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Sample records for chemical shift assignments

  1. Probabilistic validation of protein NMR chemical shift assignments

    International Nuclear Information System (INIS)

    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/

  2. 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/.

  3. Data requirements for reliable chemical shift assignments in deuterated proteins

    International Nuclear Information System (INIS)

    The information required for chemical shift assignments in large deuterated proteins was investigated using a Monte Carlo approach (Hitchens et al., 2002). In particular, the consequences of missing amide resonances on the reliability of assignments derived from Cα and CO or from Cα and Cβ chemical shifts was investigated. Missing amide resonances reduce both the number of correct assignments as well as the confidence in these assignments. More significantly, a number of undetectable errors can arise when as few as 9% of the amide resonances are missing from the spectra. However, the use of information from residue specific labeling as well as local and long-range distance constraints improves the reliability and extent of assignment. It is also shown that missing residues have only a minor effect on the assignment of protein-ligand complexes using Cα and CO chemical shifts and Cα inter-residue connectivity, provided that the known chemical shifts of the unliganded protein are utilized in the assignment process

  4. Computational Assignment of Chemical Shifts for Protein Residues

    CERN Document Server

    Bratholm, Lars A

    2013-01-01

    Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel properties. X-ray crystallography is the most common approach even with its low success rate, but lately NMR based approaches have gained popularity. The general approach involves a set of distance restraints used to guide a structure prediction, but simple NMR triple-resonance experiments often provide enough structural information to predict the structure of small proteins. Previous protein folding simulations that have utilised experimental data have weighted the experimental data and physical force field terms more or less arbitrarily, and the method is thus not generally applicable to new proteins. Furthermore a complete and near error-free assignment of chemical shifts obtained by the NMR experiments is needed, due to the static, or deterministic, assignment. In this ...

  5. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    Science.gov (United States)

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  6. 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)

    We introduce a Python-based program that utilizes the large database of 13C and 15N 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 13C–13C, 15N–13C, or 3D 15N–13C–13C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13C–13C 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.

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

    International Nuclear Information System (INIS)

    The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the 1H 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 43 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 1H 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.

  8. Chemical shift assignments of the fibronectin III like domains 7-8 of type VII collagen.

    Science.gov (United States)

    Hermsdorf, Ulrike; Seeger, Karsten

    2016-04-01

    Type VII collagen (Col7) is important for skin stability. This is underlined by the severe skin blistering phenotype in the Col7 related diseases dystrophic epidermolysis bullosa and epidermolysis bullosa acquisita (EBA). Col7 has a large N-terminal non-collagenous domain (NC1) that is followed by the triple helical collagenous domain. The NC1 domain has subdomains with homology to adhesion molecules and mediates important interactions within the extracellular matrix. An 185 amino acid long part of the NC1-subdomain termed fibronectin III like domains 7 and 8 (FNIII7-8) was investigated. Antibodies against this region are pathogenic in a mouse model of EBA and one reported missense mutations of Col7 lies within these domains. The nearly complete NMR resonance assignment of recombinant FNIII7-8 of Col7 is reported. PMID:26364055

  9. 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. PMID:24496608

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

    KAUST Repository

    Jang, Richard

    2011-01-01

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

  11. Solid state NMR chemical shift assignment and conformational analysis of a cellulose binding protein facilitated by optimized glycerol enrichment.

    Science.gov (United States)

    Ivanir, Hadar; Goldbourt, Amir

    2014-07-01

    Magic-angle spinning solid-state NMR has been applied to study CBM3b-Cbh9A (CBM3b), a cellulose binding module protein belonging to family 3b. It is a 146-residue protein having a unique nine-stranded β-sandwich fold, in which 35% of the structure is in a β-sheet conformation and the remainder of the protein is composed of loops and unstructured regions. Yet, the protein can be crystalized and it forms elongated needles. Close to complete chemical shift assignment of the protein was obtained by combining two- and three-dimensional experiments using a fully labeled sample and a glycerol-labeled sample. The use of an optimized protocol for glycerol-based sparse labeling reduces sample preparation costs and facilitates the assignment of the large number of aromatic signals in this protein. Conformational analysis shows good correlation between the NMR-predicted secondary structure and the reported X-ray crystal structure, in particular in the structured regions. Residues which show high B-factor values are situated mainly in unstructured regions, and are missing in our spectra indicating conformational flexibility rather than heterogeneity. Interestingly, long-range contacts, which could be clearly detected for tyrosine residues, could not be observed for aromatic phenylalanine residues pointing into the hydrophobic core, suggesting possible high ring mobility. These studies will allow us to further investigate the cellulose-bound form of CBM proteins. PMID:24824437

  12. Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study

    Science.gov (United States)

    Wang, Tao; Wu, Yi fang; Wang, Xue liang

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules.

  13. EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data

    International Nuclear Information System (INIS)

    For several of the proteins in the BioMagResBank larger than 200 residues, 60 % or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6 × 10260 possible assignments. In “EZ-ASSIGN”, the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281–298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592–610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335–344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested

  14. Secondary structural analysis of proteins based on 13C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database

    International Nuclear Information System (INIS)

    Magic-angle-spinning solid-state 13C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-13C,15N labeled samples. To overcome this problem, we present a method for assigning 13C chemical shifts and secondary structures from unresolved two-dimensional 13C–13C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to 13Cα, 13Cβ, and 13C′ chemical shifts and cross-peak intensities. The experimental 13C–13C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific Cα, Cβ, and C′ chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50–200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved 13C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.

  15. 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)

  16. (1)H, (13)C, and (15)N chemical shift assignments of cyanobacteriochrome NpR6012g4 in the green-absorbing photoproduct state.

    Science.gov (United States)

    Lim, Sunghyuk; Yu, Qinhong; Rockwell, Nathan C; Martin, Shelley S; Lagarias, J Clark; Ames, James B

    2016-04-01

    Cyanobacteriochromes (CBCRs) are cyanobacterial photosensory proteins with a tetrapyrrole (bilin) chromophore that belong to the phytochrome superfamily. Like phytochromes, CBCRs photoconvert between two photostates with distinct spectral properties. NpR6012g4 from Nostoc punctiforme is a model system for widespread CBCRs with conserved red/green photocycles. Atomic-level structural information for the photoproduct state in this subfamily is not known. Here, we report NMR backbone chemical shift assignments of the light-activated state of NpR6012g4 (BMRB no. 26577) as a first step toward determining its atomic resolution structure. PMID:26537963

  17. 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)

    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 1H, 13C 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 1H and 13C NMR chemical shift assignments. (author)

  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)

    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. Molecular structure and vibrational and chemical shift assignments of 3‧-chloro-4-dimethylamino azobenzene by DFT calculations

    Science.gov (United States)

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3‧-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state. The 1H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.

  20. ¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

    Science.gov (United States)

    Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

    2016-04-15

    Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations. PMID:26845204

  1. Comprehensive signal assignment of 13C-labeled lignocellulose using multidimensional solution NMR and 13C chemical shift comparison with solid-state NMR.

    Science.gov (United States)

    Komatsu, Takanori; Kikuchi, Jun

    2013-09-17

    A multidimensional solution NMR method has been developed using various pulse programs including HCCH-COSY and (13)C-HSQC-NOESY for the structural characterization of commercially available (13)C labeled lignocellulose from potatoes (Solanum tuberosum L.), chicory (Cichorium intybus), and corn (Zea mays). This new method allowed for 119 of the signals in the (13)C-HSQC spectrum of lignocelluloses to be assigned and was successfully used to characterize the structures of lignocellulose samples from three plants in terms of their xylan and xyloglucan structures, which are the major hemicelluloses in angiosperm. Furthermore, this new method provided greater insight into fine structures of lignin by providing a high resolution to the aromatic signals of the β-aryl ether and resinol moieties, as well as the diastereomeric signals of the β-aryl ether. Finally, the (13)C chemical shifts assigned in this study were compared with those from solid-state NMR and indicated the presence of heterogeneous dynamics in the polysaccharides where rigid cellulose and mobile hemicelluloses moieties existed together. PMID:24010724

  2. Protein Chemical Shift Prediction

    CERN Document Server

    Larsen, Anders S

    2014-01-01

    The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures resolved with X-ray crystallography and the corresponding experimental chemical shifts have been developed. These empirical predictors are very accurate on X-ray structures but tends to be insensitive to small structural changes. To overcome this limitation it has been suggested to make chemical shift predictors based on quantum mechanical(QM) calculations. In this thesis the development of the QM derived chemical shift predictor Procs14 is presented. Procs14 is based on 2.35 million density functional theory(DFT) calculations on tripeptides and contains corrections for hydrogen bonding, ring current and the effect of the previous and following residue. Procs14 is capable at performing predictions for the 13CA, 13CB, 13CO, 15NH, 1HN and 1HA backbone atoms. In order to benchmark Procs14, a number of QM NMR calculatio...

  3. Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone {sup 15}N or {sup 13}C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A., E-mail: fmulder@chem.au.dk [Aarhus University, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) (Denmark)

    2015-02-15

    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 {sup 1}H{sup N}, {sup 15}N{sup H}, and {sup 13}C′ resonance assignments to be completed from a single pair of 3D experiments.

  4. 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)

    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 1H, 13C and 15N 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.

  5. Geometric effects on carbon-13 chemical shifts

    International Nuclear Information System (INIS)

    In the course of our investigations on carbon-13 chemical shifts of tetracyclic dodecanes, we managed to show that a large number of chemical shift differences between members of the series and models provided by bicyclic analogs could be attributed to steric effects. There are examples, however, where this is clearly not the case. In order to investigate apparent anomalies we calculated structures of interest and looked into the relationships between molecular geometry and chemical shifts. As the assignment of some of the key structures in these analysis were made by comparison with model compounds and crucial experiments that could remove ambiguities were missing, we prepared and interpreted two spectra which are presented

  6. (1)H, (15)N and (13)C chemical shift assignment of the Gram-positive conjugative transfer protein TraHpIP501.

    Science.gov (United States)

    Fercher, Christian; Keller, Walter; Zangger, Klaus; Helge Meyer, N

    2016-04-01

    Conjugative transfer of DNA represents the most important transmission pathway in terms of antibiotic resistance and virulence gene dissemination among bacteria. TraH is a putative transfer protein of the type IV secretion system (T4SS) encoded by the Gram-positive (G+) conjugative plasmid pIP501. This molecular machine involves a multi-protein core complex spanning the bacterial envelope thereby serving as a macromolecular secretion channel. Here, we report the near complete (1)H, (13)C and (15)N resonance assignment of a soluble TraH variant comprising the C-terminal domain. PMID:26559076

  7. Backbone and Ile-δ1, Leu, Val Methyl 1H, 13C and 15N NMR chemical shift assignments for human interferon-stimulated gene 15 protein

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Cuifeng; Aramini, James M.; Ma, LiChung; Cort, John R.; Swapna, G.V.T.; Krug, R. M.; Montelione, Gaetano

    2011-10-01

    Human interferon-stimulated gene 15 protein (ISG15), also called ubiquitin cross-reactive protein (UCRP), is the first identified ubiquitin-like protein containing two ubiquitin-like domains fused in tandem. The active form of ISG15 is conjugated to target proteins via the C-terminal glycine residue through an isopeptide bond in a manner similar to ubiquitin. The biological role of ISG15 is strongly associated with the modulation of cell immune function, and there is mounting evidence suggesting that many viral pathogens evade the host innate immune response by interfering with ISG15 conjugation to both host and viral proteins in a variety of ways. Here we report nearly complete backbone 1HN, 15N, 13CO, and 13Ca, as well as side chain 13Cb, methyl (Ile-d1, Leu, Val), amide (Asn, Gln), and indole NH (Trp) NMR resonance assignments for the 157-residue human ISG15 protein. These resonance assignments provide the basis for future structural and functional solution NMR studies of the biologically important human ISG15 protein.

  8. Iboga alkaloids from Peschiera affinis (Apocynaceae) - unequivocal {sup 1}H and {sup 13}C chemical shift assignments: antioxidant activity; Alcaloides iboga de Peschiera affinis (Apocynaceae) - atribuicao inequivoca dos deslocamentos quimicos dos atomos de hidrogenio e carbono: atividade antioxidante

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Allana Kellen L.; Magalhaes, Ticiane S.; Monte, Francisco Jose Q.; Mattos, Marcos Carlos de; Oliveira, Maria Conceicao F. de; Almeida, Maria Mozarina B.; Lemos, Telma L.G.; Braz-Filho, Raimundo [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica], e-mail: tlemos@dqoi.ufc.br

    2009-07-01

    Six known alkaloids iboga type and the triterpene {alpha}- and {beta}-amyrin acetate were isolated from the roots and stems of Peschiera affinis. Their structures were characterized on the basis of spectral data mainly NMR and mass spectra. 1D and 2D NMR spectra were also used to unequivocal {sup 1}H and {sup 13}C chemical shift assignments of alkaloids. The ethanolic extract of roots, alkaloidic and no-alkaloidic fractions and iso-voacristine hydroxyindolenine and voacangine were evaluated for their antioxidative properties using an autographic assay based on {beta}-carotene bleaching on TLC plates, and also spectrophotometric detection by reduction of the stable DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical. (author)

  9. Complete assignment of 1H, 13C and 15N chemical shifts for bovine β-lactoglobulin: Secondary structure and topology of the native state is retained in a partially unfolded form

    International Nuclear Information System (INIS)

    Although β-lactoglobulin (β-LG) has been studied extensively for more than 50 years, its physical properties in solution are not yet understood fully in terms of its three-dimensional (3D) structure. For example, despite a recent high-resolution crystal structure, it is still not clear why the two common variants of bovine β-LG which differ by just two residues have different aggregation properties during milk processing. We have conducted solution-state NMR studies on a recombinant form of the A variant of β-LG at low pH conditions where the protein is partially unfolded and exists as a monomer rather than a dimer. Using a13 C,15N-labelled sample, expressed in Pichia pastoris, we have employed the standard combination of 3D heteronuclear NMR techniques to obtain near complete assignments of proton, carbon and nitrogen resonances. Using a novel pulse sequence we were able to obtain additional assignments, in particular those of methyl groups in residues preceding proline within the sequence. From chemical shifts and on the basis of inter-residue NOEs, we have inferred the secondary structure and topology of monomeric β-LG A. It includes eight antiparallel β-strands arranged in a barrel, flanked by an α-helix, which is typical of a member of the lipocalin family. A detailed comparison with the crystal structure of the dimeric form (for a mixture of A and B variants) at pH 6.5 reveals a close resemblance in both secondary structure and overall topology. Both forms have a ninth β-strand which, at the higher pH, forms part of the dimer interface. These studies represent the first full NMR assignment of β-LG and will form the basis for a complete characterisation of the solution structure and dynamics of this protein and its variants

  10. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

    Energy Technology Data Exchange (ETDEWEB)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

    2012-04-15

    The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

  11. A Short History of Three Chemical Shifts

    Science.gov (United States)

    Nagaoka, Shin-ichi

    2007-01-01

    A short history of chemical shifts in nuclear magnetic resonance (NMR), electron spectroscopy for chemical analysis (ESCA) and Mossbauer spectroscopy, which are useful for chemical studies, is described. The term chemical shift is shown to have originated in the mistaken assumption that nuclei of a given element would all undergo resonance at the…

  12. Probabilistic Approach to Determining Unbiased Random-coil Carbon-13 Chemical Shift Values from the Protein Chemical Shift Database

    International Nuclear Information System (INIS)

    We describe a probabilistic model for deriving, from the database of assigned chemical shifts, a set of random coil chemical shift values that are 'unbiased' insofar as contributions from detectable secondary structure have been minimized (RCCSu). We have used this approach to derive a set of RCCSu values for 13Cα and 13Cβ for 17 of the 20 standard amino acid residue types by taking advantage of the known opposite conformational dependence of these parameters. We present a second probabilistic approach that utilizes the maximum entropy principle to analyze the database of 13Cα and 13Cβ chemical shifts considered separately; this approach yielded a second set of random coil chemical shifts (RCCSmax-ent). Both new approaches analyze the chemical shift database without reference to known structure. Prior approaches have used either the chemical shifts of small peptides assumed to model the random coil state (RCCSpeptide) or statistical analysis of chemical shifts associated with structure not in helical or strand conformation (RCCSstruct-stat). We show that the RCCSmax-ent values are strikingly similar to published RCCSpeptide and RCCSstruct-stat values. By contrast, the RCCSu values differ significantly from both published types of random coil chemical shift values. The differences (RCCSpeptide-RCCSu) for individual residue types show a correlation with known intrinsic conformational propensities. These results suggest that random coil chemical shift values from both prior approaches are biased by conformational preferences. RCCSu values appear to be consistent with the current concept of the 'random coil' as the state in which the geometry of the polypeptide ensemble samples the allowed region of (φ,ψ)-space in the absence of any dominant stabilizing interactions and thus represent an improved basis for the detection of secondary structure. Coupled with the growing database of chemical shifts, this probabilistic approach makes it possible to refine

  13. Conformational propensities of intrinsically disordered proteins from NMR chemical shifts

    International Nuclear Information System (INIS)

    The realization that a protein can be fully functional even in the absence of a stable three-dimensional structure has motivated a large number of studies describing the conformational behaviour of these proteins at atomic resolution. Here, we review recent advances in the determination of local structural propensities of intrinsically disordered proteins (IDPs) from experimental NMR chemical shifts. A mapping of the local structure in IDPs is of paramount importance in order to understand the molecular details of complex formation, in particular, for IDPs that fold upon binding or undergo structural transitions to pathological forms of the same protein. We discuss experimental strategies for the spectral assignment of IDPs, chemical shift prediction algorithms and the generation of representative structural ensembles of IDPs on the basis of chemical shifts. Additionally, we highlight the inherent degeneracies associated with the determination of IDP sub-state populations from NMR chemical shifts alone. (authors)

  14. Constituintes químicos de Ottonia corcovadensis Miq. da floresta Amazônica: atribuição dos deslocamentos químicos dos átomos de hidrogênio e carbono Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: ¹h and 13c chemical shift assignments

    Directory of Open Access Journals (Sweden)

    Valdir A. Facundo

    2004-02-01

    Full Text Available 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-pentamethoxyflavone (1, 3',4',5,7-tetramethoxyflavone (2 and 5-hydroxy-3',4',5',7-tetramethoxyflavone (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 ¹H and 13C 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.

  15. MR chemical shift imaging of human atheroma

    International Nuclear Information System (INIS)

    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

  16. Carbon-13 magnetic resonance chemical shift additivity relationships of clinically used furocoumarins and furchromones

    International Nuclear Information System (INIS)

    The natural abundance carbon-13 nuclear magnetic resonance spectra of various clinically used furocoumarins and furochromones have been studied. The assignments of carbon chemical shift values were based on the theory of chemical shift, additivity rules, SFORD spectra and model compounds. (author)

  17. 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.

  18. Accessible surface area from NMR chemical shifts

    International Nuclear Information System (INIS)

    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

  19. Microscopic shifts of size-assigned p-cresol/H2O-cluster spectra

    Science.gov (United States)

    Pohl, M.; Schmitt, M.; Kleinermanns, K.

    1991-02-01

    p-cresol and its complexes with H2O and CH3OH were cooled in a pulsed supersonic free jet and studied by resonant multiphoton ionization with time-of-flight mass analysis. Detailed mass and concentration analysis allowed an unambiguous assignment of cluster size. The electronic origins of p-cresol (H2O)1,2,3 show irregular red- and blueshifts with change of cluster size, which is referred to the bivalent role of p-cresol as proton donor and acceptor. Ab initio and semiempirical quantum chemical calculations support this interpretation and show the spectral shifts to be essentially due to the inductive effect of the solvent molecules Y exerted on X in X-H...Y. While the vibronic bands of p-cresol (H2O)2 are quite broad, those of p-cresol (H2O)3 are sharp again. The ab initio calculations show that this may be attributed to the quite rigid ``open cyclic'' structure of p-cresol (H2O)3. Our experimental and theoretical investigations show a completely analogous behavior of phenol (H2O)1,2,3 clusters

  20. Random coil chemical shift for intrinsically disordered proteins

    DEFF Research Database (Denmark)

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

    2011-01-01

    Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical....... 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...

  1. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes che...... residues. For Rhodopsin (225 residues) a structure is found at 2.5 Å CA-RMSD from the experimental X-ray structure, and a structure is determined for the Savinase protein (269 residues) with 2.9 Å CA-RMSD from the experimental X-ray structure....

  2. Chemical shift MR imaging of the skin

    International Nuclear Information System (INIS)

    MR imaging with conventional spin-echo pulse sequences has not found wide application in the evaluation of skin pathology. This paper reports that this study was designed to determine the value of chemical shift imaging (CSI) compared with conventional pulse sequences for the noninvasive evaluation of connective tissue and neoplastic disease of the skin and underlying fascia. The studies were acquired in patients and volunteers on a whole-body system at 1.5 T and small surface coils. Comparisons were made between T1- and T2-weighted gradient-echo, spin-echo, and hybrid lipid and water-suppressed CSI series (Chopper-Dixon combined with frequency-selective pulse). CSI improves detail in the hypodermis by eliminating unwanted (lipid) signal and chemical shift misregistration artifact. The detail of water-based signal is improved in the deeper layers of the skin by improved tissue contrast and elimination of the disturbing adjacent dominant fat-based signal. MR imaging has the potential to provide information that can complement skin biopsy. A more optimal choice of pulse sequences can improve the sensitivity of MR imaging to water-based pathology and allow noninvasive visualization of deep layers. The CSI sequences may be useful in the evaluation of infiltrative and neoplastic disease of the skin, particularly as they are adapted into microimaging methods with local gradient coils

  3. RefDB: A database of uniformly referenced protein chemical shifts

    International Nuclear Information System (INIS)

    RefDB is a secondary database of reference-corrected protein chemical shifts derived from the BioMagResBank (BMRB). The database was assembled by using a recently developed program (SHIFTX) to predict protein 1H, 13C and 15N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins. The predicted shifts were then compared with the corresponding observed shifts and a variety of statistical evaluations performed. In this way, potential mis-assignments, typographical errors and chemical referencing errors could be identified and, in many cases, corrected. This approach allows for an unbiased, instrument-independent solution to the problem of retrospectively re-referencing published protein chemical shifts. Results from this study indicate that nearly 25% of BMRB entries with 13C protein assignments and 27% of BMRB entries with 15N protein assignments required significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. From this study it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC 13C and 15N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the BMRB are still being incorrectly referenced. This is cause for some concern. However, the utilization of RefDB and its companion programs may help mitigate this ongoing problem. RefDB is updated weekly and the database, along with its associated software, is freely available at http://redpoll.pharmacy.ualberta.ca and the BMRB website

  4. A procedure to validate and correct the 13C chemical shift calibration of RNA datasets

    International Nuclear Information System (INIS)

    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 13C NMR data of RNAs. Our procedure uses five 13C 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 13C calibration and detect errors or inconsistencies in RNA 13C 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–13C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable 13C 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 13C chemical shift data. This is demonstrated by a clear relationship between ribose 13C shifts and the sugar pucker, which can be used to predict a C2′- or C3′-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.

