strength.

  15. Standardized education and parental awareness are lacking for testicular torsion.

    Science.gov (United States)

    Friedman, Ariella A; Ahmed, Haris; Gitlin, Jordan S; Palmer, Lane S

    2016-06-01

    Testicular torsion leads to orchiectomy in 30-50% of cases, which may cause psychological upset and parental guilt over a potentially avertable outcome. Presentation delay is an important modifiable cause of orchiectomy; yet, families are not routinely educated about torsion or its urgency. The present study assessed parental knowledge regarding acute scrotal pain. An anonymous survey was distributed to parents in Urology and ENT offices, asking about their children's gender and scrotal pain history, urgency of response to a child's acute scrotal pain, and familiarity with testicular torsion. Surveys of 479 urology and 59 ENT parents were analyzed. The results between the two were not statistically different. Among the urology parents, 34% had heard of testicular twisting/torsion, most commonly through friends, relatives or knowing someone with torsion (35%); only 17% were informed by pediatricians (Summary Figure). Parents presenting for a child's scrotal pain were significantly more likely to have heard of torsion (69%) than those presenting for other reasons (30%, OR 5.24, P parents of boys had spoken with their children about torsion. Roughly three quarters of them would seek emergent medical attention - by day (75%) or night (82%) - for acute scrotal pain. However, urgency was no more likely among those who knew about torsion. This was the first study to assess parental knowledge of the emergent nature of acute scrotal pain in a non-urgent setting, and most closely approximating their level of knowledge at the time of pain onset. It also assessed parents' hypothetical responses to the scenario, which was markedly different than documented presentation times, highlighting a potential area for improvement in presentation times. Potential limitations included lack of respondent demographic data, potential sampling bias of a population with greater healthcare knowledge or involvement, and assessment of parents only. Parental knowledge of testicular torsion was

  16. Lanthanide shift reagents, binding, shift mechanisms and exchange

    International Nuclear Information System (INIS)

    Boer, J.W.M. de

    1977-01-01

    Paramagnetic lanthanide shift reagents, when added to a solution of a substrate, induce shifts in the nuclear magnetic resonance (NMR) spectrum of the substrate molecules. The induced shifts contain information about the structure of the shift reagent substrate complex. The structural information, however, may be difficult to extract because of the following effects: (1) different complexes between shift reagent and substrate may be present in solution, e.g. 1:1 and 1:2 complexes, and the shift observed is a weighed average of the shifts of the substrate nuclei in the different complexes; (2) the Fermi contact interaction, arising from the spin density at the nucleus, contributes to the induced shift; (3) chemical exchange effects may complicate the NMR spectrum. In this thesis, the results of an investigation into the influence of these effects on the NMR spectra of solutions containing a substrate and LSR are presented. The equations describing the pseudo contact and the Fermi contact shift are derived. In addition, it is shown how the modified Bloch equations describing the effect of the chemical exchange processes occurring in the systems studied can be reduced to the familiar equations for a two-site exchange case. The binding of mono- and bifunctional ethers to the shift reagent are reported. An analysis of the induced shifts is given. Finally, the results of the experiments performed to study the exchange behavior of dimethoxyethane and heptafluorodimethyloctanedionato ligands are presented

  17. Model of Structural Fragmentation Induced by High Pressure Torsion

    Czech Academy of Sciences Publication Activity Database

    Kratochvíl, J.; Kružík, Martin; Sedláček, R.

    2010-01-01

    Roč. 25, č. 1 (2010), s. 88-98 ISSN 1606-5131 Institutional research plan: CEZ:AV0Z10750506 Keywords : High-pressure torsion * intergranular glide * homogeneous deformation mode Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.649, year: 2010 http://library.utia.cas.cz/separaty/2010/MTR/kruzik-model of structural fragmentation induced by high pressure torsion.pdf

  18. Torsional Moment Measurement on Bucket Wheel Shaft of Giant Machine

    Directory of Open Access Journals (Sweden)

    Jiří FRIES

    2011-06-01

    Full Text Available Bucket wheel loading at the present time (torsional moment on wheel shaft, peripheral cutting force is determined from electromotor incoming power or reaction force measured on gearbox hinge. Both methods together are weighted by steel construction absorption of driving units and by inertial forces of motor rotating parts. In the article is described direct method of the torsional moment measurement, which eliminates mentioned unfavourable impacts except absorption of steel construction of bucket wheel itself.

  19. Intravitreal Phacoemulsification Using Torsional Handpiece for Retained Lens Fragments

    OpenAIRE

    Kumar, Vinod; Takkar, Brijesh

    2016-01-01

    Purpose: To evaluate the results of intravitreal phacoemulsification with torsional hand piece in eyes with posteriorly dislocated lens fragments. Methods: In this prospective, interventional case series, 15 eyes with retained lens fragments following phacoemulsification were included. All patients underwent standard three-port pars plana vitrectomy and intravitreal phacoemulsification using sleeveless, torsional hand piece (OZiL™, Alcon's Infiniti Vision System). Patients were followed up...

  20. Muscular Basis of Whisker Torsion in Mice and Rats.

    Science.gov (United States)

    Haidarliu, Sebastian; Bagdasarian, Knarik; Shinde, Namrata; Ahissar, Ehud

    2017-09-01

    Whisking mammals move their whiskers in the rostrocaudal and dorsoventral directions with simultaneous rolling about their long axes (torsion). Whereas muscular control of the first two types of whisker movement was already established, the anatomic muscular substrate of the whisker torsion remains unclear. Specifically, it was not clear whether torsion is induced by asymmetrical operation of known muscles or by other largely unknown muscles. Here, we report that mystacial pads of newborn and adult rats and mice contain oblique intrinsic muscles (OMs) that connect diagonally adjacent vibrissa follicles. Each of the OMs is supplied by a cluster of motor end plates. In rows A and B, OMs connect the ventral part of the rostral follicle with the dorsal part of the caudal follicle. In rows C-E, in contrast, OMs connect the dorsal part of the rostral follicle to the ventral part of the caudal follicle. This inverse architecture is consistent with previous behavioral observations [Knutsen et al.: Neuron 59 (2008) 35-42]. In newborn mice, torsion occurred in irregular single twitches. In adult anesthetized rats, microelectrode mediated electrical stimulation of an individual OM that is coupled with two adjacent whiskers was sufficient to induce a unidirectional torsion of both whiskers. Torsional movement was associated with protracting movement, indicating that in the vibrissal system, like in the ocular system, torsional movement is mechanically coupled to horizontal and vertical movements. This study shows that torsional whisker rotation is mediated by specific OMs whose morphology and attachment sites determine rotation direction and mechanical coupling, and motor innervation determines rotation dynamics. Anat Rec, 300:1643-1653, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  1. Torsion of the greater omentum: A rare preoperative diagnosis

    International Nuclear Information System (INIS)

    Tandon, Ankit Anil; Lim, Kian Soon

    2010-01-01

    Torsion of the greater omentum is a rare acute abdominal condition that is seldom diagnosed preoperatively. We report the characteristic computed tomography (CT) scan findings and the clinical implications of this unusual diagnosis in a 41-year-old man, who also had longstanding right inguinal hernia. Awareness of omental torsion as a differential diagnosis in the acute abdomen setting is necessary for correct patient management

  2. Measurement of the signs of methyl {sup 13}C chemical shift differences between interconverting ground and excited protein states by R{sub 1{rho}}: an application to {alpha}B-crystallin

    Energy Technology Data Exchange (ETDEWEB)

    Baldwin, Andrew J.; Kay, Lewis E., E-mail: kay@pound.med.utoronto.ca [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

    2012-05-15

    Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG RD) NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond time-scale exchange processes involving the interconversion between a visible ground state and one or more minor, sparsely populated invisible 'excited' conformational states. Recently it has also become possible to determine atomic resolution structural models of excited states using a wide array of CPMG RD approaches. Analysis of CPMG RD datasets provides the magnitudes of the chemical shift differences between the ground and excited states, {Delta}{omega}, but not the sign. In order to obtain detailed structural insights from, for example, excited state chemical shifts and residual dipolar coupling measurements, these signs are required. Here we present an NMR experiment for obtaining signs of {sup 13}C chemical shift differences of {sup 13}CH{sub 3} methyl groups using weak field off-resonance R{sub 1{rho}} relaxation measurements. The accuracy of the method is established by using an exchanging system where the invisible, excited state can be converted to the visible, ground state by altering sample conditions so that the signs of {Delta}{omega} values obtained from the spin-lock approach can be validated against those measured directly. Further, the spin-lock experiments are compared with the established H(S/M)QC approach for measuring signs of chemical shift differences and the relative strengths of each method are discussed. In the case of the 650 kDa human {alpha}B-crystallin complex where there are large transverse relaxation differences between ground and excited state spins the R{sub 1{rho}} method is shown to be superior to more 'traditional' experiments for sign determination.