  5. Pseudo 5D HN(C)N experiment to facilitate the assignment of backbone resonances in proteins exhibiting high backbone shift degeneracy

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Dinesh, E-mail: dineshcbmr@gmail.com [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India); Raikwal, Nisha [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India); Shukla, Vaibhav Kumar; Pandey, Himanshu; Arora, Ashish [Molecular and Structural Biology Division, CSIR, Central Drug Research Institute, Lucknow 226031 (India); Guleria, Anupam, E-mail: anuguleriaphy@gmail.com [Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raibareli Road, Lucknow 226014 (India)

    2014-09-30

    Graphical abstract: - Highlights: • A reduced dimensionality experiment – referred as pseudo 5D HN(C)N- is presented. • Encodes highly resolved 5D spectral information in a 3D spectrum. • Superior in terms of peak dispersion. • Facilitates assignment of crowded HSQC spectra of moderately sized proteins. • Modulated {sup 15}N chemical shifts are used to break the amide shift degeneracy. - Abstract: Assignment of protein backbone resonances is most routinely carried out using triple resonance three-dimensional NMR experiments involving amide {sup 1}H/{sup 15}N resonances. However for intrinsically unstructured proteins, alpha-helical proteins or proteins containing several disordered fragments, the assignment becomes problematic because of high-degree of backbone shift degeneracy. In this backdrop, a novel reduced-dimensionality (RD) experiment –(5, 3)D-hNCO-CANH- is presented to facilitate/validate the sequential backbone resonance assignment in such proteins. The proposed 3D NMR experiment makes use of the modulated amide {sup 15}N chemical shifts (resulting from the joint sampling along both its indirect dimensions) to resolve the ambiguity involved in connecting the neighboring amide resonances (i.e. H{sub i}N{sub i} and H{sub i−1}N{sub i−1}) for overlapping amide-NH peaks. The experiment -in combination with routine triple resonance 3D-NMR experiments involving backbone amide ({sup 1}H/{sup 15}N) and carbon ({sup 13}C{sup α}/{sup 13}C′) chemical shifts- will serve as a powerful complementary tool to achieve the nearly complete assignment of protein backbone resonances in a time efficient manner.

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

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dawei; Brüschweiler, Rafael, E-mail: bruschweiler.1@osu.edu [The Ohio State University, Campus Chemical Instrument Center (United States)

    2015-07-15

    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.

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

    International Nuclear Information System (INIS)

    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

  8. Pseudo 5D HN(C)N Experiment to Facilitate the Assignment of Backbone Resonances in Proteins Exhibiting High Backbone Shift Degeneracy

    CERN Document Server

    Kumar, Dinesh; Shukla, Vaibhav Kumar; Pandey, Himanshu; Arora, Ashish; Guleria, Anupam

    2014-01-01

    Assignment of protein backbone resonances is most routinely carried out using triple resonance three dimensional NMR experiments involving amide 1H and 15N resonances. However for intrinsically unstructured proteins, alpha-helical proteins or proteins containing several disordered fragments, the assignment becomes problematic because of high degree of backbone shift degeneracy. In this backdrop, a novel reduced dimensionality (RD) experiment -(5,3)D-hNCO-CANH- is presented to facilitate (and/or to validate) the sequential backbone resonance assignment in such proteins. The proposed 3D NMR experiment makes use of the modulated amide 15N chemical shifts (resulting from the joint sampling along both its indirect dimensions) to resolve the ambiguity involved in connecting the neighboring amide resonances (i.e. HiNi and Hi-1Ni-1) for overlapping amide NH peaks. The experiment -encoding 5D spectral information- leads to a conventional 3D spectrum with significantly reduced spectral crowding and complexity. The impr...

  9. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Labudde, D.; Leitner, D.; Krueger, M.; Oschkinat, H. [Forschungsinstitut fuer Molekulare Pharmakologie (Germany)], E-mail: oschkinat@fmp-berlin.de

    2003-01-15

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the {alpha}-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely {alpha}-helix, {beta}-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  10. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    International Nuclear Information System (INIS)

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the α-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely α-helix, β-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time

  11. Assignment of hyperfine shifted haem methyl carbon resonances in paramagnetic low-spin met-cyano complex of sperm whale myoglobin

    International Nuclear Information System (INIS)

    The hyperfine shifted resonances arising from all four individual haem carbons of the paramagnetic low-spin met-cyano complex of sperm whale myoglobin have been clearly identified and assigned for the first time with the aid of 1H-13C heteronuclear chemical shift correlated spectroscopy. Alteration of the in-plane symmetry of the electronic structure of haem induced by the ligation of proximal histidyl imidazole spreads the haem carbon resonances to 32 ppm at 220C, indicating the sensitivity of those resonances to the haem electronic/molecular structure. Those resonances are potentially powerful probes in characterizing the nature of haem electronic structure. 25 refs.; 2 figs.; 1 table

  12. Making the Shift: From Traditional Research Assignments to Guiding Inquiry Learning

    Science.gov (United States)

    Maniotes, Leslie K.; Kuhlthau, Carol C.

    2014-01-01

    The traditional research assignment is a common approach for teachers unaware of an inquiry process. In the traditional assignment, on the very first day that the work is assigned, students are given a topic or asked to choose a topic from a prepared list. They are given the parameters of the assignment, the number of sources required, the number…

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

    International Nuclear Information System (INIS)

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the 1H NMR and 13C 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 1H and 13C 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 1H and 13C 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

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

    Science.gov (United States)

    Brown, Joshua D; Summers, Michael F; Johnson, Bruce A

    2015-09-01

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR and (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 (1)H and (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 (1)H and (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. PMID:26141454

  15. 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.

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

    International Nuclear Information System (INIS)

    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 1H 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 1H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

  17. 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…

  18. An evaluation of chemical shift index-based secondary structure determination in proteins: Influence of random coil chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Mielke, S.P.; Krishnan, V.V. [Biophysics Graduate Group, University of California, Davis (United States)], E-mail: krish@llnl.gov

    2004-10-15

    Random coil chemical shifts are commonly used to detect protein secondary structural elements in chemical shift index (CSI) calculations. Though this technique is widely used and seems reliable for folded proteins, the choice of reference random coil chemical shift values can significantly alter the outcome of secondary structure estimation. In order to evaluate these effects, we present a comparison of secondary structure content calculated using CSI, based on five different reference random coil chemical shift value sets, to that derived from three-dimensional structures. Our results show that none of the reference random coil data sets chosen for evaluation fully reproduces the actual secondary structures. Among the reference values generally available to date, most tend to be good estimators only of helices. Based on our evaluation, we recommend the experimental values measured by Schwarzinger et al. (2000), and statistical values obtained by Lukin et al. (1997), as good estimators of both helical and sheet content.

  19. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim; Jensen, Jan Halborg

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...... chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the......, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction....

  20. Bayesian inference of protein structure from chemical shift data

    Directory of Open Access Journals (Sweden)

    Lars A. Bratholm

    2015-03-01

    Full Text Available Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction.

  1. 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.

  2. Counterion influence on chemical shifts in strychnine salts.

    Science.gov (United States)

    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 (1)H and (13)C 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. 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 with 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. PMID:23495106

  3. Development of reference assignment in children: a direct comparison to the performance of cognitive shift

    OpenAIRE

    Murakami, Taro; Hashiya, Kazuhide

    2014-01-01

    The referent of a deictic embedded in a particular utterance or sentence is often ambiguous. Reference assignment is a pragmatic process that enables the disambiguation of such a referent. Previous studies have demonstrated that receivers use social-pragmatic information during referent assignment; however, it is still unclear which aspects of cognitive development affect the development of referential processing in children. The present study directly assessed the relationship between perfor...

  4. 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

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

    International Nuclear Information System (INIS)

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations (13C–13C, 15N–13C, 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 13C 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 13C NMR data and almost all 15N 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 13C 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 provided

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

    Science.gov (United States)

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

    2016-02-01

    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 provided

  7. 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.

  8. Improving 3D structure prediction from chemical shift data

    International Nuclear Information System (INIS)

    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 Å RMSD from the reference)

  9. Calculations of NMR chemical shifts with APW-based methods

    Science.gov (United States)

    Laskowski, Robert; Blaha, Peter

    2012-01-01

    We present a full potential, all electron augmented plane wave (APW) implementation of first-principles calculations of NMR chemical shifts. In order to obtain the induced current we follow a perturbation approach [Pickard and Mauri, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.63.245101 63, 245101 (2001)] and extended the common APW + local orbital (LO) basis by several LOs at higher energies. The calculated all-electron current is represented in traditional APW manner as Fourier series in the interstitial region and with a spherical harmonics representation inside the nonoverlapping atomic spheres. The current is integrated using a “pseudocharge” technique. The implementation is validated by comparison of the computed chemical shifts with some “exact” results for spherical atoms and for a set of solids and molecules with available published data.

  10. 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)

  11. Anisotropy of the fluorine chemical shift tensor in UF6

    International Nuclear Information System (INIS)

    An 19F magnetic resonance study of polycrystalline UF6 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 UF6 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 UF6 molecule in the solid. (author)

  12. Magnetic shift of the chemical freezeout and electric charge fluctuations

    CERN Document Server

    Fukushima, Kenji

    2016-01-01

    We discuss the effect of a strong magnetic field on the chemical freezeout points in the ultra-relativistic heavy-ion collision. As a result of the inverse magnetic catalysis or the magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freezeout. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced especially at high baryon density. The charge conservation partially cancels the enhancement but our calculation shows that the electric charge fluctuation could serve as a magnetometer.

  13. Estimation of optical chemical shift in nuclear spin optical rotation

    International Nuclear Information System (INIS)

    Highlights: • Analytical theory of nuclear spin optical rotation (NSOR) is further developed. • Derive formula of NSOR ratio R between different nuclei in a same molecule. • Calculated results of R agree with the experiments. • Analyze influence factors on R and chemical distinction by NSOR. - Abstract: A recently proposed optical chemical shift in nuclear spin optical rotation (NSOR) is studied by theoretical comparison of NSOR magnitude between chemically non-equivalent or different element nuclei in the same molecule. Theoretical expressions of the ratio R between their NSOR magnitudes are derived by using a known semi-empirical formula of NSOR. Taking methanol, tri-ethyl-phosphite and 2-methyl-benzothiazole as examples, the ratios R are calculated and the results approximately agree with the experiments. Based on those, the important influence factors on R and chemical distinction by NSOR are discussed

  14. Chemical-shift MRI of exogenous lipoid pneumonia

    Energy Technology Data Exchange (ETDEWEB)

    Cox, J.E.; Choplin, R.H.; Chiles, C. [Wake Forest Univ., Winston-Salem, NC (United States)

    1996-05-01

    Exogenous lipoid pneumonia results from the aspiration or inhalation of fatty substances, such as mineral oil found in laxatives or nasal medications containing liquid paraffin. We present standard and lipid-sensitive (chemical-shift) MR findings in a patient with histologically confirmed lipoid pneumonia. The loss of signal intensity in an area of airspace disease on opposed-phase imaging was considered specific for the presence of lipid. 14 refs., 3 figs.

  15. Substituent effects on 61Ni NMR chemical shifts

    OpenAIRE

    Bühl, Michael; Peters, Dietmund; Herges, Rainer

    2009-01-01

    Ni-61 chemical shifts of Ni(all-trans-cdt) L (cdt = cyclododecatriene, L = none, CO, PMe3), Ni(CO)(4), Ni(C2H4)(2)(PMe3), Ni(cod)(2) (cod = cyclooctadiene) and Ni(PX3)(4) (X = Me, F, Cl) are computed at the GIAO (gauge-including atomic orbitals), BPW91, B3LYP and BHandHLYP levels, using BP86-optimised geometries and an indirect referencing scheme. For this set of compounds, substituent effects on delta(Ni-61) are better described with hybrid functionals than with the pure BPW91 functional. On...

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

    International Nuclear Information System (INIS)

    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

  17. Introducing chemical biology applications to introductory organic chemistry students using series of weekly assignments.

    Science.gov (United States)

    Kanin, Maralee R; Pontrello, Jason K

    2016-03-01

    Calls to bring interdisciplinary content and examples into introductory science courses have increased, yet strategies that involve course restructuring often suffer from the need for a significant faculty commitment to motivate change. Minimizing the need for dramatic course reorganization, the structure, reactivity, and chemical biology applications of classes of biological monomers and polymers have been integrated into introductory organic chemistry courses through three series of semester-long weekly assignments that explored (a) Carbohydrates and Oligosaccharides, (b) Amino Acids, Peptides, and Proteins, and (c) Nucleosides, Nucleotides, and Nucleic Acids. Comparisons of unannounced pre- and post tests revealed improved understanding of a reaction introduced in the assignments, and course examinations evaluated cumulative assignment topics. Course surveys revealed that demonstrating biologically relevant applications consistently throughout the semesters enhanced student interest in the connection between basic organic chemistry content and its application to new and unfamiliar bio-related examples. Covering basic material related to these classes of molecules outside of the classroom opened lecture time to allow the instructor to further build on information developed through the weekly assignments, teaching advanced topics and applications typically not covered in an introductory organic chemistry lecture course. Assignments were implemented as homework, either with or without accompanying discussion, in both laboratory and lecture organic courses within the context of the existing course structures. © 2015 by The International Union of Biochemistry and Molecular Biology, 44:168-178, 2016. PMID:26560414

  18. Accurate calculation of (31)P NMR chemical shifts in polyoxometalates.

    Science.gov (United States)

    Pascual-Borràs, Magda; López, Xavier; Poblet, Josep M

    2015-04-14

    We search for the best density functional theory strategy for the determination of (31)P nuclear magnetic resonance (NMR) chemical shifts, δ((31)P), in polyoxometalates. Among the variables governing the quality of the quantum modelling, we tackle herein the influence of the functional and the basis set. The spin-orbit and solvent effects were routinely included. To do so we analysed the family of structures α-[P2W18-xMxO62](n-) with M = Mo(VI), V(V) or Nb(V); [P2W17O62(M'R)](n-) with M' = Sn(IV), Ge(IV) and Ru(II) and [PW12-xMxO40](n-) with M = Pd(IV), Nb(V) and Ti(IV). The main results suggest that, to date, the best procedure for the accurate calculation of δ((31)P) in polyoxometalates is the combination of TZP/PBE//TZ2P/OPBE (for NMR//optimization step). The hybrid functionals (PBE0, B3LYP) tested herein were applied to the NMR step, besides being more CPU-consuming, do not outperform pure GGA functionals. Although previous studies on (183)W NMR suggested that the use of very large basis sets like QZ4P were needed for geometry optimization, the present results indicate that TZ2P suffices if the functional is optimal. Moreover, scaling corrections were applied to the results providing low mean absolute errors below 1 ppm for δ((31)P), which is a step forward in order to confirm or predict chemical shifts in polyoxometalates. Finally, via a simplified molecular model, we establish how the small variations in δ((31)P) arise from energy changes in the occupied and virtual orbitals of the PO4 group. PMID:25738630

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

    International Nuclear Information System (INIS)

    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

  20. Pitfalls of adrenal imaging with chemical shift MRI

    International Nuclear Information System (INIS)

    Chemical shift (CS) MRI of the adrenal glands exploits the different precessional frequencies of fat and water protons to differentiate the intracytoplasmic lipid-containing adrenal adenoma from other adrenal lesions. The purpose of this review is to illustrate both technical and interpretive pitfalls of adrenal imaging with CS MRI and emphasize the importance of adherence to strict technical specifications and errors that may occur when other imaging features and clinical factors are not incorporated into the diagnosis. When performed properly, the specificity of CS MRI for the diagnosis of adrenal adenoma is over 90%. Sampling the in-phase and opposed-phase echoes in the correct order and during the same breath-hold are essential requirements, and using the first echo pair is preferred, if possible. CS MRI characterizes more adrenal adenomas then unenhanced CT but may be non-diagnostic in a proportion of lipid-poor adenomas; CT washout studies may be able to diagnose these lipid-poor adenomas. Other primary and secondary adrenal tumours and supra-renal disease entities may contain lipid or gross fat and mimic adenoma or myelolipoma. Heterogeneity within an adrenal lesion that contains intracytoplasmic lipid could be due to myelolipoma, lipomatous metaplasia of adenoma, or collision tumour. Correlation with previous imaging, other imaging features, clinical history, and laboratory investigations can minimize interpretive errors

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

    International Nuclear Information System (INIS)

    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.

  2. 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.

  3. 19-Fluorine nuclear magnetic resonance chemical shift variability in trifluoroacetyl species

    OpenAIRE

    Sloop, Joseph

    2013-01-01

    Joseph C SloopSchool of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, USAAbstract: This review examines the variability of chemical shifts observed in 19-fluorine (19F) nuclear magnetic resonance spectra for the trifluoroacetyl (TFA) functional group. The range of 19F chemical shifts reported spectra for the TFA group varies generally from −85 to −67 ppm relative to CFCl3. The literature revealed several factors that impact chemical shifts of the TFA...

  4. Method of evaluating chemical shifts of X-ray emission lines in molecules and solids

    OpenAIRE

    Lomachuk, Yuriy V.; Titov, Anatoly V.

    2013-01-01

    Method of evaluating chemical shifts of X-ray emission lines for sufficiently heavy atoms (beginning from period 4 elements) in chemical compounds is developed. This method is based on the pseudopotential model and one-center restoration method (to reconstruct the proper electronic structure in heavy-atom cores). The approximations of instantaneous transition and frozen inner core spinors of the atom are used for derivation of an expression for chemical shift as a difference between mean valu...

  5. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

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

    International Nuclear Information System (INIS)

    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

  7. Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts.

    Science.gov (United States)

    Kumar, Arun V; Ali, Rehana F M; Cao, Yu; Krishnan, V V

    2015-10-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue's averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80% accuracy measured by Matthew correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with >90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments. PMID:25758094

  8. 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.

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

    International Nuclear Information System (INIS)

    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

  10. Mineral Moessbauer spectroscopy: correlations between chemical shift and quadrupole splitting parameters

    International Nuclear Information System (INIS)

    The variety of coordination numbers, symmetries, distortions and ligand environments in thermally-stable iron-bearing minerals provide wide ranges of chemical shift (δ) and quadrupole splitting (Δ) parameters, which serve to characterize the crystal chemistries and site occupancies of Fe2+ and Fe3+ ions in minerals of terrestrial and extraterrestrial origins. Correlations between ferrous and ferric chemical shifts enable thermally-induced electron delocalization behavior in mixed-valence Fe2+-Fe3+ minerals to be identified, while chemical shift versus quadrupole splitting correlations serve to identify nanophase ferric oxides and oxyhydroxides in oxidized minerals and in meteorites subjected to aqueous oxidation before and after they arrived on Earth. (orig.)

  11. 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...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...

  12. Combined Effects of Noise and Shift Work on Workers’ Physiological Parameters in a Chemical Industry

    OpenAIRE

    M. Motamedzade; S. Ghazaiee

    2003-01-01

    This study was conducted to determine the combined effects of noise and shift work on physiological parameters including body temperature, heart rate and blood pressure. This study was performed in a chemical industry in Tehran in 1993. The workers’ physiological parameters was recorded at the beginning and at the end of all work shifts. Groups under study included : day workers (n=115) , day workers with continuous noise exposure (n=44) , two-shift workers without...

  13. Chemical shifts and coupling constants of C8H10N4O2

    Science.gov (United States)

    Jain, M.

    This document is part of Subvolume D3 `Chemical Shifts and Coupling Constants for Carbon-13: Heterocycles' of Volume 35 `Nuclear Magnetic Resonance (NMR) Data' of Landolt-Börnstein Group III `Condensed Matter'

  14. Quantitative chemical-shift MR imaging cutoff value: Benign versus malignant vertebral compression – Initial experience

    Directory of Open Access Journals (Sweden)

    Dalia Z. Zidan

    2014-09-01

    Conclusion: Quantitative chemical shift MR imaging could be a valuable addition to standard MR imaging techniques and represent a rapid problem solving tool in differentiating benign from malignant vertebral compression, especially in patients with known primary malignancies.

  15. Supramolecular chemical shift reagents inducing conformational transitions: NMR analysis of carbohydrate homooligomer mixtures

    DEFF Research Database (Denmark)

    Beeren, Sophie; Meier, Sebastian

    2015-01-01

    We introduce the concept of supramolecular chemical shift reagents as a tool to improve signal resolution for the NMR analysis of homooligomers. Non-covalent interactions with the shift reagent can constrain otherwise flexible analytes inducing a conformational transition that results in signal...