  3. Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate for dual biosensing of pH with chemical exchange saturation transfer (CEST) and biosensor imaging of redundant deviation in shifts (BIRDS).

    Science.gov (United States)

    Huang, Yuegao; Coman, Daniel; Ali, Meser M; Hyder, Fahmeed

    2015-01-01

    Relaxivity-based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd(3+)) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the nonexchangeable or the exchangeable protons on the lanthanide complexes themselves. The nonexchangeable protons (e.g. -CHx, where 3 ≥ x ≥ 1) are detected using a three-dimensional chemical shift imaging method called biosensor imaging of redundant deviation in shifts (BIRDS), whereas the exchangeable protons (e.g. -OH or -NHy , where 2 ≥ y ≥ 1) are measured with chemical exchange saturation transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP(8-)) chelated with thulium (Tm(3+) ) and ytterbium (Yb(3+)). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e. 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP(5-) than with TmDOTA-4AmP(5-). In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging. Copyright © 2014 John Wiley & Sons, Ltd.

  4. Bicavitary effusion secondary to liver lobe torsion in a dog

    Directory of Open Access Journals (Sweden)

    Khan Z

    2016-04-01

    Full Text Available Zaheda Khan,1 Kathryn Gates,2 Stephen A Simpson,31Emergency and Critical Care, Animal Specialty and Emergency Center, Los Angeles, CA, 2Emergency and Critical Care, Advanced Critical Care, Emergency and Specialty Services, Culver City, CA 3Emergency and Critical Care, Southern California Veterinary Specialty Hospital, Irvine, CA, USA Abstract: We described the diagnosis and successful treatment of pleural and peritoneal effusion secondary to liver lobe torsion in a dog. A 12-year-old female spayed Borzoi dog was referred for heart failure. Emergency room thoracic and abdominal ultrasound showed a large volume of pleural effusion with mild peritoneal effusion and an abdominal mass. Pleural fluid analysis classified the effusion as exudative. A complete ultrasound revealed mild peritoneal effusion and decreased blood flow to the right liver lobe. Other causes of bicavitary effusion were ruled out based on blood work, ultrasound, echocardiogram, and computed tomography. The patient was taken to surgery and diagnosed with caudate liver lobe torsion and had a liver lobectomy. At the 2-week postoperative recheck, the patient was doing well and there was complete resolution of the pleural effusion. Liver lobe torsion is a rare occurrence in dogs and can be difficult to diagnose. Clinical signs are nonspecific for liver lobe torsion and patients may present in respiratory distress with significant pleural fluid accumulation. When assessing patients with pleural and peritoneal effusion, liver lobe torsion should be considered as a differential diagnosis.Keywords: pleural effusion, peritoneal effusion, hepatic torsion

  5. ESTIMATING TORSION OF DIGITAL CURVES USING 3D IMAGE ANALYSIS

    Directory of Open Access Journals (Sweden)

    Christoph Blankenburg

    2016-04-01

    Full Text Available Curvature and torsion of three-dimensional curves are important quantities in fields like material science or biomedical engineering. Torsion has an exact definition in the continuous domain. However, in the discrete case most of the existing torsion evaluation methods lead to inaccurate values, especially for low resolution data. In this contribution we use the discrete points of space curves to determine the Fourier series coefficients which allow for representing the underlying continuous curve with Cesàro’s mean. This representation of the curve suits for the estimation of curvature and torsion values with their classical continuous definition. In comparison with the literature, one major advantage of this approach is that no a priori knowledge about the shape of the cyclic curve parts approximating the discrete curves is required. Synthetic data, i.e. curves with known curvature and torsion, are used to quantify the inherent algorithm accuracy for torsion and curvature estimation. The algorithm is also tested on tomographic data of fiber structures and open foams, where discrete curves are extracted from the pore spaces.

  6. Torsional Vibration of a Shafting System under Electrical Disturbances

    Directory of Open Access Journals (Sweden)

    Ling Xiang

    2012-01-01

    Full Text Available Torsional vibration responses of a nonlinear shafting system are studied by a modified Riccati torsional transfer matrix combining with the Newmark-β method. Firstly, the system is modeled as a chain consisting of an elastic spring with concentrated mass points, from which a multi-segment lumped mass model is established. Secondly, accumulated errors are eliminated from the eigenfrequencies and responses of the system's torsional vibration by this newly developed procedure. The incremental transfer matrix method, combining the modified Riccati torsional transfer matrix with Newmark-β method, is further applied to solve the dynamical equations for the torsional vibration of the nonlinear shafting system. Lastly, the shafting system of a turbine-generator is employed as an illustrating example, and simulation analysis has been performed on the transient responses of the shaft's torsional vibrations during typical power network disturbances, such as three-phase short circuit, two-phase short circuit and asynchronous juxtaposition. The results validate the present method and are instructive for the design of a turbo-generator shaft.

  7. A new hybrid longitudinal–torsional magnetostrictive ultrasonic transducer

    International Nuclear Information System (INIS)

    Karafi, Mohammad Reza; Hojjat, Yousef; Sassani, Farrokh

    2013-01-01

    In this paper, a novel hybrid longitudinal–torsional magnetostrictive ultrasonic transducer (HL–TMUT) is introduced. The transducer is composed of a magnetostrictive exponential horn and a stainless steel tail mass. In this transducer a spiral magnetic field made up of longitudinal and circumferential magnetic fields is applied to the magnetostrictive horn. As a result, the magnetostrictive horn oscillates simultaneously both longitudinally and torsionally in accordance with the Joule and Wiedemann effects. The magnetostrictive exponential horn is designed in such a manner that it has the same longitudinal and torsional resonant frequency. It is made up of ‘2V Permendur’, which has isotropic magnetic properties. The differential equations of the torsional and longitudinal vibration of the horn are derived, and a HL–TMUT is designed with a resonant frequency of 20 573 Hz. The natural frequency and mode shapes of the transducer are considered theoretically and numerically. The experimental results show that this transducer resonates torsionally and longitudinally with frequencies of 20 610 Hz and 20 830 Hz respectively. The maximum torsional displacement is 1.5 mrad m −1 and the maximum longitudinal displacement is 0.6 μm. These are promising features for industrial applications. (paper)

  8. Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15N or 13C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

    International Nuclear Information System (INIS)

    Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A.

    2015-01-01

    Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone 1 H N , 15 N H , and 13 C′ resonance assignments to be completed from a single pair of 3D experiments

  9. Effectiveness of lycopene on experimental testicular torsion.

    Science.gov (United States)

    Güzel, Mahmut; Sönmez, Mehmet Fatih; Baştuğ, Osman; Aras, Necip Fazıl; Öztürk, Ayşe Betül; Küçükaydın, Mustafa; Turan, Cüneyt

    2016-07-01

    We aimed to demonstrate the long term effectiveness of lycopene, a precursor of vitamin A, on the testes for ischemia-reperfusion injury. Seventy male Wistar albino rats were used for this experiment. The rats were divided into seven groups. Group 1 served as the control group; group 2 was sham-operated; group 3 received 20mg/kg/day lycopene (intraperitoneally); in group 4, the right testes of rats were kept torted for 2hours and then were detorted and the animals lived for three days; in group 5, the right testes of rats were kept torted for 2hours and then were detorted and the animals lived for ten days; in group 6, the right testes of the rats were kept torted for 2hours and then detorted and the animals received 20mg/kg/day lycopene (intraperitoneally) for three days; in group 7, the right testes of the rats were kept torted for 2hours and then were detorted and the animals received 20mg/kg/day lycopene (intraperitoneally) for ten days. Lycopene was used intraperitoneally. Some of the testes tissues were used for biochemical analyses and the other tissues were used for histological procedures. The Johnsen's score was used for seminiferous tubule deterioration. The TUNEL method was utilized to show apoptosis of testicular tissue. Testosterone levels were measured from blood samples and SOD, MDA, TNF-α, IL-1β and IL-6 measurements were recorded from tissue samples. The results were analyzed statistically. In groups 1, 2 and 3 there was normal testicular structure. Rats in groups 4 and 5 had damaged testicular tissues. In groups 6 and 7, in which we used lycopene, the testes were not better than those in groups 4 and 5. The MSTD and JTBS values were better in group 6, but not in group 7 among the torsion groups. As a result, MDA, SOD, TNF-α and IL-1β were increased and serum testosterone and IL-6 levels were decreased in groups 4 and 5 compared to group 1. There was no improvement in the groups treated with lycopene for therapeutic purposes. It was shown that