  16. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

    International Nuclear Information System (INIS)

    We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson–Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input

  17. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

    Energy Technology Data Exchange (ETDEWEB)

    Swails, Jason [Rutgers University, Department of Chemistry and Chemical Biology and BioMaPS Institute (United States); Zhu, Tong; He, Xiao, E-mail: xiaohe@phy.ecnu.edu.cn [East China Normal University, State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science (China); Case, David A., E-mail: case@biomaps.rutgers.edu [Rutgers University, Department of Chemistry and Chemical Biology and BioMaPS Institute (United States)

    2015-10-15

    We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson–Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.

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

    International Nuclear Information System (INIS)

    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.)

  20. From NMR chemical shifts to amino acid types: Investigation of the predictive power carried by nuclei

    International Nuclear Information System (INIS)

    An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP (Grzesiek and Bax, J. Biomol. NMR, 3, 185-204, 1993) RESCUE (Pons and Delsuc, J. Biomol. NMR, 15, 15-26, 1999) and PLATON (Labudde et al., J. Biomol. NMR, 25, 41-53, 2003) and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are Cβ and Hβ, in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: Hβ, Cβ, Cα and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids

  1. Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.

    Science.gov (United States)

    Markwick, Phineus R L; Cervantes, Carla F; Abel, Barrett L; Komives, Elizabeth A; Blackledge, Martin; McCammon, J Andrew

    2010-02-01

    A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range. PMID:20063881

  2. Ontogenetic shift in response to prey-derived chemical cues in prairie rattlesnakes Crotalus viridis viridis

    Directory of Open Access Journals (Sweden)

    Anthony J. SAVIOLA, David CHISZAR, Stephen P. MACKESSY

    2012-08-01

    Full Text Available Snakes often have specialized diets that undergo a shift from one prey type to another depending on the life stage of the snake. Crotalus viridis viridis (prairie rattlesnake takes different prey at different life stages, and neonates typically prey on ectotherms, while adults feed almost entirely on small endotherms. We hypothesized that elevated rates of tongue flicking to chemical stimuli should correlate with particular prey consumed, and that this response shifts from one prey type to another as individuals age. To examine if an ontogenetic shift in response to chemical cues occurred, we recorded the rate of tongue flicking for 25 neonate, 20 subadult, and 20 adult (average SVL = 280.9, 552, 789.5 mm, respectively wild-caught C. v. viridis to chemical stimuli presented on a cotton-tipped applicator; water-soluble cues from two ectotherms (prairie lizard, Sceloporus undulatus, and house gecko, Hemidactylus frenatus, two endotherms (deer mouse, Peromyscus maniculatus and lab mouse, Mus musculus, and water controls were used. Neonates tongue flicked significantly more to chemical cues of their common prey, S. undulatus, than to all other chemical cues; however, the response to this lizard’s chemical cues decreased in adult rattlesnakes. Subadults tongue flicked with a higher rate of tongue flicking to both S. undulatus and P. maniculatus than to all other treatments, and adults tongue flicked significantly more to P. maniculatus than to all other chemical cues. In addition, all three sub-classes demonstrated a greater response for natural prey chemical cues over chemical stimuli of prey not encountered in the wild (M. musculus and H. frenatus. This shift in chemosensory response correlated with the previously described ontogenetic shifts in C. v. viridis diet. Because many vipers show a similar ontogenetic shift in diet and venom composition, we suggest that this shift in prey cue discrimination is likely a general phenomenon among viperid

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu [Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055 (United States)

    2015-10-14

    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), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 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) {sup 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 {sup 1}H–{sup 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

  4. 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)

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

    International Nuclear Information System (INIS)

    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 1H 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 13C 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)

  6. Chemical Constituents of Lecythispisonis (Lecythidaceae)--A New Saponin and Complete 1H and 13C Chemical Shift Assignments.

    Science.gov (United States)

    Duarte, Rennê C; Matos, Carlos R R; Braz-Filho, Raimundo; Mathias, Leda

    2015-06-01

    A novel triterpenoid saponin 3-O-β-D-glucuronopyranosyl-(1' --> 3)-2α,19α-dihydroxyolean-12-en-28-oic acid [3-O-β-D-glucuronopyranosyl-(1' --> 3)-arjunic acid, 1], ten known compounds [six triterpenoids: α-amyrin (2), β-amyrin (3), germanicol (4), lupeol (5), friedelin (6), friedelanol (7); four steroids--campesterol (8), stigmasterol (9), sitosterol (10), cholesterol (11)], and a long chain alcohol n-eicosan-1-ol (12) were identified in the bark of Lecythis pisonis. The structures were established by 1D and 2D NMR spectroscopy (1H and 13C-NMR, DEPTQ, 1H-1H-COSY, NOESY, HSQC and HMBC), low (CG-MS) and high resolution mass spectrometry (HR-ESI-MS), and infrared (IR) spectral data involving comparison with the literature. PMID:26197504

  7. Effect of shifting cultivation on soil physical and chemical properties in Bandarban hill district, Bangladesh

    Institute of Scientific and Technical Information of China (English)

    Khandakar Showkat Osman; M. Jashimuddin; S. M. Sirajul Haque; Sohag Miah

    2013-01-01

    This study reports the effects of shifting cultivation at slashing stage on soil physicochemical properties at Bandarban Sadar Upazila in Chittagong Hill Tracts of Bangladesh. At this initial stage of shifting cultivation no general trend was found for moisture content, maximum water holding capacity, field capacity, dry and moist bulk density, parti-cle density for some chemical properties between shifting cultivated land and forest having similar soil texture. Organic matter was significantly (p≤0.05) lower in 1-year and 3-year shifting cultivated lands and higher in 2-year shifting cultivation than in adjacent natural forest. Significant differences were also found for total N, exchangeable Ca, Mg and K and in CEC as well as for available P. Slashed area showed higher soil pH. Deterioration in land quality starts from burning of slashing materials and continues through subsequent stages of shifting cultivation.

  8. Method for evaluating chemical shifts of x-ray emission lines in molecules and solids

    Science.gov (United States)

    Lomachuk, Yuriy V.; Titov, Anatoly V.

    2013-12-01

    A method of evaluating chemical shifts of x-ray emission lines for period four and heavier elements is developed. This method is based on the relativistic pseudopotential model and one-center restoration approach [Int. J. Quantum Chem.IJQCB20020-760810.1002/qua.20418 104, 223 (2005)] to recover a proper electronic structure in heavy-atom cores after the pseudopotential simulation of chemical compounds. The approximations of instantaneous transition and frozen core are presently applied to derive an expression for chemical shift as a difference between mean values of certain effective operator. The method allows one to avoid evaluation of small quantities (chemical shifts ˜0.01-1 eV) as differences of very large values (transition energies ˜1-100 keV in various compounds). The results of our calculations of chemical shifts for the Kα1, Kα2, and L transitions of group-14 metal cations with respect to neutral atoms are presented. Calculations of Kα1-line chemical shifts for the Pb core transitions in PbO and PbF2 with respect to those in the Pb atom are also performed and discussed. The accuracy of approximations used is estimated and the quality of the calculations is analyzed.

  9. Method of evaluating chemical shifts of X-ray emission lines in molecules and solids

    CERN Document Server

    Lomachuk, Yuriy V

    2013-01-01

    Method of evaluating chemical shifts of X-ray emission lines for sufficiently heavy atoms (beginning from period 4 elements) in chemical compounds is developed. This method is based on the pseudopotential model and one-center restoration method (to reconstruct the proper electronic structure in heavy-atom cores). The approximations of instantaneous transition and frozen inner core spinors of the atom are used for derivation of an expression for chemical shift as a difference between mean values of some effective operator. The method allows one to avoid evaluating small values (chemical shifts ~ 0.01{\\div}1 eV) as differences of very large values (transition energies ~ 1{\\div}100 keV in various compounds). The results of our calculations of chemical shifts for the K_{\\alpha1,2} and L transitions of the group 14 metal cations with respect to neutral atoms are presented. The calculations of chemical shift of K_{\\alpha1}-line in the Pb-core transition within PbO and PbF_2 with respect to the neutral Pb are also p...

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

    International Nuclear Information System (INIS)

    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/χ1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C' 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/χ1 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 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C', respectively, including outliers

  11. Differential diagnosis of adrenal masses by chemical shift and dynamic gadolinium enhanced MR imaging

    International Nuclear Information System (INIS)

    Chemical shift MRI is widely used for identifying adenomas, but it is not a perfect method. We determined whether combined dynamic MRI methods can lead to improved diagnostic accuracy. Fifty-seven adrenal masses were examined by chemical shift and dynamic MR imaging using 2 MR systems. The masses included 38 adenomas and 19 non-adenomas. In chemical shift MRI studies, the signal intensity index (SI) was calculated, and the lesions classified into 5 types in the dynamic MRI studies. Of the 38 adenomas studied, 37 had an SI greater than 0. In the dynamic MRI, 34 of 38 adenomas showed a benign pattern (type 1). If the SI for the adenomas in the chemical shift MRI was considered to be greater than 0, the positive predictive value was 0.9, and the negative predictive value was 0.94 and κ=0.79. If type 1 was considered to indicate adenomas in the dynamic MRI, the corresponding values were 0.94, 0.81 and κ=0.77 respectively. The results obtained when the 2 methods were combined were 1, 0.95 and κ=0.96 respectively. The chemical shift MRI was found to be useful for identifying adenomas in most cases. If the adrenal mass had a low SI (0< SI<5), dynamic MRI was also found to be helpful for making a differential diagnosis. (author)

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

    Directory of Open Access Journals (Sweden)

    Anders S Christensen

    Full Text Available 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 QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94. ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3J(NC' spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.

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

    CERN Document Server

    Christensen, Anders S; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H

    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 QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this...

  14. Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Hansen, Poul Erik

    2015-01-01

    The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static......” and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N−. The paper will be deal with both secondary...... and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles...

  15. Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis

    DEFF Research Database (Denmark)

    Modig, K.; Jürgensen, Vibeke Würtz; Lindorff-Larsen, K.;

    2007-01-01

    A simple alternative method for obtaining "random coil" chemical shifts by intrinsic referencing using the protein's own peptide sequence is presented. These intrinsic random coil backbone shifts were then used to calculate secondary chemical shifts, that provide important information on the resi...

  16. Pulse NMR in solids: chemical shift, lead fluoride, and thorium hydride

    International Nuclear Information System (INIS)

    The fluorine chemical shift of a single crystal CaF2 was measured up to 4 kilobar at room temperature using multiple pulse NMR. The pressure dependence of the shift is found to be --1.7 +- 1 ppM/kbar, while an overlap model predicts a shift of --0.46 ppM/kbar.The chemical shift tensor is separated into ''geometrical'' and ''chemical'' contributions, and comparison of the proposed model calculations with recent data on hydroxyl proton chemical shift tensors shows that the geometrical portion accounts for the qualitative features of the measured tensors. A study of fluoride ion motion in β-PbF2 doped with NaF was conducted by measurement of the 19F transverse relaxation time (T2), spin lattice relaxation time (T1) and the spin lattice relaxation time in the rotating frame (T/sub 1r). Two samples of Th4H15, prepared under different conditions but both having the proper ratio of H/Th (to within 1 percent), were studied. The structure of the Th4H15 suggested by x-ray measurements is confirmed through a moment analysis of the rigid lattice line shape

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

    International Nuclear Information System (INIS)

    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 13Cα 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 13Cα 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 Rfree factors similar to those of the deposited X-ray structure, the 13Cα 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 13Cα 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 13Cα 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 13Cα 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 13Cα 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 accuracy as good as

  18. Proton Magnetic Resonance and Human Thyroid Neoplasia III. Ex VivoChemical-Shift Microimaging

    Science.gov (United States)

    Rutter, Allison; Künnecke, Basil; Dowd, Susan; Russell, Peter; Delbridge, Leigh; Mountford, Carolyn E.

    1996-03-01

    Magnetic-resonance chemical-shift microimaging, with a spatial resolution of 40 × 40 μm, is a modality which can detect alterations to cellular chemistry and hence markers of pathological processes in human tissueex vivo.This technique was used as a chemical microscope to assess follicular thyroid neoplasms, lesions which are unsatisfactorily investigated using standard histopathological techiques or water-based magnetic-resonance imaging. The chemical-shift images at the methyl frequency (0.9 ppm) identify chemical heterogeneity in follicular tumors which are histologically homogeneous. The observed changes to cellular chemistry, detectable in foci of approximately 100 cells or less, support the existence of a preinvasive state hitherto unidentified by current pathological techniques.

  19. 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

    this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that...... changes 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......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...

  20. 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 re...... implanted in silica are found to be in excellent agreement with experimental data, providing support for the proposed atomic geometry....

  1. Chemical shifts in transition metal dithiocarbamates from infrared and X-ray photoelectron spectroscopies

    Science.gov (United States)

    Payne, R.; Magee, R. J.; Liesegang, J.

    1982-11-01

    Measurements of the IR stretching frequencies of the NC and MS bonds in transition-metal (M) dithiocarbamates show significant correlation with measurement of core level XPS chemical shifts. This is believed to be the first demonstration of such a correlation for a series of solid-phase compounds.

  2. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    DEFF Research Database (Denmark)

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;

    2011-01-01

    Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation. This me...

  3. Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

    NARCIS (Netherlands)

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

    NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a

  4. 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.

  5. Elucidating the Link between NMR Chemical Shifts and Electronic Structure in d(0) Olefin Metathesis Catalysts.

    Science.gov (United States)

    Halbert, Stéphanie; Copéret, Christophe; Raynaud, Christophe; Eisenstein, Odile

    2016-02-24

    The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δiso) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δiso. This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σMC and π*MC orbitals under the action of the magnetic field, is analogous to that resulting from coupling σCC and π*CC in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δiso in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σMC and π*MC vs this between σCC and π*CC in ethylene. This effect also explains why the highest value of δiso is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to πMX) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δiso. PMID:26787258

  6. Noninvasive Temperature Mapping With MRI Using Chemical Shift Water-Fat Separation

    OpenAIRE

    Soher, Brian J.; Wyatt, Cory; Reeder, Scott B.; MacFall, James R.

    2010-01-01

    Tissues containing both water and lipids, e.g., breast, confound standard MR proton reference frequency-shift methods for mapping temperatures due to the lack of temperature-induced frequency shift in lipid protons. Generalized Dixon chemical shift–based water-fat separation methods, such as GE’s iterative decomposition of water and fat with echo asymmetry and least-squares estimation method, can result in complex water and fat images. Once separated, the phase change over time of the water s...

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

    International Nuclear Information System (INIS)

    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 (KD) 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 KD 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 1H–15N 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 (koff). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, koff ∼ 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 koff 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 koff values over a wide range, from 100 to 15,000 s−1. The validity of line shape analysis for koff values approaching intermediate exchange (∼100 s−1), may be facilitated by more accurate KD measurements from NMR-monitored chemical shift

  8. Introducing Chemical Biology Applications to Introductory Organic Chemistry Students Using Series of Weekly Assignments

    Science.gov (United States)

    Kanin, Maralee R.; Pontrello, Jason K.

    2016-01-01

    Calls to bring interdisciplinary content and examples into introductory science courses have increased, yet strategies that involve course restructuring often suffer from the need for a significant faculty commitment to motivate change. Minimizing the need for dramatic course reorganization, the structure, reactivity, and chemical biology…

  9. Phosphorus-31 nuclear magnetic resonance of double- and triple-helical nucleic acids. Phosphorus-31 chemical shifts as a probe of phosphorus-oxygen ester bond torsional angles

    International Nuclear Information System (INIS)

    The temperature dependence to the 31P NMR spectra of poly[d(GC)]-poly[d(GC)], d(GC)4, phenylalanine tRNA (yeast) and mixtures of poly(A) + oligo(U) is presented. The 31P NMR spectra of mixtures of complementary RNA and of the poly d(GC) self-complementary DNA provide torsional information on the phosphate ester conformation in the double, triple, and ''Z'' helix. The increasing downfield shift with temperature for the single-strand nucleic acids provides a measure of the change in the phosphate ester conformation in the single helix to coil conversion. A seperate upfield peak (20-26% of the total phosphates) is observed at lower temperatures in the oligo(U)-poly(A) mixtures which is assigned to the double helix/triple helix. Proton NMR and UV spectra confirm the presence of the multistrand forms. The 31P chemical shift for the double helix/triple helix is 0.2-0.5 ppm upfield from the chemical shift for the single helix which in turn is 1.0 ppm upfield from the chemical shift for the random coil conformation

  10. Alterations in chemical shifts and exchange broadening upon peptide boronic acid inhibitor binding to α-lytic protease

    International Nuclear Information System (INIS)

    α-Lytic protease, a bacterial serine protease of 198 aminoacids (19800 Da), has been used as a model system for studies of catalytic mechanism, structure-function relationships, and more recently for studies of pro region-assisted protein folding. We have assigned the backbones of the enzyme alone, and of its complex with the tetrahedral transition state mimic N-tert-butyloxycarbonyl-Ala-Pro-boroVal, using double- and triple-resonance 3D NMR spectroscopy on uniformly15N- and 13C/15N-labeled protein.Changes in backbone chemical shifts between the uncomplexed and inhibited form of the protein are correlated with distance from the inhibitor, the displacement of backbone nitrogens, and change in hydrogen bond strength upon inhibitor binding (derived from previously solved crystal structures).A comparison of the solution secondary structure of the uninhibited enzyme with that of the X-ray structure reveals no significant differences.Significant line broadening, indicating intermediate chemical exchange, was observed in many of the active site amides (including three broadened to invisibility), and in a majority of cases the broadening was reversed upon addition of the inhibitor. Implications and possible mechanisms of this line broadening are discussed

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

    International Nuclear Information System (INIS)

    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.

  12. Substituent Chemical Shifts of (E)-1-Aryl-3-thienylpropen-1-ones

    International Nuclear Information System (INIS)

    Substituent chemical shifts were examined for the 2- and 3-thiophene derivatives of chalcone and compared to the thiophene series of derivatives with the phenyl series. The chemical shift values for the α-carbons of the enones showed and inverse correlation with the Hammett σ values, but the correlation coefficients were moderate (r = 0.836 - 0.878). On the other hand, the β-carbons showed a normal correlation with excellent correlation coefficients (r = 0.994). The absolute magnitude of the ρ values for the α-carbon are about half of those of the β-carbon. The observation may be the result of a through-space transition of the electronic effect of the substituents in addition to the through bond transition

  13. 1H chemical shift imaging characterization of human brain tumor and edema

    International Nuclear Information System (INIS)

    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) 1H chemical shift imaging results at different repetition times (TR=1500 and 5000 ms; T1: n=19) and echo times (TE=135 and 270 ms; T2: n=7). Metabolite T1 and T2 relaxation times in unaffected brain tissue corresponded with those published for healthy volunteers. T2 relaxation times were reduced in tumor (choline, N-acetyl aspartate) and edema (choline, creatine) compared with unaffected brain tissue (p1H chemical shift imaging is most suited in the use of choline elevation as tumor marker. (orig.)

  14. Four-Component Relativistic DFT Calculations of (13)C Chemical Shifts of Halogenated Natural Substances.

    Science.gov (United States)

    Casella, Girolamo; Bagno, Alessandro; Komorovsky, Stanislav; Repisky, Michal; Saielli, Giacomo

    2015-12-14

    We have calculated the (13)C NMR chemical shifts of a large ensemble of halogenated organic molecules (81 molecules for a total of 250 experimental (13)C NMR data at four different levels of theory), ranging from small rigid organic compounds, used to benchmark the performance of various levels of theory, to natural substances of marine origin with conformational degrees of freedom. Carbon atoms bonded to heavy halogen atoms, particularly bromine and iodine, are known to be rather challenging when it comes to the prediction of their chemical shifts by quantum methods, due to relativistic effects. In this paper, we have applied the state-of-the-art four-component relativistic density functional theory for the prediction of such NMR properties and compared the performance with two-component and nonrelativistic methods. Our results highlight the necessity to include relativistic corrections within a four-component description for the most accurate prediction of the NMR properties of halogenated organic substances. PMID:26541625

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

    International Nuclear Information System (INIS)

    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 (φ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ1 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

  16. 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.

  17. Using Neural Networks for 13C NMR Chemical Shift Prediction-Comparison with Traditional Methods

    Science.gov (United States)

    Meiler, Jens; Maier, Walter; Will, Martin; Meusinger, Reinhard

    2002-08-01

    Interpretation of 13C chemical shifts is essential for structure elucidation of organic molecules by NMR. In this article, we present an improved neural network approach and compare its performance to that of commonly used approaches. Specifically, our recently proposed neural network ( J. Chem. Inf. Comput. Sci. 2000, 40, 1169-1176) is improved by introducing an extended hybrid numerical description of the carbon atom environment, resulting in a standard deviation (std. dev.) of 2.4 ppm for an independent test data set of ˜42,500 carbons. Thus, this neural network allows fast and accurate 13C NMR chemical shift prediction without the necessity of access to molecule or fragment databases. For an unbiased test dataset containing 100 organic structures the accuracy of the improved neural network was compared to that of a prediction method based on the HOSE code ( hierarchically ordered spherical description of environment) using S PECI NFO. The results show the neural network predictions to be of quality (std. dev.=2.7 ppm) comparable to that of the HOSE code prediction (std. dev.=2.6 ppm). Further we compare the neural network predictions to those of a wide variety of other 13C chemical shift prediction tools including incremental methods (C HEMD RAW, S PECT OOL), quantum chemical calculation (G AUSSIAN, C OSMOS), and HOSE code fragment-based prediction (S PECI NFO, ACD/CNMR, P REDICTI T NMR) for the 47 13C-NMR shifts of Taxol, a natural product including many structural features of organic substances. The smallest standard deviations were achieved here with the neural network (1.3 ppm) and S PECI NFO (1.0 ppm).

  18. Relationship between electrophilicity index, Hammett constant and nucleus-independent chemical shift

    Indian Academy of Sciences (India)

    M Elango; R Parthasarathi; G Karthik Narayanan; A Md Sabeelullah; U Sarkar; N S Venkatasubramaniyan; V Subramanian; P K Chattaraj

    2005-01-01

    Inter-relationships between the electrophilicity index (), Hammett constant (ó) and nucleusindependent chemical shift (NICS (1) - NICS value one å ngstrom above the ring centre) have been investigated for a series of meta- and para-substituted benzoic acids. Good linear relationships between Hammett constant vs electrophilicity and Hammett constant vs NICS (1) values have been observed. However, the variation of NICS (1) against shows only a low correlation coefficient.

  19. Chemical shifts and EXAFS in some rare-earth metals and compounds

    International Nuclear Information System (INIS)

    The positions of the Lsub(111) absorption edge and accompanying Kossel and EXAFS oscillations of terbium, dysprosium and holmium in metals and compounds (acetate, carbonate, chloride, fluoride, nitrate, oxalate, oxide, phosphate and sulphate) have been measured. The chemical shifts of the main edge range from about 1 eV to about 10 eV and the EXAFS are observed up to about 150 eV. (author)

  20. Automated prediction of 15N, 13Cα, 13Cβ and 13C' chemical shifts in proteins using a density functional database

    International Nuclear Information System (INIS)

    A database of peptide chemical shifts, computed at the density functional level, has been used to develop an algorithm for prediction of 15N and 13C shifts in proteins from their structure; the method is incorporated into a program called SHIFTS (version 4.0). The database was built from the calculated chemical shift patterns of 1335 peptides whose backbone torsion angles are limited to areas of the Ramachandran map around helical and sheet configurations. For each tripeptide in these regions of regular secondary structure (which constitute about 40% of residues in globular proteins) SHIFTS also consults the database for information about sidechain torsion angle effects for the residue of interest and for the preceding residue, and estimates hydrogen bonding effects through an empirical formula that is also based on density functional calculations on peptides. The program optionally searches for alternate side-chain torsion angles that could significantly improve agreement between calculated and observed shifts. The application of the program on 20 proteins shows good consistency with experimental data, with correlation coefficients of 0.92, 0.98, 0.99 and 0.90 and r.m.s. deviations of 1.94, 0.97, 1.05, and 1.08 ppm for 15N, 13Cα, 13Cβ and 13C', respectively. Reference shifts fit to protein data are in good agreement with 'random-coil' values derived from experimental measurements on peptides. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement

  1. On the bathochromic shift of the absorption by astaxanthin in crustacyanin: a quantum chemical study

    Science.gov (United States)

    Durbeej, Bo; Eriksson, Leif A.

    2003-06-01

    The structural origin of the bathochromic shift assumed by the electronic absorption spectrum of protein-bound astaxanthin, the carotenoid that upon binding to crustacyanin is responsible for the blue colouration of lobster shell, is investigated by means of quantum chemical methods. The calculations suggest that the bathochromic shift is largely due to one of the astaxanthin C4 keto groups being hydrogen-bonded to a histidine residue of the surrounding protein, and that the effect of this histidine is directly dependent on its protonation state. Out of the different methodologies (CIS, TD-DFT, and ZINDO/S) employed to calculate wavelengths of maximum absorption, the best agreement with experimental data is obtained using the semiempirical ZINDO/S method.

  2. 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.

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

    International Nuclear Information System (INIS)

    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 13Cβ 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 13Cβ atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ15N, δ13C', δ13Cα, δ13Cβ, δ1Hα and δ1HN, 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.

  4. Simulations of Xe-129 NMR chemical shift of atomic xenon dissolved in liquid benzene

    Czech Academy of Sciences Publication Activity Database

    Standara, Stanislav; Kulhánek, P.; Marek, R.; Horníček, Jan; Bouř, Petr; Straka, Michal

    2011-01-01

    Roč. 129, 3/5 (2011), s. 677-684. ISSN 1432-881X R&D Projects: GA ČR GA203/09/2037; GA ČR GAP208/11/0105 Grant ostatní: AV ČR(CZ) M200550902; European Reintegration Grant(XE) 230955; European Community(XE) 205872 Institutional research plan: CEZ:AV0Z40550506 Keywords : Xe-129 NMR chemical shift * dynamical averaging * density functional theory * Breit-Pauli perturbation theory * relativistic effects Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.162, year: 2011

  5. Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition

    Science.gov (United States)

    Grodzka, P.; Facemire, B.

    1977-01-01

    Three investigations conducted aboard Skylab IV and Apollo-Soyuz involved phenomena that are of interest to the biochemistry community. The formaldehyde clock reaction and the equilibrium shift reaction experiments conducted aboard Apollo Soyuz demonstrate the effect of low-g foams or air/liquid dispersions on reaction rate and chemical equilibrium. The electrodeposition reaction experiment conducted aboard Skylab IV demonstrate the effect of a low-g environment on an electrochemical displacement reaction. The implications of the three space experiments for various applications are considered.

  6. 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.

  7. Model analysis of influences of the high-temperature reactor on location shifting in chemical industry

    International Nuclear Information System (INIS)

    An analysis is presented of the influences of High-Temperature Reactor on probable location shifting of big chemical plants, in the future. This is done by a spatial location model, that includes an investigation on 116 industrial locations within the first six countries of Common Market. The results of a computerized program show differences in location qualities when furnished either with traditional or with nuclear energy systems. In addition to location factor energy some other important factors, as subventions, taxes, labour, and transport costs are analysed, and their influence on industrial location is quantified. (orig.)

  8. NMR Chemical Shift Ranges of Urine Metabolites in Various Organic Solvents.

    Science.gov (United States)

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

    Signal stability is essential for reliable multivariate data analysis. Urine samples show strong variance in signal positions due to inter patient differences. Here we study the exchange of the solvent of a defined urine matrix and how it affects signal and integral stability of the urinary metabolites by NMR spectroscopy. The exchange solvents were methanol, acetonitrile, dimethyl sulfoxide, chloroform, acetone, dichloromethane, and dimethyl formamide. Some of these solvents showed promising results with a single batch of urine. To evaluate further differences between urine samples, various acid, base, and salt solutions were added in a defined way mimicking to some extent inter human differences. Corresponding chemical shift changes were monitored. PMID:27598217

  9. Association between airborne PM2.5 chemical constituents and birth weight—implication of buffer exposure assignment

    International Nuclear Information System (INIS)

    Several papers reported associations between airborne fine particulate matter (PM2.5) and birth weight, though findings are inconsistent across studies. Conflicting results might be due to (1) different PM2.5 chemical structure across locations, and (2) various exposure assignment methods across studies even among the studies that use ambient monitors to assess exposure. We investigated associations between birth weight and PM2.5 chemical constituents, considering issues arising from choice of buffer size (i.e. distance between residence and pollution monitor). We estimated the association between each pollutant and term birth weight applying buffers of 5 to 30 km in Connecticut (2000–2006), in the New England region of the USA. We also investigated the implication of the choice of buffer size in relation to population characteristics, such as socioeconomic status. Results indicate that some PM2.5 chemical constituents, such as nitrate, are associated with lower birth weight and appear more harmful than other constituents. However, associations vary with buffer size and the implications of different buffer sizes may differ by pollutant. A homogeneous pollutant level within a certain distance is a common assumption in many environmental epidemiology studies, but the validity of this assumption may vary by pollutant. Furthermore, we found that areas close to monitors reflect more minority and lower socio-economic populations, which implies that different exposure approaches may result in different types of study populations. Our findings demonstrate that choosing an exposure method involves key tradeoffs of the impacts of exposure misclassification, sample size, and population characteristics. (letter)

  10. 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...

  11. Qualitative Study of Substituent Effects on NMR 15N and 17O Chemical Shifts

    Science.gov (United States)

    Contreras, Rubén H.; Llorente, Tomás; Pagola, Gabriel I.; Bustamante, Manuel G.; Pasqualini, Enrique E.; Melo, Juan I.; Tormena, Cláudio F.

    2009-08-01

    A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-β substituent effects on both 15N and 17O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and σ-hyperconjugative interactions in saturated multicyclic compounds.

  12. Qualitative study of substituent effects on NMR (15)N and (17)O chemical shifts.

    Science.gov (United States)

    Contreras, Rubén H; Llorente, Tomás; Pagola, Gabriel I; Bustamante, Manuel G; Pasqualini, Enrique E; Melo, Juan I; Tormena, Cláudio F

    2009-09-10

    A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-beta substituent effects on both (15)N and (17)O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and sigma-hyperconjugative interactions in saturated multicyclic compounds. PMID:19685922

  13. 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

    differences are due to different conformational behavior of the OH and OCH3 groups; while the ortho-disubstituted OH group remains planar in polyphenols due to hydrogen bonding and conjugative stabilization, the steric congestion in ortho-disubstituted anisoles outweighs the conjugative effects and forces the......Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2) to...... 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...

  14. Water-fat imaging and general chemical shift imaging with spectrum modeling

    Science.gov (United States)

    An, Li

    Water-fat chemical shift imaging (CSI) has been an active research area in magnetic resonance imaging (MRI) since the early 1980's. There are two main reasons for water- fat imaging. First, water-fat imaging can serve as a fat- suppression method. Removing the usually bright fatty signals not only extends the useful dynamic range of an image, but also allows better visualization of lesions or injected contrast, and removes chemical shift artifacts, which may contribute to improved diagnosis. Second, quantification of water and fat provides useful chemical information for characterizing tissues such as bone marrow, liver, and adrenal masses. A milestone in water- fat imaging is the Dixon method that can produce separate water and fat images with only two data acquisitions. In practice, however, the Dixon method is not always successful due to field inhomogeneity problems. In recent years, many variations of the Dixon method have been proposed to overcome the field inhomogeneity problem. In general, these methods can at best separate water and fat without identifying the two because the water and fat magnetization vectors are sampled symmetrically, only parallel and anti-parallel. Furthermore, these methods usually depend on two-dimensional phase unwrapping which itself is sensitive to noise and artifacts, and becomes unreliable when the images have disconnected tissues in the field-of-view (FOV). We will first introduce the basic principles of nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) in chapter 1, and briefly review the existing water-fat imaging techniques in chapter 2. In chapter 3, we will introduce a new method for water-fat imaging. With three image acquisitions, a general direct phase encoding (DPE) of the chemical shift information is achieved, which allows an unambiguous determination of water and fat on a pixel by pixel basis. Details of specific implementations and noise performance will be discussed. Representative results

  15. Chemical potential shift in organic field-effect transistors identified by soft X-ray operando nano-spectroscopy

    Science.gov (United States)

    Nagamura, Naoka; Kitada, Yuta; Tsurumi, Junto; Matsui, Hiroyuki; Horiba, Koji; Honma, Itaru; Takeya, Jun; Oshima, Masaharu

    2015-06-01

    A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO2 (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying -30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping.

  16. Chemical potential shift in organic field-effect transistors identified by soft X-ray operando nano-spectroscopy

    International Nuclear Information System (INIS)

    A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO2 (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying −30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping

  17. Chemical potential shift in organic field-effect transistors identified by soft X-ray operando nano-spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Nagamura, Naoka, E-mail: NAGAMURA.Naoka@nims.go.jp; Kitada, Yuta; Honma, Itaru [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Tsurumi, Junto; Matsui, Hiroyuki; Takeya, Jun [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561 (Japan); Horiba, Koji [Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Oshima, Masaharu [Synchrotron Radiation Research Organization, The University of Tokyo, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2015-06-22

    A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO{sub 2} (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying −30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping.

  18. Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Bermel, Wolfgang [Bruker BioSpin GmbH (Germany); Bruix, Marta [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain); Felli, Isabella C., E-mail: felli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Kumar, M.V. Vasantha [University of Florence, Magnetic Resonance Center (Italy); Pierattelli, Roberta, E-mail: pierattelli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Serrano, Soraya [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain)

    2013-03-15

    Intrinsically disordered proteins (IDPs) have recently attracted the attention of the scientific community challenging the well accepted structure-function paradigm. In the characterization of the dynamic features of proteins nuclear magnetic resonance spectroscopy (NMR) is a strategic tool of investigation. However the peculiar properties of IDPs, with the lack of a unique 3D structure and their high flexibility, have a strong impact on NMR observables (low chemical shift dispersion, efficient solvent exchange broadening) and thus on the quality of NMR spectra. Key aspects to be considered in the design of new NMR experiments optimized for the study of IDPs are discussed. A new experiment, based on direct detection of {sup 13}C{sup {alpha}}, is proposed.

  19. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    Energy Technology Data Exchange (ETDEWEB)

    Sweany, M; Bernstein, A; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, S M

    2011-09-21

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 {+-} 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 {+-} 0.03 for Carbostyril-124, and 1.20 {+-} 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modeled, resulting in a simulated gain within 9% of the experimental gain at 1 ppm concentration. Finally, we report an increase in neutron detection performance of a large-scale (3.5 kL) gadolinium-doped water Cherenkov detector at a 4-Methylumbelliferone concentration of 1 ppm.

  20. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    International Nuclear Information System (INIS)

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultraviolet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as 1.88±0.02 for 4-Methylumbelliferone, stable within 0.5% over 50 days, 1.37±0.03 for Carbostyril-124, and 1.20±0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modeled, resulting in a simulated gain within 9% of the experimental gain at 1 ppm concentration. Finally, we report an increase in neutron detection performance of a large-scale (3.5 kL) gadolinium-doped water Cherenkov detector at a 4-Methylumbelliferone concentration of 1 ppm.

  1. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    CERN Document Server

    Sweany, M; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, M

    2011-01-01

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 $\\pm$ 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 $\\pm$ 0.03 for Carbostyril-124, and 1.20 $\\pm$ 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modele...

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

    International Nuclear Information System (INIS)

    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.)

  3. A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory.

    Science.gov (United States)

    Shaghaghi, Hoora; Ebrahimi, Hossein Pasha; Fathi, Fariba; Bahrami Panah, Niloufar; Jalali-Heravi, Mehdi; Tafazzoli, Mohsen

    2016-05-30

    The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of (13) C(α) chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of (13) C(β) , and (1) H(α) chemical shifts nor on the variation of absolute deviation of (13) C(α) chemical shifts relative to ψ dihedral angle. The (13) C(α) absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of highly accurate calculations, priori knowledge of protein structure and structural refinement. Comparison of Full-DFT and ONIOM(DFT:HF) approaches illustrates that the trend of (13) C(α) ADCC plots are independent of computational method but not of basis set valence shell type. © 2016 Wiley Periodicals, Inc. PMID:26940760

  4. Fragment-based (13)C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods.

    Science.gov (United States)

    Hartman, Joshua D; Monaco, Stephen; Schatschneider, Bohdan; Beran, Gregory J O

    2015-09-14

    We assess the quality of fragment-based ab initio isotropic (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 (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. PMID:26374002

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

    International Nuclear Information System (INIS)

    We assess the quality of fragment-based ab initio isotropic 13C 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 13C 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

  6. Chemical shifts of the X-ray L3 absorption edge of europium in its trivalent halides

    International Nuclear Information System (INIS)

    Position of the Eu-L3 absorption edge has been studied in pure metal and in its trivalent halides, EuF3, EuCl3, EuBr3, and EuI3, employing a simple X-ray spectrometer with an LiF single crystal as the analyser. A linear relationship was established between the chemical shift and the effective charge on the absorbing rare earth atom. The chemical shifts have also been correlated to Moessbauer isomer shifts. The results have been discussed in terms of nature of chemical bonding, effective atomic charge on the absorbing atom and some other parameters relevant to the immediate local environment of the absorbing atom. (author)

  7. Attainable entanglement of unitary transformed thermal states in liquid-state nuclear magnetic resonance with the chemical shift

    CERN Document Server

    Ota, Y; Ohba, I; Yoshida, N; Mikami, Shuji; Ohba, Ichiro; Ota, Yukihiro; Yoshida, Noriyuki

    2006-01-01

    Recently, Yu, Brown, and Chuang [Phys. Rev. A {\\bf 71}, 032341 (2005)] investigated the entanglement attainable from unitary transformed thermal states in liquid-state nuclear magnetic resonance (NMR). Their research gave an insight into the role of the entanglement in a liquid-state NMR quantum computer. Moreover, they attempted to reveal the role of mixed-state entanglement in quantum computing. However, they assumed that the Zeeman energy of each nuclear spin which corresponds to a qubit takes a common value for all; there is no chemical shift. In this paper, we research a model with the chemical shifts and analytically derive the physical parameter region where unitary transformed thermal states are entangled, by the positive partial transposition (PPT) criterion with respect to any bipartition. We examine the effect of the chemical shifts on the boundary between the separability and the nonseparability, and find it is negligible.

  8. Shifts in microbial and chemical patterns within the marine sponge Aplysina aerophoba during a disease outbreak.

    Science.gov (United States)

    Webster, Nicole S; Xavier, Joana R; Freckelton, Marnie; Motti, Cherie A; Cobb, Rose

    2008-12-01

    The microbial community composition in affected and unaffected portions of diseased sponges and healthy control sponges of Aplysina aerophoba was assessed to ascertain the role of microbes in the disease process. Sponge secondary metabolites were also examined to assess chemical shifts in response to infection. The microbial profile and aplysinimine levels in unaffected tissue near the lesions closely reflected those of healthy sponge tissue, indicating a highly localized disease process. DGGE detected multiple sequences that were exclusively present in diseased sponges. Most notably, a Deltaproteobacteria sequence with high homology to a coral black band disease strain was detected in all sponge lesions and was absent from all healthy and unaffected regions of diseased sponges. Other potential pathogens identified by DGGE include an environmental Cytophaga strain and a novel Epsilonproteobacteria strain with no known close relatives. The disease process also caused a major shift in prokaryote community structure at a very high taxonomic level. Using 16S rRNA gene sequence analysis, only the diseased sponges were found to contain sequences belonging to the Epsilonproteobacteria and Firmicutes, and there was a much greater number of Bacteroidetes sequences within the diseased sponges. In contrast, only the healthy sponges contained sequences corresponding to the cyanobacteria and 'OP1' candidate division, and the healthy sponges were dominated by Chloroflexi and Gammaproteobacteria sequences. Overall bacterial diversity was found to be considerably higher in diseased sponges than in healthy sponges. These results provide a platform for future cultivation-based experiments to isolate the putative pathogens from A. aerophoba and perform re-infection trials to define the disease aetiology. PMID:18783385

  9. Nuclear magnetic resonance shielding constants and chemical shifts in linear 199Hg compounds: a comparison of three relativistic computational methods.

    Science.gov (United States)

    Arcisauskaite, Vaida; Melo, Juan I; Hemmingsen, Lars; Sauer, Stephan P A

    2011-07-28

    We investigate the importance of relativistic effects on NMR shielding constants and chemical shifts of linear HgL(2) (L = Cl, Br, I, CH(3)) compounds using three different relativistic methods: the fully relativistic four-component approach and the two-component approximations, linear response elimination of small component (LR-ESC) and zeroth-order regular approximation (ZORA). LR-ESC reproduces successfully the four-component results for the C shielding constant in Hg(CH(3))(2) within 6 ppm, but fails to reproduce the Hg shielding constants and chemical shifts. The latter is mainly due to an underestimation of the change in spin-orbit contribution. Even though ZORA underestimates the absolute Hg NMR shielding constants by ∼2100 ppm, the differences between Hg chemical shift values obtained using ZORA and the four-component approach without spin-density contribution to the exchange-correlation (XC) kernel are less than 60 ppm for all compounds using three different functionals, BP86, B3LYP, and PBE0. However, larger deviations (up to 366 ppm) occur for Hg chemical shifts in HgBr(2) and HgI(2) when ZORA results are compared with four-component calculations with non-collinear spin-density contribution to the XC kernel. For the ZORA calculations it is necessary to use large basis sets (QZ4P) and the TZ2P basis set may give errors of ∼500 ppm for the Hg chemical shifts, despite deceivingly good agreement with experimental data. A Gaussian nucleus model for the Coulomb potential reduces the Hg shielding constants by ∼100-500 ppm and the Hg chemical shifts by 1-143 ppm compared to the point nucleus model depending on the atomic number Z of the coordinating atom and the level of theory. The effect on the shielding constants of the lighter nuclei (C, Cl, Br, I) is, however, negligible. PMID:21806118

  10. Comparison of Computed Tomography Histogram Analysis and Chemical-Shift Magnetic Resonance Imaging for Adrenal Mass Characterization

    International Nuclear Information System (INIS)

    Background: Computed tomography (CT) histogram analysis and chemical-shift magnetic resonance imaging (MRI) are currently used modalities for adrenal mass characterization. However, it is not yet clear which modality can be regarded as most sensitive in terms of adrenal mass characterization. Purpose: To prospectively compare CT histogram analysis and chemical-shift MRI in the characterization of adrenal masses. Material and Methods: Between May 2007 and November 2008, 93 patients (45 males, 48 females; mean age 56.7 years, range 22-85 years) with 109 adrenal masses prospectively underwent both unenhanced CT and chemical-shift MRI examinations. These masses consisted of 67 adenomas and 42 metastases. Histogram analysis was applied with a circular region of interest (ROI) that recorded mean attenuation, total number of pixels, number of negative pixels, and the percentage of negative pixels on unenhanced CT images for each adrenal mass. In the CT histogram analysis, a 10% negative pixel threshold for unenhanced CT was calculated. In chemical-shift MRI, signal intensity drop between in-phase and opposed-phase images was quantitatively calculated so that adrenal-to-spleen chemical-shift ratios and adrenal signal intensity indexes were determined for each of the adrenal masses. A mass was regarded as an adenoma if it contained more than 10% negative pixels by CT histogram analysis, showed an adrenal-to-spleen chemical-shift ratio of less than 0.71, and had an adrenal signal intensity index of more than 16.5% by chemical-shift MRI. The results were compared to reveal which method was most sensitive in the diagnosis of adrenal masses and whether or not a correlation exists between these two modalities. Final diagnoses were based on imaging follow-up of minimum 6 months, biopsy, surgery, and adrenal washout study. Results: On unenhanced CT examinations, all of the 67 adenomas and 21 out of 42 metastases exhibited negative pixels. None of the metastases showed more than 10

  11. Comparison of Computed Tomography Histogram Analysis and Chemical-Shift Magnetic Resonance Imaging for Adrenal Mass Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Halefoglu, A.M.; Yasar, A.; Bas, N.; Ozel, A.; Erturk, S.M.; Basak, M. (Dept. of Radiology, Sisli Etfal Training and Research Hospital, Sisli, Istanbul (Turkey))

    2009-11-15

    Background: Computed tomography (CT) histogram analysis and chemical-shift magnetic resonance imaging (MRI) are currently used modalities for adrenal mass characterization. However, it is not yet clear which modality can be regarded as most sensitive in terms of adrenal mass characterization. Purpose: To prospectively compare CT histogram analysis and chemical-shift MRI in the characterization of adrenal masses. Material and Methods: Between May 2007 and November 2008, 93 patients (45 males, 48 females; mean age 56.7 years, range 22-85 years) with 109 adrenal masses prospectively underwent both unenhanced CT and chemical-shift MRI examinations. These masses consisted of 67 adenomas and 42 metastases. Histogram analysis was applied with a circular region of interest (ROI) that recorded mean attenuation, total number of pixels, number of negative pixels, and the percentage of negative pixels on unenhanced CT images for each adrenal mass. In the CT histogram analysis, a 10% negative pixel threshold for unenhanced CT was calculated. In chemical-shift MRI, signal intensity drop between in-phase and opposed-phase images was quantitatively calculated so that adrenal-to-spleen chemical-shift ratios and adrenal signal intensity indexes were determined for each of the adrenal masses. A mass was regarded as an adenoma if it contained more than 10% negative pixels by CT histogram analysis, showed an adrenal-to-spleen chemical-shift ratio of less than 0.71, and had an adrenal signal intensity index of more than 16.5% by chemical-shift MRI. The results were compared to reveal which method was most sensitive in the diagnosis of adrenal masses and whether or not a correlation exists between these two modalities. Final diagnoses were based on imaging follow-up of minimum 6 months, biopsy, surgery, and adrenal washout study. Results: On unenhanced CT examinations, all of the 67 adenomas and 21 out of 42 metastases exhibited negative pixels. None of the metastases showed more than 10

  12. Chemical shift imaging and localised magnetic resonance spectroscopy in full-term asphyxiated neonates

    International Nuclear Information System (INIS)

    Diagnosis of brain lesions after birth anoxia-ischemia is essential for appropriate management. Clinical evaluation is not sufficient. MRI has been proven to provide useful information. To compare abnormalities observed with MRI, including diffusion-weighted imaging (DWI), localised magnetic resonance spectroscopy (MRS) and chemical shift imaging (CSI) and correlate these findings with the clinical outcome. Fourteen full-term neonates with birth asphyxia were studied. MRI, MRS and CSI were performed within the first 4 days of life. Lesions observed with DWI were correlated with outcome, but the apparent diffusion coefficient (ADC) did improve diagnostic confidence. The mean value of Lac/Cr for the neonates with a favourable outcome was statically lower than for those who died (0.22 vs 1.04; P = 0.01). The same results were observed for the Lac/NAA ratio (0.21 vs 1.23; P = 0.01). Data obtained with localised MRS and CSI were correlated for the ratio N-acetyl-aspartate/choline, but not for the other metabolites. No correlation was found between the ADC values and the metabolite ratios. Combination of these techniques could be helpful in our understanding of the physiopathological events occurring in neonates with asphyxia. (orig.)