  10. Magnetic resonance imaging findings in adnexial torsion

    Energy Technology Data Exchange (ETDEWEB)

    Trindade, Ronald Meira Castro; Quadros, Marianne Siquara de [Hospital Albert Einstein, Sao Paulo, SP (Brazil). Instituto de Ensino e Pesquisa], e-mail: rtrindade@einstein.br; Baroni, Ronaldo Hueb; Rosemberg, Michelle; Racy, Marcelo de Castro Jorge; Tachibana, Adriano [Hospital Albert Einstein, Sao Paulo, SP (Brazil); Funari, Marcelo Buarque de Gusmao [Hospital Albert Einstein, Sao Paulo, SP (Brazil). Imaging Service

    2010-01-15

    Adnexial torsion is an unusual event, but a major cause of abdominal pain in women. It is often associated with ovarian tumor or cyst, but can occur in normal ovaries, especially in children. The twisting of adnexial structures may involve the ovary or tube, but frequently affects both. In most cases, it is unilateral, with slight predilection for the right size. In imaging findings, increased ovarian volume and adnexial masses are observed, with reduced or absent vascularisation. In cases of undiagnosed or untreated complete twist, hemorrhagic necrosis may occur leading to complications; in that, peritonitis is the most frequent. Early diagnosis helps preventing irreversible damage with conservative treatment, thereby saving the ovary. Limitations in performing physical examination, possible inconclusive results in ultrasound and exposure to radiation in computed tomography makes magnetic resonance imaging a valuable tool in emergency assessment of gynecological diseases. The objective of this study was to report two confirmed cases of adnexial twist, emphasizing the contribution of magnetic resonance imaging in the diagnosis of this condition. (author)

  11. Market shifting

    Energy Technology Data Exchange (ETDEWEB)

    Forst, Michael

    2013-11-01

    After years of oversupply and artificially low module pricing, market analysts believe that the solar industry will begin to stabilize by 2017. While the market activities are shifting from Europe to the Asia Pacific region and the United States, the solar shakeout continues to be in full swing including solar cell and module manufacturing. (orig.)

  12. Tough Shift

    DEFF Research Database (Denmark)

    Brewer, Robert S.; Verdezoto, Nervo; Holst, Thomas

    2015-01-01

    people to change their behavior at home. Leveraging prior research on encouraging reductions in residential energy use through game play, we introduce ShareBuddy: a casual mobile game intended to encourage players not only to reduce, but also to shift their electricity use. We conducted two field studies...... real-world resource use into a game....

  13. On unified field theories, dynamical torsion and geometrical models: II

    International Nuclear Information System (INIS)

    Cirilo-Lombardo, D.J.

    2011-01-01

    We analyze in this letter the same space-time structure as that presented in our previous reference (Part. Nucl, Lett. 2010. V.7, No.5. P.299-307), but relaxing now the condition a priori of the existence of a potential for the torsion. We show through exact cosmological solutions from this model, where the geometry is Euclidean RxO 3 ∼ RxSU(2), the relation between the space-time geometry and the structure of the gauge group. Precisely this relation is directly connected with the relation of the spin and torsion fields. The solution of this model is explicitly compared with our previous ones and we find that: i) the torsion is not identified directly with the Yang-Mills type strength field, ii) there exists a compatibility condition connected with the identification of the gauge group with the geometric structure of the space-time: this fact leads to the identification between derivatives of the scale factor a with the components of the torsion in order to allow the Hosoya-Ogura ansatz (namely, the alignment of the isospin with the frame geometry of the space-time), and iii) of two possible structures of the torsion the 'tratorial' form (the only one studied here) forbid wormhole configurations, leading only to cosmological instanton space-time in eternal expansion

  14. Torsion of wandering spleen in patient with horseshoe kidney

    International Nuclear Information System (INIS)

    Molski, St.; Zurada, A.; Meder, G.; Lasek, W.