  13. Repeatability of long and short echo-time in vivo proton chemical-shift imaging

    International Nuclear Information System (INIS)

    We carried out long (145 ms) and short (25 ms) echo time spectroscopic imaging of the brain (chemical-shift imaging, CSI) on two occasions 1 week apart on 15 healthy individuals. We found coefficients of variation (CVs) generally in the range 10-25% for long and 15-30% for short echo-time measurements. The CVs of metabolite ratios were higher by about 5-10%. Limits of agreement (defined as mean±2 SD of the week 1-week 2 differences) were wider at the shorter echo time. The modest repeatability may be due in part to the difficulty of repositioning spectroscopic voxels at a scale of 1 mm. The generally higher CVs and wider limits of agreement at TE25 ms suggest that the increased spectral complexity more than offsets the theoretical advantage of increased signal at short echo-times. Analysis of variance general linear modelling of metabolites and metabolite ratios showed that, in general, the subject, region of the brain and hemisphere were more important than the occasion in explaining the variability of results. Unless information on short-T2 metabolites is specifically required, better results can probably be achieved with longer echo-times. The magnitude of the CVs needs to be taken into account in the calculation of sample size for cross-sectional or linear studies. (orig.)

  14. Clinical evaluation of the cerebral energy metabolism with 31P chemical shift imaging in neurosurgical disorders

    International Nuclear Information System (INIS)

    Cerebral energy metabolism was evaluated by means of 31P chemical shift imaging (CSI) using the 2.0 T whole-body MRIS system. 31P CSI was carried out by means of Spectroscopic Imaging by Dephasing Amplitude Changing method, four-dimensional CSI, and three-dimensional CSI. Twenty three patients with cerebral infarction and 21 patients with hypertensive intracerebral hemorrhage were examined. In cerebral infarction, an acute infarction was seen as a low-signal area in the PCr and ATP images and as a high-signal area in the Pi image. A subacute and chronic infarction was seen as a low-signal area in all the images -- 31P, PCr, ATP, Pi, PDE and PME. Intracellular acidosis was noticed within 2 days after onset. The intracellular pH became alkaline at the subacute and chronic stages of infarction. The chronological changes in the phosphorus metabolites were evaluated by means of these methods. In hypertensive intracerebral hemorrhage, hematoma and perifocal edema in the acute stage were seen as low-signal areas in the 31P, PCr, and ATP images, and as high-signal areas in the Pi image. In the chronic stage, a hematoma was seen as a low-signal area in all the images -- 31P, PCr, ATP and Pi. 31P CSI is thus a practical tool for studying phosphate metabolites clinically. Changes in the phosphorus metabolism relative to the anatomy of interest were detected by the use of these methods. (author)

  15. Correlation of 1H NMR Chemical Shift for Aqueous Solutions by Statistical Associating Fluid Theory Association Model

    Institute of Scientific and Technical Information of China (English)

    许波; 李浩然; 王从敏; 许映杰; 韩世钧

    2005-01-01

    1H NMR chemical shifts of binary aqueous mixtures of acylamide, alcohol, dimethyl sulphoxide (DMSO), and acetone are correlated by statistical associating fluid theory (SAFT) association model. The comparison between SAFT association model and Wilson equation shows that the former is better for dealing with aqueous solutions. Finally, the specialties of both models are discussed.

  16. 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; Spielman, D.M.

    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...... concentration error (<15%). Magn Reson Med 44:10-18, 2000....

  17. 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.

  18. {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.)

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

    International Nuclear Information System (INIS)

    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)

  20. 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.

  1. Anomalous chemical shifts in X-ray photoelectron spectra of sulfur-containing compounds of silver (I) and (II)

    International Nuclear Information System (INIS)

    Highlights: • Ag 3d5/2 binding energy for Ag(II)SO4 is as large as 370.1 eV. • This is the largest value ever measured for a silver (II) compound. • Large shift is connected with the extreme oxidizing nature of Ag(II) species. • Ag(I)2S2O7 exhibits both positive and negative shifts with respect to metallic Ag. • Two distinct Ag(I) sites are responsible for large BE difference of 3.6 eV. - Abstract: Anomalous chemical shifts, i.e. cases when binding energy decreases with the increase of the oxidation state, have been well-documented for selected compounds of silver, and well understood based on analysis of initial- and final-state effects in the XPS spectra. Here we report two examples of even more exotic behaviour of chemical shifts for two silver compounds. The first one is Ag2S2O7 which exhibits both positive and negative substantial shifts with respect to metallic Ag for two distinct Ag(I) sites in its crystal structure, which differ by as much as 3.6 eV. Another is AgSO4, a rare example of oxo silver (II) salt, which exhibits “normal” chemical shift but the Ag 3d5/2 binding energy takes the largest value measured for a silver (II) compound (370.1 eV). This property is connected predominantly with the extremely strongly oxidizing nature of Ag(II) species

  2. Anomalous chemical shifts in X-ray photoelectron spectra of sulfur-containing compounds of silver (I) and (II)

    Energy Technology Data Exchange (ETDEWEB)

    Grzelak, A. [Faculty of Chemistry, University of Warsaw, Pasteur 1, 02093 Warsaw (Poland); Jaroń, T. [Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland); Mazej, Z. [Department of Inorganic Chemistry and Technology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Michałowski, T. [Faculty of Chemistry, University of Warsaw, Pasteur 1, 02093 Warsaw (Poland); Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland); Szarek, P. [Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland); Grochala, W., E-mail: w.grochala@cent.uw.edu.pl [Faculty of Chemistry, University of Warsaw, Pasteur 1, 02093 Warsaw (Poland); Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland)

    2015-07-15

    Highlights: • Ag 3d{sub 5/2} binding energy for Ag(II)SO{sub 4} is as large as 370.1 eV. • This is the largest value ever measured for a silver (II) compound. • Large shift is connected with the extreme oxidizing nature of Ag(II) species. • Ag(I){sub 2}S{sub 2}O{sub 7} exhibits both positive and negative shifts with respect to metallic Ag. • Two distinct Ag(I) sites are responsible for large BE difference of 3.6 eV. - Abstract: Anomalous chemical shifts, i.e. cases when binding energy decreases with the increase of the oxidation state, have been well-documented for selected compounds of silver, and well understood based on analysis of initial- and final-state effects in the XPS spectra. Here we report two examples of even more exotic behaviour of chemical shifts for two silver compounds. The first one is Ag{sub 2}S{sub 2}O{sub 7} which exhibits both positive and negative substantial shifts with respect to metallic Ag for two distinct Ag(I) sites in its crystal structure, which differ by as much as 3.6 eV. Another is AgSO{sub 4}, a rare example of oxo silver (II) salt, which exhibits “normal” chemical shift but the Ag 3d{sub 5/2} binding energy takes the largest value measured for a silver (II) compound (370.1 eV). This property is connected predominantly with the extremely strongly oxidizing nature of Ag(II) species.

  3. Evaluation of vertebral bone marrow fat content by chemical-shift MRI in osteoporosis

    International Nuclear Information System (INIS)

    To quantitatively evaluate vertebral bone marrow fat content and investigate its association with osteoporosis with chemical-shift magnetic resonance imaging (CS-MRI). Fifty-six female patients (age range 50-65 years) with varying bone mineral densities as documented with dual x-ray absorptiometry (DXA) were prospectively included in the study. According to the DXA results, the patients were grouped as normal bone density, osteopenic, or osteoporotic. In order to calculate fat content, the lumbar region was visualized in the sagittal plane by CS-MRI sequence. ''Region of interest'' (ROI)s were placed within L3 vertebral bodies and air (our reference point) at different time points by different radiologists. Fat content was calculated through ''signal intensity (SI) suppression rate'' and ''SI Index''. The quantitative values were compared statistically with those obtained from DXA examinations. Kruskal-Wallis, and Mann-Whitney U tests were used for comparisons between groups. The reliability of the measurements performed by two radiologists was evaluated with the ''intraclass correlation coefficient''. This study was approved by an institutional review board and all participants provided informed consent to participate in the study. Eighteen subjects with normal bone density (mean T score, 0.39 ± 1.3 [standard deviation]), 20 subjects with osteopenia (mean T score, -1.79 ± 0.38), and 18 subjects with osteoporosis (mean T score, -3 ± 0.5) were determined according to DXA results. The median age was 55.9 (age range 50-64 years) in the normal group, 55.5 (age range 50-64 years) in the osteopenic group, and 55.1 (age range 50-65 years) in the osteoporotic group (p = 0.872). In the CS-MRI examination, the values of ''SI suppression ratio'' and ''SI Index'' (median [min:max]) were calculated by the first and second reader, independently. There was no statistically significant difference between the groups with regard to vertebral bone marrow fat content (p > 0

  4. Predicting 15N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from φ, ψi-1, and χ1torsion angles

    International Nuclear Information System (INIS)

    Empirical shielding surfaces are most commonly used to predict chemical shifts in proteins from known backbone torsion angles, φ and ψ. However, the prediction of 15N chemical shifts using this technique is significantly poorer, compared to that for the other nuclei such as 1Hα, 13Cα, and 13Cβ. In this study, we investigated the effects from the preceding residue and the side-chain geometry, χ1, on 15N chemical shifts by statistical methods. For an amino acid sequence XY, the 15N chemical shift of Y is expressed as a function of the amino acid types of X and Y, as well as the backbone torsion angles, φ and ψi-1. Accordingly, 380 empirical 'Preceding Residue Specific Individual (PRSI)' 15N chemical shift shielding surfaces, representing all the combinations of X and Y (except for Y=Pro), were built and used to predict 15N chemical shift from φ and ψi-1. We further investigated the χ1 effects, which were found to account for differences in 15N chemical shifts by ∼5 ppm for amino acids Val, Ile, Thr, Phe, His, Tyr, and Trp. Taking the χ1 effects into account, the χ1-calibrated PRSI shielding surfaces (XPRSI) were built and used to predict 15N chemical shifts for these amino acids. We demonstrated that 15N chemical shift predictions are significantly improved by incorporating the preceding residue and χ1 effects. The present PRSI and XPRSI shielding surfaces were extensively compared with three recently published programs, SHIFTX (Neal et al., 2003), SHIFTS (Xu and Case, 2001 and 2002), and PROSHIFT (Meiler, 2003) on a set of ten randomly selected proteins. A set of Java programs using XPRSI shielding surfaces to predict 15N chemical shifts in proteins were developed and are freely available for academic users at http://www.pronmr.com or by sending email to one of the authors Yunjun Wang

  5. A Paradigm Shift: Supply Chain Collaboration and Competition in and between Europe’s Chemical Clusters

    OpenAIRE

    Wassenhove, Luk; Lebreton, Baptiste; Letizia, Paolo

    2007-01-01

    textabstractWith the attention of the chemical industry focused on exploiting the low cost feedstocks in the Middle East and the growth markets of Brazil, Russia, India, China and South East Asia, this report provides a timely reminder to policy makers, chemical companies and logistics service providers of the significant opportunities for improving business potential in Europe’s chemical clusters. Europe is still the largest, most sophisticated global market for chemical products, with a wel...

  6. Determination of nuclear distances and chemical-shift anisotropy from 1H MAS NMR sideband patterns of surface OH groups

    Science.gov (United States)

    Fenzke, Dieter; Hunger, Michael; Pfeifer, Harry

    A procedure is described which allows a separate determination of the proton-aluminum distance and of the chemical-shift anisotropy for the bridging OH groups of crystalline molecular sieves from their 'H MAS NMR sideband patterns. For the bridging OH groups which point into the 6-rings of the framework (line "c"), the 1H- 27Al distance could be determined to be 0.237 ± 0.004 and 0.234 ± 0.004 nm for molecular sieves of type H-Y and SAPO-5, respectively. In contrast, for the bridging OH groups of the 12-rings (line "b"), the corresponding distances are equal and distinctly larger, 0.248 ± 0.004 nm. Within the limits of error, the values of the chemical-shift anisotropy are equal (about 19 ± 2 ppm) except for line b of SAPO-5, which exhibits a much smaller value of 14.5 ± 2 ppm.

  7. Hash: a program to accurately predict protein H{sup {alpha}} shifts from neighboring backbone shifts

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Jianyang, E-mail: zengjy@gmail.com [Tsinghua University, Institute for Interdisciplinary Information Sciences (China); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2013-01-15

    Chemical shifts provide not only peak identities for analyzing nuclear magnetic resonance (NMR) data, but also an important source of conformational information for studying protein structures. Current structural studies requiring H{sup {alpha}} chemical shifts suffer from the following limitations. (1) For large proteins, the H{sup {alpha}} chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of C{sup {alpha}} that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict H{sup {alpha}} chemical shifts. Predicting accurate H{sup {alpha}} chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict H{sup {alpha}} chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate H{sup {alpha}} chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins.

  8. Multiple pancreatic metastases from clear cell renal carcinoma: diagnosis with chemical shift magnetic resonance imaging before surgery

    International Nuclear Information System (INIS)

    We present a case in which multiple pancreatic tumours were diagnosed as metastatic clear cell renal carcinomas with chemical shift MRI (CSI) before surgery. Radiologists may be unable to recognize the loss of intensity on CSI macroscopically. We believe that it is useful to make subtraction images and calculate signal intensity on CSI, even if the lesions are multiple metastatic tumours Copyright (2005) Blackwell Publishing Asia Pty Ltd

  9. 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.

  10. Distinguishing between cystic teratomas and endometriomas of the ovary using chemical shift gradient echo magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Ishijima Hideyuki; Ishizaka Hiroshi; Inoue Tomio [Gunma University Hospital, Gunma (Japan). Depts. of Diagnostic Radiaology and Nuclear Medicine

    1996-02-01

    The purpose of this study was to evaluate the efficacy of chemical shift gradient echo magnetic resonance imaging (MRI) in distinguishing between cystic teratomas and endometriomas of the ovary, using a 1.5 T magnet. The study included 22 patients with 31 ovarian lesions (15 cystic teratomas and 16 endometriomas), which showed high signal intensity on T1-weighted spin echo images. Chemical shift gradient echo images with three different echo times (TE = 2.5, 4.5 and 6.5 ms) were obtained in all cases. Indices were calculated on the basis of the signal intensities of lesions on the chemical shift gradient echo images. All endometriomas had signal intensity indices of less than 2.1, while all cystic teratomas had signal intensity indices of 18.1 or greater. It was concluded that the method used in this study presents the following advantages: the acquisition time is short; it needs no special software; and it does not depend on magnetic field homogeneity. 11 refs., 4 figs.

  11. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation

    Indian Academy of Sciences (India)

    D Joseph; A K Yadav; S N Jha; D Bhattacharyya

    2013-11-01

    Mn and Cr K X-ray absorption edges were measured in various compounds containing Mn in Mn2+, Mn3+ and Mn4+ oxidation states and Cr in Cr3+ and Cr6+ oxidation states. Few compounds possess tetrahedral coordination in the 1st shell surrounding the cation while others possess octahedral coordination. Measurements have been carried out at the energy dispersive EXAFS beamline at INDUS-2 Synchrotron Radiation Source at Raja Ramanna Centre for Advanced Technology, Indore. Energy shifts of ∼8–16 eV were observed for Mn K edge in the Mn-compounds while a shift of 13–20 eV was observed for Cr K edge in Cr-compounds compared to values in elementalMn and Cr, respectively. The different chemical shifts observed for 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 Mn and Cr cations in the above compounds.

  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. A First Exploration of Health Impact Assessment of Chemical Exposure: Assigning Weights to Subclinical Effects Based on Animal Studies

    NARCIS (Netherlands)

    Burg, W. ter; Bokkers, B.G.H.; Kroese, E.D.; Schuur, A.G.

    2015-01-01

    ABSTRACT: Health impact assessments (HIA) have become an important tool for applying evidence-based policy. Recently, the concept of HIA has been introduced in the field of chemical substances. Two main issues are encountered, i.e., the focus of risk assessment is deriving safe levels and on first s

  14. A tracked approach for automated NMR assignments in proteins (TATAPRO)

    International Nuclear Information System (INIS)

    A novel automated approach for the sequence specific NMR assignments of 1HN, 13Cα, 13Cβ, 13C'/1Hα and 15N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate 1HN and 15N chemical shifts with those of 13Cα, 13Cβ and 13C'/1Hα. The information derived from such correlations is used to create a 'masterlist' consisting of all possible sets of 1HNi, 15Ni, 13Cαi, 13Cβi, 13C'i/1Hαi, 13Cαi-1, 13Cβi-1 and 13C'i-1/ 1Hαi-1 chemical shifts. On the basis of an extensive statistical analysis of 13Cα and 13Cβ chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the masterlist and also to translate the protein primary sequence into an array called ppsarray. The program then uses the masterlist to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so, each assigned residue is tracked in an array called assigarray, with the two-digit code assigned earlier. The assigarray is then mapped onto the ppsarray for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18-42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the masterlist

  15. 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. PMID:27335085

  16. 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

  17. Polynomial Assignments

    OpenAIRE

    Guillemin, Victor; Sabatini, Silvia; Zara, Catalin

    2013-01-01

    The concept of assignments was introduced in [GGK99] as a method for extracting geometric information about group actions on manifolds from combinatorial data encoded in the infinitesimal orbit-type stratification. In this paper we will answer in the affirmative a question posed in [GGK99] by showing that the equivariant cohomology ring of $M$ is to a large extent determined by this data.

  18. Linear correlation of the barriers to pyramidal inversion of phosphorus with the 31P chemical shifts of acylphosphines

    International Nuclear Information System (INIS)

    The dependence of the inversion barriers (ΔG) of phosphorus compounds directly on a parameter of the inversion center, i.e., the chemical shift of the nucleus (delta31 P) were studied. The possibility of such an approach was justified by the correlation both of ΔG, and of delta31 P for phosphorus compounds with one and the same characteristics (the bond angles and electronegativities of the substituent). The acylphosphines (I-IX) were investigated in the range of variation of ΔG, accessible to dynamic NMR and in a fairly wide range of delta31 P

  19. Gradient-echo in-phase and opposed-phase chemical shift imaging: Role in evaluating bone marrow

    International Nuclear Information System (INIS)

    Chemical shift imaging (CSI) provides valuable information for assessing the bone marrow, while adding little to total examination time. In this article, we review the uses of CSI for evaluating bone marrow abnormalities. CSI can be used for differentiating marrow-replacing lesions from a range of non-marrow-replacing processes, although the sequence is associated with technical limitations and pitfalls. Particularly at 3 T, susceptibility artefacts are prevalent, and optimal technical parameters must be implemented with appropriate choices for echo times

  20. The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis.

    Science.gov (United States)

    Chikayama, Eisuke; Shimbo, Yudai; Komatsu, Keiko; Kikuchi, Jun

    2016-04-14

    NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites. PMID:26963288

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

    Directory of Open Access Journals (Sweden)

    Simone Di Micco

    2013-12-01

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

  2. High resolution spectroscopy and chemical shift imaging of hyperpolarized 129Xe dissolved in the human brain in vivo at 1.5 tesla

    Science.gov (United States)

    Rao, Madhwesha; Stewart, Neil J.; Norquay, Graham; Griffiths, Paul D.

    2016-01-01

    Purpose Upon inhalation, xenon diffuses into the bloodstream and is transported to the brain, where it dissolves in various compartments of the brain. Although up to five chemically distinct peaks have been previously observed in 129Xe rat head spectra, to date only three peaks have been reported in the human head. This study demonstrates high resolution spectroscopy and chemical shift imaging (CSI) of 129Xe dissolved in the human head at 1.5 Tesla. Methods A 129Xe radiofrequency coil was built in‐house and 129Xe gas was polarized using spin‐exchange optical pumping. Following the inhalation of 129Xe gas, NMR spectroscopy was performed with spectral resolution of 0.033 ppm. Two‐dimensional CSI in all three anatomical planes was performed with spectral resolution of 2.1 ppm and voxel size 20 mm × 20 mm. Results Spectra of hyperpolarized 129Xe dissolved in the human head showed five distinct peaks at 188 ppm, 192 ppm, 196 ppm, 200 ppm, and 217 ppm. Assignment of these peaks was consistent with earlier studies. Conclusion High resolution spectroscopy and CSI of hyperpolarized 129Xe dissolved in the human head has been demonstrated. For the first time, five distinct NMR peaks have been observed in 129Xe spectra from the human head in vivo. Magn Reson Med 75:2227–2234, 2016. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:27080441

  3. Anisotropy of the Chemical Shift Tensor for Fluorines in UF6 : Application to the Fluorine Atom Movement Model

    International Nuclear Information System (INIS)

    R. Blinc et al. have made an initial study of polycrystalline uranium hexafluoride using the magnetic resonance of fluorine at 40 Mc/s. The low-temperattire spectrum (t 6 octahedron has one long axis and two short axes, the fluorine atoms are divided among two different types of site. The change in the spectrum with temperature (coalescence of the two lines) suggests movement of the fluorine atoms between the two types of site. By repeating these experiments at 56.4 Mc/s and 94 Mc/s, we have been able to demonstrate the existence of considerable axial anisotropy of the chemical shift tensor (about 650 ppm). The absorption line obtained for a powder in these conditions is complex, and to study it we must envisage a line-shape function f(h), which is the probability that a grain of powder is so orientated that it resonates for the value h of the field. In the absence of movement (low-temperature spectrum) the line-shape function for each of the two lines (corresponding to the two types of site) is of the form obtained for equivalent atoms. It is known that the parameters of chemical shift tensors give information on chemical bond character. We are thus led, for example, to attribute a considerable ionic character (I ≃ 1/2) to the bonds between the uranium and the two most distant fluorine atoms. In the presence of movement the line-shape function is very different, and depends on the type of movement. For UF6, study of the shape of the single line (t > 20°C) in cases where we have anisotropy, shows that the fluorine atoms of the same molecule interchange with each other, each atom remaining in each of the positions for about 5 μsec at 30°C, with an activation energy of about 0.5 eV. (author)

  4. Liver fat quantification: Comparison of dual-echo and triple-echo chemical shift MRI to MR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Satkunasingham, Janakan; Besa, Cecilia [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Bane, Octavia [Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Shah, Ami [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Oliveira, André de; Gilson, Wesley D.; Kannengiesser, Stephan [Siemens AG, Healthcare Sector, Erlangen (Germany); Taouli, Bachir, E-mail: bachir.taouli@mountsinai.org [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States)

    2015-08-15

    Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T{sub 2} corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T{sub 2}{sup *} shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T{sub 2} corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T{sub 2}{sup *} imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T{sub 2}{sup *} and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T{sub 2}{sup *}, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of

  5. Liver fat quantification: Comparison of dual-echo and triple-echo chemical shift MRI to MR spectroscopy

    International Nuclear Information System (INIS)

    Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T2 corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T2* shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T2 corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T2* imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T2* and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T2*, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of liver fat in the clinical environment, even in the presence of

  6. Characterization of interface abruptness and material properties in catalytically grown III-V nanowires: exploiting plasmon chemical shift

    International Nuclear Information System (INIS)

    We have studied the assessment of chemical composition changes in III-V heterostructured semiconductor nanowires (NWs) with nanometric spatial resolution using transmission electron microscopy methods. These materials represent a challenge for conventional spectroscopy techniques due to their high sensitivity to electron beam irradiation. Radiation damage strongly limits the exposure time to a few (5-10) s, which reduces the sensitivity of the traditionally used x-ray spectroscopy. The rather low counting statistics results in significant errors bars for EDS chemical quantification (5-10%) and interface width determination (few nanometers). Plasmon chemical shift is ideal in this situation, as its measurement requires very short exposure times (∼100 ms) and the plasmon peak energy can be measured with high precision (∼20 meV in this work). This high sensitivity allows the detection of subtle changes (1-2%) in composition or even the detection of a small plasmon energy (33 ± 7) meV change along usually assumed pure and homogeneous InAs segments. We have applied this approach to measure interface widths in heterostructure InAs/InP NWs grown using metal catalysts and also to determine the timescale (∼10 s) in which beam irradiation induces material damage in these wires. In particular, we have detected small As concentrations (4.4 ± 0.5)% in the final InP segment close to the Au catalyst, which leads to the conclusion that As diffuses through the metal nanoparticle during growth.

  7. Acetylcholinesterase(AChE)-catalyzed hydrolysis of long-chain thiocholine esters:shift to a new chemical mechanism

    International Nuclear Information System (INIS)

    The kinetic and chemical mechanisms of AChE-catalyzed hydrolysis of short-chain thiocholine esters are relatively well documented. Up to propanoylthiocholine (PrTCh) the chemical mechanism is general acid-base catalysis by the active site catalytic triad. The chemical mechanism for the enzyme-catalyzed butyrylthio-choline(BuTCh) hydrolysis shifts to a parallel mechanism in which general base catalysis by E199 of direct water attack to the carbonyl carbon of the substrate. (Selwood, T., et al. J. Am. Chem. Soc. 1993, 115, 10477-10482) The long chain thiocholine esters such as hexanoylthiocholine (HexTCh), heptanoylthiocholine (HepTCh), and octanoylthiocholine (OcTCh) are hydrolyzed by electric eel acetylcholinesterase (AChE). The kinetic parameters are determined to show that these compounds have a lower Michaelis constant than BuTCh and the pH-Rate profile showed that the mechanism is similar to that of BuTCh hydrolysis. The solvent isotope effect and proton inventory of AChE-catalyzed hydrolysis of HexTCh showed that one proton transfer is involved in the transition state of the acylation stage. The relationship between the dipole moment and the Michaelis constant of the long chain thiocholine esters showed that the dipole moment is the most important factor for the binding of a substrate to the enzyme active site

  8. Acetylcholinesterase(AChE)-catalyzed hydrolysis of long-chain thiocholine esters:shift to a new chemical mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Dai Il; Shin, Young Ju [Donga Univ., Busan (Korea, Republic of); Lee, Eun Seok; Lee, Bong Ho [Hanbat National Univ., Daejon (Korea, Republic of); Moon, Tae Sung; Yoon, Chang No [Korea Institute of Science and Technology, Seoul (Korea, Republic of)

    2003-01-01

    The kinetic and chemical mechanisms of AChE-catalyzed hydrolysis of short-chain thiocholine esters are relatively well documented. Up to propanoylthiocholine (PrTCh) the chemical mechanism is general acid-base catalysis by the active site catalytic triad. The chemical mechanism for the enzyme-catalyzed butyrylthio-choline(BuTCh) hydrolysis shifts to a parallel mechanism in which general base catalysis by E199 of direct water attack to the carbonyl carbon of the substrate. (Selwood, T., et al. J. Am. Chem. Soc. 1993, 115, 10477-10482) The long chain thiocholine esters such as hexanoylthiocholine (HexTCh), heptanoylthiocholine (HepTCh), and octanoylthiocholine (OcTCh) are hydrolyzed by electric eel acetylcholinesterase (AChE). The kinetic parameters are determined to show that these compounds have a lower Michaelis constant than BuTCh and the pH-Rate profile showed that the mechanism is similar to that of BuTCh hydrolysis. The solvent isotope effect and proton inventory of AChE-catalyzed hydrolysis of HexTCh showed that one proton transfer is involved in the transition state of the acylation stage. The relationship between the dipole moment and the Michaelis constant of the long chain thiocholine esters showed that the dipole moment is the most important factor for the binding of a substrate to the enzyme active site.

  9. Automated protein backbone assignment using the projection-decomposition approach

    International Nuclear Information System (INIS)

    Spectral projection experiments by NMR in conjunction with decomposition analysis have been previously introduced for the backbone assignment of proteins; various pulse sequences as well as the behaviour with low signal-to-noise or chemical shift degeneracy have been illustrated. As a guide for routine applications of this combined tool, we provide here a systematic analysis on different types of proteins using welldefined run-time parameters. As a second result of this study, the backbone assignment module SHABBA was extensively rewritten and improved. Calculations on ubiquitin yielded again fully correct and nearly complete backbone and CHβ assignments. For the 128 residue long azurin, missing assignments mostly affect Hα and Hβ. Among the remaining backbone (plus Cβ) nuclei 97.5% could be assigned with 1.0% differences to a reference. Finally, the new SHABBA algorithm was applied to projections recorded for a yeast histone protein domain at room temperature, where the protein is subject to partial unfolding: this leads to unobservable resonances (about a dozen missing signals in a normal 15N-HSQC) and extensive degeneracy among the resonances. From the clearly observable residues, 97.5% of the backbone and CHβresonances could be assigned, of which only 0.8 % showed differences to published shifts. An additional study on the protein MMP20, which exhibits spectral difficulties to an even larger extent, explores the limitations of the approach.

  10. Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

    Science.gov (United States)

    Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko

    2014-04-28

    Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds. PMID:24655374

  11. NMR chemical shift analysis of the conformational transition between the monomer and tetramer of melittin in an aqueous solution.

    Science.gov (United States)

    Miura, Yoshinori

    2016-05-01

    It is known that melittin in an aqueous solution undergoes a conformational transition between the monomer and tetramer by variation in temperature. The transition correlates closely with isomers of the proline residue; monomeric melittin including a trans proline peptide bond (trans-monomer) is involved directly in the transition, whereas monomeric melittin having a cis proline peptide bond (cis-monomer) is virtually not. The transition has been explored by using nuclear magnetic resonance spectroscopy in order to clarify the stability of the tetrameric conformation and the cooperativity of the transition. In the light of temperature dependence of chemical shifts of resonances from the isomeric monomers, we qualitatively estimate the temperature-, salt-, and concentration-dependence of the relative equilibrium populations of the trans-monomer and tetramer, and show that the tetramer has a maximum conformational stability at 30-45 °C and that the transition cooperativity is very low. PMID:26658745

  12. Microscopic structures of ionic liquids 1-ethyl-3-methylimidazolium tetrafluoroborate in water probed by the relative chemical shift

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The relative chemical shifts (△δ) △δwere put forward to investigate the microscopic structure of 1-ethyl-3-methyl-imidazolium tetrafluoroborate (EmimBF4) during the dilution process with water.The concentration-dependent △δ(C2)H-(C4)H,△δ(C2)H-(C5)H and △δ(C4)H-(C5)H were analyzed.The results reveal that the variations of the microscopic structures of three aromatic protons are inconsistent.The strength of the H-bond between water and three aromatic protons follows the order:(C2)H···O > (C4)H···O > (C5)H···O.The concentration-dependent △δ(C6)H-(C7)H and △δ(C6)H-(C8)H indicate the formation of the H-bonds of (Calkyl)H···O is impossible,and more water is located around (C6)H than around (C7)H or (C8)H.The concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H both increase rapidly when xwater > 0.9 or so,suggesting the ionic pairs of EmimBF4 are dissociated rapidly.The turning points of concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H indicate that some physical properties of the EmimBF4/water mixtures also change at the corresponding concentration point.The microscopic structures of EmimBF4 in water could be clearly detected by the relative chemical shifts.

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

    International Nuclear Information System (INIS)

    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

  14. Thickness-Dependent Binding Energy Shift in Few-Layer MoS2 Grown by Chemical Vapor Deposition.

    Science.gov (United States)

    Lin, Yu-Kai; Chen, Ruei-San; Chou, Tsu-Chin; Lee, Yi-Hsin; Chen, Yang-Fang; Chen, Kuei-Hsien; Chen, Li-Chyong

    2016-08-31

    The thickness-dependent surface states of MoS2 thin films grown by the chemical vapor deposition process on the SiO2-Si substrates are investigated by X-ray photoelectron spectroscopy. Raman and high-resolution transmission electron microscopy suggest the thicknesses of MoS2 films to be ranging from 3 to 10 layers. Both the core levels and valence band edges of MoS2 shift downward ∼0.2 eV as the film thickness increases, which can be ascribed to the Fermi level variations resulting from the surface states and bulk defects. Grainy features observed from the atomic force microscopy topographies, and sulfur-vacancy-induced defect states illustrated at the valence band spectra imply the generation of surface states that causes the downward band bending at the n-type MoS2 surface. Bulk defects in thick MoS2 may also influence the Fermi level oppositely compared to the surface states. When Au contacts with our MoS2 thin films, the Fermi level downshifts and the binding energy reduces due to the hole-doping characteristics of Au and easy charge transfer from the surface defect sites of MoS2. The shift of the onset potentials in hydrogen evolution reaction and the evolution of charge-transfer resistances extracted from the impedance measurement also indicate the Fermi level varies with MoS2 film thickness. The tunable Fermi level and the high chemical stability make our MoS2 a potential catalyst. The observed thickness-dependent properties can also be applied to other transition-metal dichalcogenides (TMDs), and facilitates the development in the low-dimensional electronic devices and catalysts. PMID:27488185

  15. Chemical shift measurements of chlorine K X-ray spectra using a high-resolution PIXE system

    International Nuclear Information System (INIS)

    A high-efficiency high-resolution wavelength-dispersive spectrograph with a von-Hamos configuration was developed for chemical state identification of elements in environmental samples using PIXE analysis. To evaluate the performance of this system, chlorine K X-ray spectra for NaCl, NH4Cl and polyvinylchloride (PVC) targets were measured and compared. Also, to study the applicability to environmental mixed samples, mixtures of NaCl and NH4Cl with different mixing ratios were measured. Through observation of Cl Kα1 X-ray from NaCl, the energy resolution of the system was determined to be 1.1 eV. For the NaCl sample, a Kβx line was observed at an energy, which is higher than that of the Kβ main peak by 2 eV, whereas no Kβx emission was observed for the NH4Cl sample. The chemical shift of the Kβ main peak for PVC relative to that for NaCl was about 1.2 eV. For NaCl-NH4Cl mixture targets, the relative intensity of Kβx satellite to the Kβ main line provided an indication of mixing ratio. Energies and relative intensity of Cl Kβ X-ray satellites for NaCl and NH4Cl samples calculated by a simple molecular-orbital method agreed only qualitatively with the experimental results

  16. Development of multicomponent hybrid density functional theory with polarizable continuum model for the analysis of nuclear quantum effect and solvent effect on NMR chemical shift

    International Nuclear Information System (INIS)

    We have developed the multicomponent hybrid density functional theory [MC-(HF+DFT)] method with polarizable continuum model (PCM) for the analysis of molecular properties including both nuclear quantum effect and solvent effect. The chemical shifts and H/D isotope shifts of the picolinic acid N-oxide (PANO) molecule in chloroform and acetonitrile solvents are applied by B3LYP electron exchange-correlation functional for our MC-(HF+DFT) method with PCM (MC-B3LYP/PCM). Our MC-B3LYP/PCM results for PANO are in reasonable agreement with the corresponding experimental chemical shifts and isotope shifts. We further investigated the applicability of our method for acetylacetone in several solvents

  17. An optimized buffer system for NMR-based urinary metabonomics with effective pH control, chemical shift consistency and dilution minimization.

    Science.gov (United States)

    Xiao, Chaoni; Hao, Fuhua; Qin, Xiaorong; Wang, Yulan; Tang, Huiru

    2009-05-01

    NMR-based metabonomics has been widely employed to understand the stressor-induced perturbations to mammalian metabolism. However, inter-sample chemical shift variations for metabolites remain an outstanding problem for effective data mining. In this work, we systematically investigated the effects of pH and ionic strength on the chemical shifts for a mixture of 9 urinary metabolites. We found that the chemical shifts were decreased with the rise of pH but increased with the increase of ionic strength, which probably resulted from the pH- and ionic strength-induced alteration to the ionization equilibrium for the function groups. We also found that the chemical shift variations for most metabolites were reduced to less than 0.004 ppm when the pH was 7.1-7.7 and the salt concentration was less than 0.15 M. Based on subsequent optimization to minimize chemical shift variation, sample dilution and maximize the signal-to-noise ratio, we proposed a new buffer system consisting of K(2)HPO(4) and NaH(2)PO(4) (pH 7.4, 1.5 M) with buffer-urine volume ratio of 1 : 10 for human urinary metabonomic studies; we suggest that the chemical shifts for the proton signals of citrate and aromatic signals of histidine be corrected prior to multivariate data analysis especially when high resolution data were employed. Based on these, an optimized sample preparation method has been developed for NMR-based urinary metabonomic studies. PMID:19381385

  18. High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of dilutable microemulsions. Part 1 - Proof of concept.

    Science.gov (United States)

    Hoffman, Roy E; Darmon, Eliezer; Aserin, Abraham; Garti, Nissim

    2016-02-01

    In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique. PMID:25113928

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

    Czech Academy of Sciences Publication Activity Database

    Czernek, Jiří; Brus, Jiří

    2014-01-01

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

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

    International Nuclear Information System (INIS)

    The effects of heteroatoms Eh(Eh=O, S, Se, Te) on 13C chemical shifts in eleven isological series of R1-Eh-R2 unsaturated compounds are compared. A linear relation between 13C nuclei screening and tEh electronegativity is observed. An assumption is suggested that both likeness of the effects of 6A and 7A group elements on 13C chemical shifts of R1 and R2 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. Shifts in controls on the temporal coherence of throughfall chemical flux in Acadia National Park, Maine, USA

    Science.gov (United States)

    Nelson, Sarah J.; Webster, Katherine E.; Loftin, Cynthia S.; Weathers, Kathleen C.

    2013-01-01

    Major ion and mercury (Hg) inputs to terrestrial ecosystems include both wet and dry deposition (total deposition). Estimating total deposition to sensitive receptor sites is hampered by limited information regarding its spatial heterogeneity and seasonality. We used measurements of throughfall flux, which includes atmospheric inputs to forests and the net effects of canopy leaching or uptake, for ten major ions and Hg collected during 35 time periods in 1999–2005 at over 70 sites within Acadia National Park, Maine to (1) quantify coherence in temporal dynamics of seasonal throughfall deposition and (2) examine controls on these patterns at multiple scales. We quantified temporal coherence as the correlation between all possible site pairs for each solute on a seasonal basis. In the summer growing season and autumn, coherence among pairs of sites with similar vegetation was stronger than for site-pairs that differed in vegetation suggesting that interaction with the canopy and leaching of solutes differed in coniferous, deciduous, mixed, and shrub or open canopy sites. The spatial pattern in throughfall hydrologic inputs across Acadia National Park was more variable during the winter snow season, suggesting that snow re-distribution affects net hydrologic input, which consequently affects chemical flux. Sea-salt corrected calcium concentrations identified a shift in air mass sources from maritime in winter to the continental industrial corridor in summer. Our results suggest that the spatial pattern of throughfall hydrologic flux, dominant seasonal air mass source, and relationship with vegetation in winter differ from the spatial pattern of throughfall flux in these solutes in summer and autumn. The coherence approach applied here made clear the strong influence of spatial heterogeneity in throughfall hydrologic inputs and a maritime air mass source on winter patterns of throughfall flux. By contrast, vegetation type was the most important influence on

  2. Effect of spectra recording conditions on the example of chemical shifts calculation in CMR spectra of 1-pentylbenzoylformate

    OpenAIRE

    Mizyuk, Volodymyr; Shibanov, Volodymyr

    2011-01-01

    The concept of "compatible" and "incompatible" CMR spectra has been introduced. Application of compatibility increments (IC) allows to calculate the chemical shifts of C and C3 atoms of pentyloxyl fragment in 1-pentylbenzoylformate with a sufficiently good accuracy. Введено поняття "сумісних " і "несумісних " ЯМР спектрів. Застосування "інкрементів узгодження " дало можливість з достатньою точністю розрахувати хімічні зсуви атомів С2 і С пентилоксильного фрагменту в 1-пентилбензоїлформіаті....