    2005-01-01

    Wandering spleen is rare pathology, mostly occurring in young women. Disease may be congenital or acquired. Absence or laxity of ligaments leads to spleen pathologic mobility and may cause torsion of its pedicle, resulting in ischemia or infarct even haemorrhagic shock and patients death. We report a case of young woman previously diagnosed (and treated nonoperative) with wandering spleen who presented acute abdomen after minor blunt trauma. She was evaluated with abdominal ultrasound (US) and spiral computed tomography (CT). Torsion of splenic pedicle and splenic rupture was diagnosed and a horseshoe kidney as well. Laparotomy followed by splenectomy confirmed the existence of an intrapelvic torsioned wandering spleen. The only definitive treatment of wandering spleen is operative since nonoperative treatment is associated with high complication rate. Earlier diagnosis of wandering spleen in asymptomatic patients lets to direct diagnosis when patient starts to present with acute abdomen. CT and abdominal US play most important role in diagnosing splenic pedicle torsion. To our knowledge this is a first case of torsion of splenic pedicle in patient with horseshoe kidney. We consider this coincidence to be a congenital defect as both conditions may develop in second month gestation. (author)

  15. Torsion of abdominal appendages presenting with acute abdominal pain

    International Nuclear Information System (INIS)

    Al-Jaberi, Tareq M.; Gharabeih, Kamal I.; Yaghan, Rami J.

    2000-01-01

    Diseases of abnormal appendages are rare causes of abdominal pain in all age groups. Nine patients with torsion and infraction of abdominal appendages were retrospectively reviewed. Four patients had torsion and infarction of the appendices epiploicae, four patients had torsion and infarction of the falciform ligament. The patient with falciform ligament disease represents the first reported case of primary torsion and infarction of the falciform ligament, and the patient with the transverse colon epiplocia represents the first reported case of vibration-induced appendix epiplocia torsion and infarction. The patient with the falciform ligament disease presented with a tender upper abdominal mass and the remaining patients were operated upon with the preoperative diagnosis of acute appendicitis. The presence of normal appendix with free serosanguinous fluid in the peritoneal cavity should raise the possibility of a disease and calls for further evaluation of the intra-abdominal organs. If the diagnosis is suspected preoperatively, CT scan and ultrasound may lead to a correct diagnosis and possibly conservative management. Laparoscopy is playing an increasing diagnostic and therapeutic role in such situations. (author)

  16. Prune belly syndrome, splenic torsion, and malrotation: a case report.

    Science.gov (United States)

    Tran, Sifrance; Grossman, Eric; Barsness, Katherine A

    2013-02-01

    An 18 year old male with a history of prune belly syndrome (PBS) presented with acute abdominal pain and palpable left upper quadrant mass. Computed tomography (CT) of the abdomen revealed a medialized spleen with a "whirl sign" in the splenic vessels, consistent with splenic torsion. Coincidentally, the small bowel was also noted to be on the right side of the abdomen, while the colon was located on the left, indicative of malrotation. Emergent diagnostic laparoscopy confirmed splenic torsion and intestinal malrotation. Successful laparoscopic reduction of the splenic torsion was achieved, however, conversion to an open procedure by a vertical midline incision was necessary owing to the patient's unique anatomy. Open splenopexy with a mesh sling and Ladd's procedure were subsequently performed. Malrotation and wandering spleen are known, rare associated anomalies in PBS; however, both have not been reported concurrently in a patient with PBS in the literature. In patients with PBS, acute abdominal pain, and an abdominal mass, high clinical suspicion for gastrointestinal malformations and prompt attention can result in spleen preservation and appropriate malrotation management. We present a case of a teenager who presented with a history of PBS, acute abdominal pain, and a palpable abdominal mass. The patient was found to have splenic torsion and intestinal malrotation. The clinical findings, diagnostic imaging, and surgical treatment options of splenic torsion are reviewed. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Elevated temperature axial and torsional fatigue behavior of Haynes 188

    Science.gov (United States)

    Bonacuse, Peter J.; Kalluri, Sreeramesh

    1992-06-01

    The results of high-temperature axial and torsional low-cycle fatigue experiments performed on Haynes 188, a wrought cobalt-base superalloy, are reported. Fatigue tests were performed at 760 C in air on thin-walled tubular specimens at various ranges under strain control. Data are also presented for coefficient of thermal expansion, elastic modulus, and shear modulus at various temperatures from room to 1000 C, and monotonic and cyclic stress-strain curves in tension and in shear at 760 C. The data set is used to evaluate several multiaxial fatigue life models (most were originally developed for room temperature multiaxial life prediction) including von Mises equivalent strain range (ASME boiler and pressure vessel code), Manson-Halford, Modified Multiaxiality Factor (proposed here), Modified Smith-Watson-Topper, and Fatemi-Socie-Kurath. At von Mises equivalent strain ranges (the torsional strain range divided by the square root of 3, taking the Poisson's ratio to be 0.5), torsionally strained specimens lasted, on average, factors of 2 to 3 times longer than axially strained specimens. The Modified Multiaxiality Factor approach shows promise as a useful method of estimating torsional fatigue life from axial fatigue data at high temperatures. Several difficulties arose with the specimen geometry and extensometry used in these experiments. Cracking at extensometer probe indentations was a problem at smaller strain ranges. Also, as the largest axial and torsional strain range fatigue tests neared completion, a small amount of specimen buckling was observed.