  3. Cytoplasmic fat detection utilizing chemical shift gradient. Echo MR imaging in cases of clear cell renal cell carcinoma

    International Nuclear Information System (INIS)

    We investigated whether cytoplasmic fat in clear cell renal cell carcinoma (CCC) can be identified by chemical shift gradient-echo magnetic resonance imaging (CSI). CSI was performed for 22 cases of CCC and 30 cases of other renal tumors (including 16 cases of non-CCC), all of which were surgically proven. Signal reduction in out-of-phase images of these tumors was retrospectively evaluated and compared. The signal loss ratio (SLR) was defined and calculated. Fat staining of specimens from 16 tumors was performed and correlated with SLR. SLR was found to be significantly higher in CCC than in non-CCC (p<0.002). There was a significant correlation between the degree of fat staining positively of the specimens and SLR (p<0.01). When signal reduction in out-of-phase images suggested a diagnosis of CCC, a correct diagnosis of this entity was made in the resected renal tumors with a sensitivity, specificity, and accuracy of 82%, 93%, and 88%, respectively. CSI can demonstrate cytoplasmic fat in CCC, which helps to differentiate this entity from other renal tumors. (author)

  4. Quantitative evaluation of norcholesterol scintigraphy, CT attenuation value, and chemical-shift MR imaging for characterizing adrenal adenomas

    International Nuclear Information System (INIS)

    The objective of our study was to evaluate diagnostic ability and features of quantitative indices of three modalities: uptake rate on norcholesterol scintigraphy, computed tomography (CT) attenuation value, and fat suppression on chemical-shift magnetic resonance imaging (MRI) for characterizing adrenal adenomas. Image findings of norcholesterol scintigraphy, CT, and MRI were reviewed for 78 patients with functioning (n=48) or nonfunctioning (n=30) adrenal masses. The norcholesterol uptake rate, attenuation value on unenhanced CT, and suppression on in-phase to opposed-phase MRI were measured for adrenal masses. The norcholesterol uptake rate, CT attenuation value, and MR suppression index showed the sensitivity of 60%, 82%, and 100%, respectively, for functioning adenomas of <2.0 cm, and 96%, 79%, and 67%, respectively, for those of ≥2.0 cm. A statistically significant correlation was observed between size and norcholesterol uptake, and between CT attenuation value and MR suppression index. Regarding norcholesterol uptake, the adenoma-to-contralateral gland ratio was significantly higher in cortisol releasing than in aldosterone-releasing adenomas. The norcholesterol uptake rate was reliable for characterization of adenomas among adrenal masses of ≥2.0 cm. CT attenuation value and MR suppression index were well correlated with each other, and were useful regardless of mass size. (author)

  5. The study on temporal lobe epilepsy with single-voxel proton MR spectroscopy and chemical shift imaging

    International Nuclear Information System (INIS)

    Objective: To investigate the value of different proton MR spectroscopy techniques including single-voxel spectroscopy (SVS) and chemical shift imaging (CSI) in diagnosing patients with temporal lobe epilepsy. Methods: Sixty cases (40 normal, 20 temporal lobe epilepsy) experienced SVS and CSI. The volume of interest (VOI) of SVS was placed over the anterior hippocampus formation (HF) region, including part of the head and body of the HF. The VOI of CSI encompassed bilateral HF and the head, body and tail of HF. The VOI was divided into 5 voxels from anterior to posterior. The metabolite data of both SVS and CSI were obtained and the ratios of NAA/Cr and NAA/(Cho+Cr) were recorded or calculated. Results: The ipsilateral hippocampus to the seizure of TLE patients had lower ratios of NAA/(Cho+Cr) and NAA/Cr, and the differences compared with those of the normal group and contralateral subgroup were statistically significant (F=41.958, P1HMRS study improved the diagnostic yield of MR evaluation in TLE patients. There was a correlation between the ratio of NAA/(Cho+Cr) and the location of HF. Regional variation must be considered when interpreting proton spectra of the HF. (author)

  6. Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm

    International Nuclear Information System (INIS)

    A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra (“good connections”), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra (“bad connections”), and minimizing the number of assigned peaks that have no matching peaks in the other spectra (“edges”). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct

  7. 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.

  8. Phosphorus Chemical Shifts in Drew-Dickerson Dodecamer and DNA Hairpin from MD-DFT Calculations: NMR Based Force Field Validation

    Czech Academy of Sciences Publication Activity Database

    Přecechtělová, J.; Munzarová, M. L.; Vaara, J.; Novák, P.; Dračínský, Martin; Sklenář, V.

    Ireland : University College Dublin, 2012. s. 72-72. [EUROMAR 2012. Magnetic Resonance Conference. 01.07.2012-05.07.2012, Dublin] Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR spectroscopy * phosphorus chemical shift * DFT calculations Subject RIV: CC - Organic Chemistry

  9. Probing the solvent shell with 195Pt chemical shifts: density functional theory molecular dynamics study of Pt(II) and Pt(IV) anionic complexes in aqueous solution.

    Science.gov (United States)

    Truflandier, Lionel A; Autschbach, Jochen

    2010-03-17

    Ab initio molecular dynamics (aiMD) simulations based on density functional theory (DFT) were performed on a set of five anionic platinum complexes in aqueous solution. (195)Pt nuclear magnetic shielding constants were computed with DFT as averages over the aiMD trajectories, using the two-component relativistic zeroth-order regular approximation (ZORA) in order to treat relativistic effects on the Pt shielding tensors. The chemical shifts obtained from the aiMD averages are in good agreement with experimental data. For Pt(II) and Pt(IV) halide complexes we found an intermediate solvent shell interacting with the complexes that causes pronounced solvent effects on the Pt chemical shifts. For these complexes, the magnitude of solvent effects on the Pt shielding constant can be correlated with the surface charge density. For square-planar Pt complexes the aiMD simulations also clearly demonstrate the influence of closely coordinated non-equatorial water molecules on the Pt chemical shift, relating the structure of the solution around the complex to the solvent effects on the metal NMR chemical shift. For the complex [Pt(CN)(4)](2-), the solvent effects on the Pt shielding constant are surprisingly small. PMID:20166712

  10. Enhanced spectral resolution in RNA HCP spectra for measurement of 3JC2'P and 3JC4'P couplings and 31P chemical shift changes upon weak alignment

    International Nuclear Information System (INIS)

    The 'out-and-back' 3D HCP experiment, using gradient- and sensitivity-enhanced detection, provides a convenient method for assignment of the 31P NMR spectra and accurate measurement of the 31P chemical shifts of ribonucleic acids. The 13C resolution in such spectra can be doubled, at the cost of a 50% reduction in sensitivity, by combining 13C evolution during the 13C-31P de- and rephasing periods. The multiple connectivities observable for a given 31P, including correlations to the intranucleotide C5'H2 and C4'H groups, and the C2'H, C3'H and C4'H groups of the preceding nucleotide, permit independent measurements of the 31P shift. The 13C spectrum of these groups is typically crowded for an RNA molecule in isotropic solution and overlap becomes more problematic in media used to achieve partial alignment. However, many of these correlations are resolvable in the combined-evolution HCP spectrum. The difference in 31P chemical shift between isotropic solution and a medium containing liquid crystalline Pf1 provides information on the orientation of phosphate groups. The intensities measured in the 3D HCP spectrum, obtained for an isotropic sample, yield values for the 3JC2'P and 3JC4'P couplings, thereby providing important restraints for the backbone torsion angles ε and β. The experiments are illustrated for a uniformly 13C-enriched, 24-residue stem-loop RNA sequence, and results for the helical stem region show close agreement between observed Δδ(31P) values and those predicted for a model A-form RNA helix when using a uniform 31P CSA tensor. This confirms that Δδ(31P) values can be used directly as restraints in refining nucleic acid structures

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

    Energy Technology Data Exchange (ETDEWEB)

    Kohl, Chad A. [Mayo Clinic, Department of Radiology, Phoenix, AZ (United States); Radiology Ltd., Tucson, AZ (United States); Chivers, F.S.; Lorans, Roxanne; Roberts, Catherine C.; Kransdorf, Mark J. [Mayo Clinic, Department of Radiology, Phoenix, AZ (United States)

    2014-08-15

    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.)

  12. 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)

    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

  13. 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)

    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.)

  14. Exploiting image registration for automated resonance assignment in NMR

    International Nuclear Information System (INIS)

    Analysis of protein NMR data involves the assignment of resonance peaks in a number of multidimensional data sets. To establish resonance assignment a three-dimensional search is used to match a pair of common variables, such as chemical shifts of the same spin system, in different NMR spectra. We show that by displaying the variables to be compared in two-dimensional plots the process can be simplified. Moreover, by utilizing a fast Fourier transform cross-correlation algorithm, more common to the field of image registration or pattern matching, we can automate this process. Here, we use sequential NMR backbone assignment as an example to show that the combination of correlation plots and segmented pattern matching establishes fast backbone assignment in fifteen proteins of varying sizes. For example, the 265-residue RalBP1 protein was 95.4 % correctly assigned in 10 s. The same concept can be applied to any multidimensional NMR data set where analysis comprises the comparison of two variables. This modular and robust approach offers high efficiency with excellent computational scalability and could be easily incorporated into existing assignment software

  15. Reproducibility of 31P MR spectroscopy detection in human liver with two-dimensional chemical shift imaging

    International Nuclear Information System (INIS)

    Objective: To study the reproducibility of relative quantification of phosphorus metabolites in human liver with two-dimensional chemical shift imaging(2D CSI). Methods: Using 2D CSI with FOV 200 mm and average times 40, 500 ml phosphate (NaH2PO4) solution phantom with 0.05 mol/L concentration was scanned 6 times, changing FOV to 280 mm, five healthy volunteers were scanned 6 times under respiration gating. The relative quantification of metabolites was derived from the integral values of peaks on the spectra, and then the errors of metabolite detection were obtained through data analysis. Results: (1) With FOV 200 mm and average times 40, phosphate solution phantom had a good reproducibility with the error less than 5.38%. Under respiration gating, the largest detection error of metabolites within five volunteers was phosphomonoesters (PME) 39.5%, inorganic phosphate (Pi) 40.4%, phosphodiesters (PDE) 23.2%, adenosine triphosphate; γ-ATP 24.3%, α-ATP 20.1%, β-ATP 24.9%, respectively. (2) The baseline of spectra was smoother and the error was less with respiration gating than that without respiration gating. (3) During the phantom test, with average times 40, change FOV to 280 mm and 400 mm, the detection errors were 4.96% and 4.47%. With FOV 200 mm and average times 20, 40, 80, the detection errors were 8.86%, 5.38% and 4.40%, corresponding acquisition time were 1.27 min, 2.53 min and 5.06 min. Conclusion: Detection of phosphorus metabolites in human liver with 2D CSI is a stable and useful technique. Scan parameters should be carefully selected, and other influencing factors of detection must be also noticed during examination. (authors)

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

    Indian Academy of Sciences (India)

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

    2014-05-01

    Uranium L3 X-ray absorption edge was measured in various compounds containing uranium in U4+, U5+ and U6+ 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 L3 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.

  17. Multilayer MoS2 prepared by one-time and repeated chemical vapor depositions: anomalous Raman shifts and transistors with high ON/OFF ratio

    Science.gov (United States)

    Wu, Chong-Rong; Chang, Xiang-Rui; Chang, Shu-Wei; Chang, Chung-En; Wu, Chao-Hsin; Lin, Shih-Yen

    2015-11-01

    We show that multilayer molybdenum disulfide (MoS2) grown with the chemical vapor deposition (CVD) may exhibit quite distinct behaviors of Raman shifts from those of exfoliated ones. The anomalous Raman shifts depend on CVD growth modes and are attributed to the modified dielectric screening and interlayer coupling of MoS2 in various growth conditions. With repeated CVD growths, we demonstrated the precise control over the layer number of MoS2. A decently large drain current, high ON/OFF ratio of 105, and enhanced field-effect mobility can be achieved in transistors fabricated on the six-layer MoS2.

  18. A tracked approach for automated NMR assignments in proteins (TATAPRO)

    Energy Technology Data Exchange (ETDEWEB)

    Atreya, H.S.; Sahu, S.C.; Chary, K.V.R.; Govil, Girjesh [Tata Institute of Fundamental Research, Department of Chemical Sciences (India)

    2000-06-15

    A novel automated approach for the sequence specific NMR assignments of {sup 1}H{sup N}, {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C'/{sup 1}H{sup {alpha}} and {sup 15}N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate {sup 1}H{sup N} and {sup 15}N chemical shifts with those of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}} and {sup 13}C'/{sup 1}H{sup {alpha}}. The information derived from such correlations is used to create a 'master{sub l}ist' consisting of all possible sets of {sup 1}H{sup N}{sub i}, {sup 15}N{sub i}, {sup 13}C{sup {alpha}}{sub i}, {sup 13}C{sup {beta}}{sub i}, {sup 13}C'{sub i}/{sup 1}H{sup {alpha}}{sub i}, {sup 13}C{sup {alpha}}{sub i-1}, {sup 13}C{sup {beta}}{sub i-1} and {sup 13}C'{sub i-1}/ {sup 1}H{sup {alpha}}{sub i-1} chemical shifts. On the basis of an extensive statistical analysis of {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master{sub l}ist and also to translate the protein primary sequence into an array called pps{sub a}rray. The program then uses the master{sub l}ist to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so, each assigned residue is tracked in an array called assig{sub a}rray, with the two-digit code assigned earlier. The assig{sub a}rray is then mapped onto the pps{sub a}rray for sequence specific resonance assignment. The program has been tested using

  19. First-principles calculation of spectral features, chemical shift and absolute threshold of ELNES and XANES using a plane wave pseudopotential method

    International Nuclear Information System (INIS)

    Spectral features, chemical shifts, and absolute thresholds of electron energy loss near-edge structure (ELNES) and x-ray absorption near-edge structure (XANES) for selected compounds, i.e. TiO2 (rutile), TiO2 (anatase), SrTiO3, Ti2O3, Al2O3, AlN and β-Ga2O3, were calculated by a plane wave pseudopotential method. Experimental ELNES/XANES of those compounds were well reproduced when an excited pseudopotential, which includes a core hole, was used. In addition to the spectral features, it was found that chemical shifts among different compounds were also reproduced by correcting the contribution of the excited pseudopotentials to the energy of the core orbital.

  20. Deciphering Noncovalent Interactions Accompanying 7,7,8,8-Tetracyanoquinodimethane Encapsulation within Biphene[n]arenes: Nucleus-Independent Chemical Shifts Approach.

    Science.gov (United States)

    Lande, Dipali N; Rao, Soniya S; Gejji, Shridhar P

    2016-07-18

    Binding of novel biphene[n]arene hosts to antiaromatic 7,7,8,8-tetracyanoquinodimethane (TCNQ) are investigated by DFT. Biphene[4]arene favors the inclusion complex through noncovalent interactions, such as hydrogen bonding, π-π stacking, C-H⋅⋅⋅π, and C-H⋅⋅⋅H-C dihydrogen bonding. Donor-acceptor complexation renders aromatic character to the guest through charge transfer. The formation of TCNQ anionic radicals through supramolecular π stacking significantly influences its chemical and photophysical behavior. Electron density reorganization consequent to encapsulation of TCNQ reflects in the shift of characteristic vibrations in the IR spectra. The accompanying aromaticities arising from the induced ring currents are analyzed by employing nucleus-independent chemical shifts based profiles. PMID:27028656

  1. Correlation between 1H NMR chemical shifts of hydroxyl protons in n-hexanol/cyclohexane and molecular association properties investigated using density functional theory

    Science.gov (United States)

    Flores, Mario E.; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

    2016-01-01

    Association of n-hexanol molecules in cyclohexane forming clusters is studied by DFT and 1H NMR. Geometry optimization, corrected binding energies, charge distributions, charge transfer energies, and 1H NMR chemical shifts have been obtained. The calculated chemical shifts of hydroxyl protons have been correlated to experimental data obtained in the range of n-hexanol molar fraction between 0.002 and 0.2, showing that n-hexanol molecules at a molar fraction around 0.1, where well-structured hydrogen bond networks are observed, tend to form linear pentamers and hexamers. The experimental data are consistent with the continuous linear association thermodynamic model, showing a dimensionless association constant of 284.

  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. 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: 4.493, year: 2014 http://pubs.rsc.org/en/content/articlepdf/2015/cp/c5cp04214c

  4. Orientational constraints as three-dimensional structural constraints from chemical shift anisotropy: the polypeptide backbone of gramicidin A in a lipid bilayer.

    OpenAIRE

    Mai, W.; Hu, W; Wang, C; Cross, T A

    1993-01-01

    Chemical shifts observed from samples that are uniformly aligned with respect to the magnetic field can be used as very high-resolution structural constraints. This constraint takes the form of an orientational constraint rather than the more familiar distance constraint. The accuracy of these constraints is dependent upon the quality of the tensor characterization. Both tensor element magnitudes and tensor orientations with respect to the molecular frame need to be considered. Here these con...

  5. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA

    International Nuclear Information System (INIS)

    The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment and structure calculation with CYANA under a variety of conditions on the basis of the experimental NMR data sets of ten proteins. To evaluate the robustness of the algorithm, the original high-quality experimental data sets were modified in different ways to simulate the effect of data imperfections, i.e. incomplete or erroneous chemical shift assignments, missing NOESY cross peaks, inaccurate peak positions, inaccurate peak intensities, lower dimensionality NOESY spectra, and higher tolerances for the matching of chemical shifts and peak positions. The results show that the algorithm is remarkably robust with regard to imperfections of the NOESY peak lists and the chemical shift tolerances but susceptible to lacking or erroneous resonance assignments, in particular for nuclei that are involved in many NOESY cross peaks

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

    International Nuclear Information System (INIS)

    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 (NaH2PO4) 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

  7. NMR assignments of mitochondrial cyclophilin Cpr3 from Saccharomyces cerevisiae.

    Science.gov (United States)

    Shukla, Vaibhav Kumar; Singh, Jai Shankar; Trivedi, Dipesh; Hosur, Ramakrishna V; Kumar, Ashutosh

    2016-04-01

    Cyclophilins regulate protein folding, transport and signalling through catalysis of proline isomerization, and are ubiquitously expressed in both prokaryotes and eukaryotes. Cpr3 is the yeast mitochondrial cyclophilin and it is structurally and biophysically uncharacterized so far. Yeast cyclophilin gene cpr3 is essential for the lactate metabolism. Here, we report (1)H, (13)C, and (15)N chemical shift assignments of Cpr3 protein determined by various 2D and 3D heteronuclear NMR experiments at pH 6.5, and temperature 298 K. PMID:26897529

  8. 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.

  9. BTEC Integrative Assignments.

    Science.gov (United States)

    Foot, G. E.

    1992-01-01

    To equip electrical engineering students with common and transferable work skills, a program of integrative assignments was created to develop communication and teamwork skills. Discusses assignment components; the log book, a personal account of each assignment; assessment; conversion of "common skills" to competence statements, and performance…

  10. 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.

  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)

    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. Effects of structural differences on the NMR chemical shifts in cinnamic acid derivatives: Comparison of GIAO and GIPAW calculations

    Science.gov (United States)

    Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika; Wawer, Iwona

    2016-06-01

    In this article we report the results of combined theoretical and experimental structural studies on cinnamic acid derivatives (CADs), one of the main groups of secondary metabolites present in various medicinal plant species and food products of plant origin. The effects of structural differences in CADs on their spectroscopic properties were studied in detail by both: solid-state NMR and GIAO/GIPAW calculations. Theoretical computations were used in order to perform signal assignment in 13C CP/MAS NMR spectra of the cinnamic, o-coumaric, m-coumaric, p-coumaric, caffeic, ferulic, sinapic and 3,4-dimethoxycinnamic acids, and to evaluate the accuracy of GIPAW and GIAO methodology.

  13. 129Xe-NMR of xenon adsorbed on zeolites: determination of the dimensions of the void space from the chemical shift δ(129Xe)

    International Nuclear Information System (INIS)

    The chemical shift δS of xenon adsorbed on zeolite and extrapolated to zero concentration depends only on the internal void space of the solid. The smaller the channels or cavities, or the more restricted the diffusion, the greater δS becomes. We have calculated the theoretical values of the mean free path l-bar of xenon adsorbed in various zeolites. We deduce from them the dependence of the δS on l-bar. It is now possible to determine the dimensions of any void space in which xenon can be adsorbed. 4 refs.; 2 figs.; 3 tabs

  14. Molecular formula assignment for dissolved organic matter (DOM) using high-field FT-ICR-MS: chemical perspective and validation of sulphur-rich organic components (CHOS) in pit lake samples.

    Science.gov (United States)

    Herzsprung, Peter; Hertkorn, Norbert; von Tümpling, Wolf; Harir, Mourad; Friese, Kurt; Schmitt-Kopplin, Philippe

    2016-04-01

    Molecular formula assignment is one of the key challenges in processing high-field Fourier transform ion cyclotron resonance mass spectrometric (FT-ICR-MS) datasets. The number of potential solutions for an elemental formula increases exponentially with increasing molecular mass, especially when non-oxygen heteroatoms like N, S or P are included. A method was developed from the chemical perspective and validated using a Suwannee River Fulvic Acid (SRFA) dataset which is dominated by components consisting exclusively of C, H and O (78 % CHO). In order to get information on the application range and robustness of this method, we investigated a FT-ICR-MS dataset which was merged from 18 mine pit lake pore waters and 3 river floodplain soil waters. This dataset contained 50 % CHO and 18 % CHOS on average, whereas the former SRFA dataset contained only 1.5 % CHOS. The mass calculator was configured to allow up to five nitrogen atoms and up to one sulphur atom in assigning formulas to mass peaks. More than 50 % multiple-formula assignments were found for peaks with masses > 650 Da. Based on DBE - O frequency diagrams, many CHO, CHOS1, CHON1 and CHON1S1 molecular series were ultimately assigned to many m/z and considered to be reliable solutions. The unequivocal data pool could thus be enlarged by 523 (6.8 %) CHOS1 components. In contrast to the method validation with CHO-rich SRFA, validation with sulphur-rich pit lake samples showed that formulas with a higher number of non-oxygen heteroatoms can be more reliable assignments in many cases. As an example: CHOS molecular series were reliable and the CHO classes were unreliable amongst other molecular classes in many multiple-formula assignments from the sulphur-rich pit lake samples. Graphical abstract An exemplary frequency versus DBE - O diagram. CHOS components but not CHO (and not CHON2 or CHON2S) components were considered here reliable. PMID:26883969

  15. 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 s...