  18. Residual torsional properties of composite shafts subjected to impact loadings

    International Nuclear Information System (INIS)

    Sevkat, Ercan; Tumer, Hikmet

    2013-01-01

    Highlights: • Impact loading reduces the torsional strength of composite shaft. • Impact energy level determines the severity of torsional strength reduction. • Hybrid composite shafts can be manufactured by mixing two types of filament. • Maximum torque capacity of shafts can be estimated using finite element method. - Abstract: This paper presents an experimental and numerical study to investigate residual torsional properties of composite shafts subjected to impact loadings. E-glass/epoxy, carbon/epoxy and E-glass–carbon/epoxy hybrid composite shafts were manufactured by filament winding method. Composite shafts were impacted at 5, 10, 20 and 40 J energy levels. Force–time and energy–time histories of impact tests were recorded. One composite shaft with no impact, and four composite shafts with impact damage, five in total, were tested under torsion. Torque-twisting angle relations for each test were obtained. Reduction at maximum torque and maximum twisting angle induced by impact loadings were calculated. While 5 J impact did not cause significant reduction at maximum torque and maximum twisting angle, remaining impact loadings caused 34–67% reduction at maximum torque, and 30–61% reduction at maximum twisting angle. Reductions increased with increasing energy levels and varied depending on the material of composite shafts. The 3-D finite element (FE) software, Abaqus, incorporated with an elastic orthotropic model, was then used to simulate the torsion tests. Good agreement between experimental and numerical results was achieved

  19. Torsion as a dark matter candidate from the Higgs portal

    Science.gov (United States)

    Belyaev, Alexander S.; Thomas, Marc C.; Shapiro, Ilya L.

    2017-05-01

    Torsion is a metric-independent component of gravitation, which may provide a more general geometry than the one taking place within general relativity. On the other hand, torsion could lead to interesting phenomenology in both particle physics and cosmology. In the present work it is shown that a torsion field interacting with the SM Higgs doublet and having a negligible coupling to standard model (SM) fermions is protected from decaying by a Z2 symmetry, and therefore becomes a promising dark matter (DM) candidate. This model provides a good motivation for Higgs portal vector DM scenario. We evaluate the DM relic density and explore direct DM detection and collider constraints on this model to understand its consistency with experimental data and establish the most up-to-date limits on its parameter space. We have found in the model when the Higgs boson is only partly responsible for the generation of torsion mass, there is a region of parameter space where torsion contributes 100% to the DM budget of the Universe. Furthermore, we present the first results on the potential of the LHC to probe the parameter space of minimal scenario with Higgs portal vector DM using mono-jet searches and have found that LHC at high luminosity will be sensitive to the substantial part of model parameter space which cannot be probed by other experiments.

  20. Crack path in aeronautical titanium alloy under ultrasonic torsion loading

    Directory of Open Access Journals (Sweden)

    A. Nikitin

    2016-01-01

    Full Text Available This paper discusses features of fatigue crack initiation and growth in aeronautical VT3-1 titanium alloy under pure torsion loading in gigacycle regime. Two materials: extruded and forged VT3-1 titanium alloys were studied. Torsion fatigue tests were performed up to fatigue life of 109 cycles. The results of the torsion tests were compared with previously obtained results under fully reversed axial loading on the same alloys. It has been shown that independently on production process as surface as well subsurface crack initiation may appear under ultrasonic torsion loading despite the maximum stress amplitude located at the specimen surface. In the case of surface crack initiation, a scenario of crack initiation and growth is similar to HCF regime except an additional possibility for internal crack branching. In the case of subsurface crack, the initiation site is located below the specimen surface (about 200 μm and is not clearly related to any material flaw. Internal crack initiation is produced by shear stress in maximum shear plane and early crack growth is in Mode II. Crack branching is limited in the case of internal crack initiation compared to surface one. A typical ‘fish-eye’ crack can be observed at the torsion fracture surface, but mechanism of crack initiation seems not to be the same than under axial fatigue loading.