  16. DFT Studies on Thermal Stabilities,Electronic Structures, and 13C Chemical Shifts of C24O2 Based on Fullerene C24(D6)

    Institute of Scientific and Technical Information of China (English)

    WANG Zhen; ZHANG Jing

    2011-01-01

    Quantum chemical calculations on some possible equilibrium geometries of C2402 isomers derived from C24 (D6) and C240 have been performed using density functional theory (DFT) method. The geometric and electronic structures as well as the relative energies and thermal stabilities of various C2402 isomers at the ground state have been calculated at the B3LYP/6-31G(d) level of theory. And the 1,4,2,5-C2402 isomer was found to be the most stable geometry where two oxygen atoms were added to the longest carbon-carbon bonds in the same pentagon from a thermodynamic point of view. Based on the optimized neutral geometries, the vertical ionization potential and vertical electron affinity have been obtained. Meanwhile, the vibrational frequencies,IR spectrum, and 13C chemical shifts of various C2402 isomers have been calculated and analyzed.

  17. Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development in Inga, a genus of tropical trees.

    Science.gov (United States)

    Wiggins, Natasha L; Forrister, Dale L; Endara, María-José; Coley, Phyllis D; Kursar, Thomas A

    2016-01-01

    Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few-week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment

  18. Final Technical Report: A Paradigm Shift in Chemical Processing: New Sustainable Chemistries for Low-VOC Coatings

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Kenneth F.

    2006-07-26

    The project employed new processes to make emulsion polymers from reduced levels of petroleum-derived chemical feedstocks. Most waterborne paints contain spherical, emulsion polymer particles that serve as the film-forming binder phase. Our goal was to make emulsion polymer particles containing 30 percent feedstock that would function as effectively as commercial emulsions made from higher level feedstock. The processes developed yielded particles maintained their film formation capability and binding capacity while preserving the structural integrity of the particles after film formation. Rohm and Haas Company (ROH) and Archer Daniels Midland Company (ADM) worked together to employ novel polymer binders (ROH) and new, non-volatile, biomass-derived coalescing agents (ADM). The University of Minnesota Department of Chemical Engineering and Material Science utilized its unique microscopy capabilities to characterize films made from the New Emulsion Polymers (NEP).

  19. Comparative molecular field analysis and comparative molecular similarity index analysis studies on 1H NMR chemical shift of NH group of diaryl triazene derivatives.

    Science.gov (United States)

    Rofouie, M K; Salahinejad, M; Ghasemi, J B; Aghaei, A

    2013-05-01

    Comparative molecular field analysis (CoMFA), comparative molecular field analysis region focusing (CoMFA-RF) for optimizing the region for the final partial least square analysis, and comparative molecular similarity indices analysis (CoMSIA) methods were employed to develop three-dimensional quantitative structure-activity relationship (3D-QSAR) models of (1)H NMR chemical shift of NH proton of diaryl triazene derivatives. The best orientation was searched by all-orientation search (AOS) strategy to minimize the effect of the initial orientation of the structures. The predictive abilities of CoMFA-RF and CoMSIA models were determined using a test set of ten compounds affording predictive correlation coefficients of 0.721 and 0.754, respectively, indicating good predictive power. For further model validation, cross validation (leave one out), progressive scrambling, and bootstrapping were also applied. The accuracy and speed of obtained 3D-QSAR models for the prediction of (1)H NMR chemical shifts of NH group of diaryl triazene derivatives were greater compared to some computational well-known procedures. PMID:23456682

  20. 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.

  1. Analyzing Tenant Assignment Policies

    OpenAIRE

    Kaplan, Edward H.

    1987-01-01

    This paper discusses two popular policies used by housing authorities to assign applicants to housing projects: first available unit and priority assignment policies. The policies are compared according to their abilities to integrate housing projects, applicant assignment probabilities, and mean waiting times. Our results show that priority policies can successfully integrate public housing projects while first available unit policies can exacerbate segregation. These results support the rep...

  2. Brain temperature and pH measured by 1H chemical shift imaging of a thulium agent

    OpenAIRE

    Coman, Daniel; Trubel, Hubert K.; Rycyna, Robert E.; Hyder, Fahmeed

    2009-01-01

    Temperature and pH are two of the most important physiological parameters and are believed to be tightly regulated because they are intricately related to energy metabolism in living organisms. Temperature and/or pH data in mammalian brain are scarce, however, mainly due to lack of precise and non-invasive methods. At 11.7T, we demonstrate that a thulium-based macrocyclic complex infused through the blood stream can be used to obtain temperature and pH maps of rat brain in vivo by 1H chemical...

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

    DEFF Research Database (Denmark)

    Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek;

    2016-01-01

    Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for non-relativistic 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 4-component Dirac-Coulomb Hamiltonian using Dyall’s acv4z basis sets. The relativistic corrections to the nuclear magnetic...... shieldings and chemical shifts are combined with non-relativistic 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 corrections obtained at the CCSD...

  4. 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

    shifts can in principle report the conformations of aliphatic side chains in disordered proteins and in order to examine this two model systems were chosen: the acid denatured state of acyl-CoA binding protein (ACBP) and the intrinsically disordered activation domain of the activator for thyroid hormone...... allow a quantitative analysis of the ensemble of ¿(2)-angles of especially leucine residues in disordered proteins. The changes in the rotamer distributions upon denaturation correlate to the changes upon helix induction by the co-solvent trifluoroethanol, suggesting that the side chain conformers are......The peptide backbones of disordered proteins are routinely characterized by NMR with respect to transient structure and dynamics. Little experimental information is, however, available about the side chain conformations and how structure in the backbone affects the side chains. Methyl chemical...

  5. 1H chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter

    International Nuclear Information System (INIS)

    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 spectroscopy revealed guanidinoacetate (GAA) in the absence of creatine. New is that GAA signals are more prominent in gray matter than in white. In the prevailing view, that enzyme deficiency is localized in liver and pancreas and that all GAA is transported into the brain from the blood and the cerebrospinal fluid, this would be compatible with a more limited uptake and/or better clearance of GAA from the white matter compared to the grey matter. (orig.)

  6. Chemical shifts of 17O, 183W NMR and state of [ZW10O36]n-heteropolyanions in aqueous solutions

    International Nuclear Information System (INIS)

    By 17O, 183W NMR aqueous solutions of Na- and K-salts of heteropolyanions (HPA) [ZW10O36]n-, where Z = La3+-Er3+, Ce3+, Th4+, U4+, have been studied. HPA in aqueous solution exist as inert in the NMR time scale (1-100 ms) complexes, moreover, coordination sphere of Z is filled with O atoms of oxotungstate ligands, as in crystal state. The character of paramagnetic shifts (LIS) of all HPA atoms has been defined - in O and W atoms nearest to Z in LIS contact contribution prevails, for W-O-W bridge atoms and internal O atom dipole contribution prevails, for the rest atoms the dipole and contact contributions are comparable. The change in chemical shifts in lanthanide series depends not only on magnetic properties of element, but also on structural change in HPA. The width of 17O NMR lines for HPA studied (except HPA containing gadolinium) is determined by quadrupole mechanism of nuclear magnetic relaxation. 24 refs., 2 figs., 3 tabs

  7. Probing structural patterns of ion association and solvation in mixtures of imidazolium ionic liquids with acetonitrile by means of relative (1)H and (13)C NMR chemical shifts.

    Science.gov (United States)

    Marekha, Bogdan A; Kalugin, Oleg N; Bria, Marc; Idrissi, Abdenacer

    2015-09-21

    Mixtures of ionic liquids (ILs) with polar aprotic solvents in different combinations and under different conditions (concentration, temperature etc.) are used widely in electrochemistry. However, little is known about the key intermolecular interactions in such mixtures depending on the nature of the constituents and mixture composition. In order to systematically address the intermolecular interactions, the chemical shift variation of (1)H and (13)C nuclei has been followed in mixtures of imidazolium ILs 1-n-butyl-3-methylimidazolium tetrafluoroborate (BmimBF4), 1-n-butyl-3-methylimidazolium hexafluorophosphate (BmimPF6), 1-n-butyl-3-methylimidazolium trifluoromethanesulfonate (BmimTfO) and 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimTFSI) with molecular solvent acetonitrile (AN) over the entire composition range at 300 K. The concept of relative chemical shift variation is proposed to assess the observed effects on a unified and unbiased scale. We have found that hydrogen bonds between the imidazolium ring hydrogen atoms and electronegative atoms of anions are stronger in BmimBF4 and BmimTfO ILs than those in BmimTFSI and BmimPF6. Hydrogen atom at position 2 of the imidazolium ring is substantially more sensitive to interionic hydrogen bonding than those at positions 4-5 in the case of BmimTfO and BmimTFSI ILs. These hydrogen bonds are disrupted upon dilution in AN due to ion dissociation which is more pronounced at high dilutions. Specific solvation interactions between AN molecules and IL cations are poorly manifested. PMID:26278514

  8. 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)

    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 31P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders 31P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.)

  9. Assignment strategies for aliphatic protons in the solid-state in randomly protonated proteins

    International Nuclear Information System (INIS)

    Biological solid-state nuclear magnetic resonance spectroscopy developed rapidly in the past two decades and emerged as an important tool for structural biology. Resonance assignment is an essential prerequisite for structure determination and the characterization of motional properties of a molecule. Experiments, which rely on carbon or nitrogen detection, suffer, however, from low sensitivity. Recently, we introduced the RAP (Reduced Adjoining Protonation) labeling scheme, which allows to detect backbone and sidechain protons with high sensitivity and resolution. We present here a 1H-detected 3D (H)CCH experiment for assignment of backbone and sidechain proton resonances. Resolution is significantly improved by employing simultaneous 13CO and 13Cβ J-decoupling during evolution of the 13Cα chemical shift. In total, ∼90% of the 1Hα-13Cα backbone resonances of chicken α-spectrin SH3 could be assigned.

  10. Assignment strategies for aliphatic protons in the solid-state in randomly protonated proteins

    Energy Technology Data Exchange (ETDEWEB)

    Asami, Sam; Reif, Bernd, E-mail: reif@tum.de [Leibniz-Institut fuer Molekulare Pharmakologie (FMP) (Germany)

    2012-01-15

    Biological solid-state nuclear magnetic resonance spectroscopy developed rapidly in the past two decades and emerged as an important tool for structural biology. Resonance assignment is an essential prerequisite for structure determination and the characterization of motional properties of a molecule. Experiments, which rely on carbon or nitrogen detection, suffer, however, from low sensitivity. Recently, we introduced the RAP (Reduced Adjoining Protonation) labeling scheme, which allows to detect backbone and sidechain protons with high sensitivity and resolution. We present here a {sup 1}H-detected 3D (H)CCH experiment for assignment of backbone and sidechain proton resonances. Resolution is significantly improved by employing simultaneous {sup 13}CO and {sup 13}C{beta} J-decoupling during evolution of the {sup 13}C{alpha} chemical shift. In total, {approx}90% of the {sup 1}H{alpha}-{sup 13}C{alpha} backbone resonances of chicken {alpha}-spectrin SH3 could be assigned.

  11. Historical WBAN ID Assignments

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — 4"x6" index cards represent the first written assignments of Weather Bureau Army Navy (WBAN) station identifier numbers by the National Climatic Data Center....

  12. Extensive de novo solid-state NMR assignments of the 33 kDa C-terminal domain of the Ure2 prion

    International Nuclear Information System (INIS)

    We present the de novo resonance assignments for the crystalline 33 kDa C-terminal domain of the Ure2 prion using an optimized set of five 3D solid-state NMR spectra. We obtained, using a single uniformly 13C, 15N labeled protein sample, sequential chemical-shift information for 74% of the N, Cα, Cβ triples, and for 80% of further side-chain resonances for these spin systems. We describe the procedures and protocols devised, and discuss possibilities and limitations of the assignment of this largest protein assigned today by solid-state NMR, and for which no solution-state NMR shifts were available. A comparison of the NMR chemical shifts with crystallographic data reveals that regions with high crystallographic B-factors are particularly difficult to assign. While the secondary structure elements derived from the chemical shift data correspond mainly to those present in the X-ray crystal structure, we detect an additional helical element and structural variability in the protein crystal, most probably originating from the different molecules in the asymmetric unit, with the observation of doubled resonances in several parts, including entire stretches, of the protein. Our results provide the point of departure towards an atomic-resolution structural analysis of the C-terminal Ure2p domain in the context of the full-length prion fibrils.

  13. Extensive de novo solid-state NMR assignments of the 33 kDa C-terminal domain of the Ure2 prion

    Energy Technology Data Exchange (ETDEWEB)

    Habenstein, Birgit [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France); Wasmer, Christian [Harvard Medical School (United States); Bousset, Luc; Sourigues, Yannick [UPR 3082 CNRS, Laboratoire d' Enzymologie et Biochimie Structurales (France); Schuetz, Anne [ETH Zurich, Physical Chemistry (Switzerland); Loquet, Antoine [Max Planck Institute for Biophysical Chemistry (Germany); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Melki, Ronald, E-mail: melki@lebs.cnrs-gif.fr [UPR 3082 CNRS, Laboratoire d' Enzymologie et Biochimie Structurales (France); Boeckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France)

    2011-11-15

    We present the de novo resonance assignments for the crystalline 33 kDa C-terminal domain of the Ure2 prion using an optimized set of five 3D solid-state NMR spectra. We obtained, using a single uniformly {sup 13}C, {sup 15}N labeled protein sample, sequential chemical-shift information for 74% of the N, C{alpha}, C{beta} triples, and for 80% of further side-chain resonances for these spin systems. We describe the procedures and protocols devised, and discuss possibilities and limitations of the assignment of this largest protein assigned today by solid-state NMR, and for which no solution-state NMR shifts were available. A comparison of the NMR chemical shifts with crystallographic data reveals that regions with high crystallographic B-factors are particularly difficult to assign. While the secondary structure elements derived from the chemical shift data correspond mainly to those present in the X-ray crystal structure, we detect an additional helical element and structural variability in the protein crystal, most probably originating from the different molecules in the asymmetric unit, with the observation of doubled resonances in several parts, including entire stretches, of the protein. Our results provide the point of departure towards an atomic-resolution structural analysis of the C-terminal Ure2p domain in the context of the full-length prion fibrils.

  14. Dynamics-based selective 2D {sup 1}H/{sup 1}H chemical shift correlation spectroscopy under ultrafast MAS conditions

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu [Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055 (United States)

    2015-05-28

    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 {sup 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 {sup 1}H/{sup 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.

  15. Reduced Dimensionality (4,3)D-hnCOCANH Experiment: An Efficient Backbone Assignment tool for NMR studies of Proteins

    CERN Document Server

    Kumar, Dinesh

    2013-01-01

    Sequence specific resonance assignment and secondary structure determination of proteins form the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone (1H, 15N, 13Ca and 13C') resonances and secondary structure determination of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality (RD) experiment -(4,3)D-hnCOCANH and exploits the linear combinations of backbone (13Ca and 13C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text) for efficient and rapid data analysis. Further, the experiment leads to the spectrum with direct distinction of self (intra-residue) and sequential (inter-residue) carbon correlation peaks; these appear opposite in signs and therefore can easily be discriminated without using an additional complementary experiment. On ...

  16. My Favorite Assignment.

    Science.gov (United States)

    Hebert, Margaret; And Others

    1991-01-01

    Contains seven brief articles which offer assignments designed to help students perform job searches, write job application letters, answer difficult questions, write letters of resignation, alleviate fears of public speaking, use the interview effectively in the business communication, and develop listening skills. (PRA)

  17. 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.

  18. The value of 15-minute delayed contrast-enhanced CT to differentiate hyperattenuating adrenal masses compared with chemical shift MR imaging

    International Nuclear Information System (INIS)

    To investigate the diagnostic performance of 15-min delayed contrast-enhanced computed tomography (15-DECT) compared with that of chemical shift magnetic resonance (CSMR) imaging in differentiating hyperattenuating adrenal masses and to perform subgroup analysis in underlying malignancy and non-malignancy. This study included 478 adrenal masses in 453 patients examined with 15-DECT and 235 masses in 217 patients examined with CSMR. Relative percentage washout (RPW) and absolute percentage washout (APW) on 15-DECT, and signal intensity index (SII) and adrenal-to-spleen ratio (ASR) on CSMR were measured. Sensitivity, specificity and accuracy of 15-DECT and CSMR were analysed for characterisation of adrenal adenoma. Subgroup analyses were performed in patients with and without underlying malignancy. Attenuation and size of the masses on unenhanced CT correlated with the risk of non-adenoma. RPW calculated from 15-DECT showed the highest diagnostic performance for characterising hyperattenuating adrenal masses regardless of underlying malignancy, and the sensitivity, specificity and accuracy were 91.7 %, 74.8 % and 88.1 %, respectively in all patients. The risk of non-adenoma increased approximately threefold as mass size increased 1 cm or as its attenuation value increased by 10 Hounsfield units. 15-DECT was more accurate than CSMR in characterising hyperattenuating adrenal masses regardless of underlying malignancy. (orig.)

  19. 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.

  20. The value of 15-minute delayed contrast-enhanced CT to differentiate hyperattenuating adrenal masses compared with chemical shift MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Koo, Hyun Jung; Choi, Hyuck Jae; Cho, Kyoung-Sik [Asan Medical Center, University of Ulsan College of Medicine, Department of Radiology and Research Institute of Radiology, Seoul (Korea, Republic of); Kim, Hwa Jung; Kim, Sun-Ok [Asan Medical Center, University of Ulsan College of Medicine, Cancer Center, Department of Clinical Epidemiology and Biostatistics, Seoul (Korea, Republic of)

    2014-06-15

    To investigate the diagnostic performance of 15-min delayed contrast-enhanced computed tomography (15-DECT) compared with that of chemical shift magnetic resonance (CSMR) imaging in differentiating hyperattenuating adrenal masses and to perform subgroup analysis in underlying malignancy and non-malignancy. This study included 478 adrenal masses in 453 patients examined with 15-DECT and 235 masses in 217 patients examined with CSMR. Relative percentage washout (RPW) and absolute percentage washout (APW) on 15-DECT, and signal intensity index (SII) and adrenal-to-spleen ratio (ASR) on CSMR were measured. Sensitivity, specificity and accuracy of 15-DECT and CSMR were analysed for characterisation of adrenal adenoma. Subgroup analyses were performed in patients with and without underlying malignancy. Attenuation and size of the masses on unenhanced CT correlated with the risk of non-adenoma. RPW calculated from 15-DECT showed the highest diagnostic performance for characterising hyperattenuating adrenal masses regardless of underlying malignancy, and the sensitivity, specificity and accuracy were 91.7 %, 74.8 % and 88.1 %, respectively in all patients. The risk of non-adenoma increased approximately threefold as mass size increased 1 cm or as its attenuation value increased by 10 Hounsfield units. 15-DECT was more accurate than CSMR in characterising hyperattenuating adrenal masses regardless of underlying malignancy. (orig.)

  1. Determination of NH proton chemical shift anisotropy with 14N-1H heteronuclear decoupling using ultrafast magic angle spinning solid-state NMR

    Science.gov (United States)

    Pandey, Manoj Kumar; Nishiyama, Yusuke

    2015-12-01

    The extraction of chemical shift anisotropy (CSA) tensors of protons either directly bonded to 14N nuclei (I = 1) or lying in their vicinity using rotor-synchronous recoupling pulse sequence is always fraught with difficulty due to simultaneous recoupling of 14N-1H heteronuclear dipolar couplings and the lack of methods to efficiently decouple these interactions. This difficulty mainly arises from the presence of large 14N quadrupolar interactions in comparison to the rf field that can practically be achieved. In the present work it is demonstrated that the application of on-resonance 14N-1H decoupling with rf field strength ∼30 times weaker than the 14N quadrupolar coupling during 1H CSA recoupling under ultrafast MAS (90 kHz) results in CSA lineshapes that are free from any distortions from recoupled 14N-1H interactions. With the use of extensive numerical simulations we have shown the applicability of our proposed method on a naturally abundant L-Histidine HCl·H2O sample.

  2. 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…

  3. Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex.

    Science.gov (United States)

    Puthenpurackal Narayanan, Sunilkumar; Maeno, Akihiro; Wada, Yuji; Tate, Shin-Ichi; Akasaka, Kazuyuki

    2016-04-01

    Occasionally, a mutation in an exposed loop region causes a significant change in protein function and/or stability. A single mutation Gly67Val of E. coli dihydrofolate reductase (DHFR) in the exposed CD loop is such an example. We have carried out the chemical shift assignments for H(N), N(H), C(α) and C(β) atoms of the Gly67Val mutant of E. coli DHFR complexed with folate at pH 7.0, 35 °C, and then evaluated the H(N), N(H), C(α) and C(β) chemical shift changes caused by the mutation. The result indicates that, while the overall secondary structure remains the same, the single mutation Gly67Val causes site-specific conformational changes of the polypeptide backbone restricted around the adenosine-binding subdomain (residues 38-88) and not in the distant catalytic domain. PMID:26482924

  4. Amino acid selective unlabeling for sequence specific resonance assignments in proteins

    Energy Technology Data Exchange (ETDEWEB)

    Krishnarjuna, B.; Jaipuria, Garima; Thakur, Anushikha [Indian Institute of Science, NMR Research Centre (India); D' Silva, Patrick, E-mail: patrick@biochem.iisc.ernet.in [Indian Institute of Science, Department of Biochemistry (India); Atreya, Hanudatta S., E-mail: hsatreya@sif.iisc.ernet.in [Indian Institute of Science, NMR Research Centre (India)

    2011-01-15

    Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective 'unlabeling' or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly {sup 13}C/{sup 15}N labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {l_brace}{sup 12}CO{sub i}-{sup 15}N{sub i+1}{r_brace}-filtered HSQC, which aids in linking the {sup 1}H{sup N}/{sup 15}N resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i - 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to {sup 2}H labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of {sup 14}N at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies.

  5. SAFT缔合模型关联含水体系的1H NMR%Correlation of 1H NMR Chemical Shift for Aqueous Solutions by Statistical Associating Fluid Theory Association Model

    Institute of Scientific and Technical Information of China (English)

    许波; 李浩然; 王从敏; 许映杰; 韩世钧

    2005-01-01

    1H NMR chemical shifts of binary aqueous mixtures of acylamide, alcohol, dimethyl sulphoxide (DMSO), and acetone are correlated by statistical associating fluid theory (SAFT) association model. The comparison between SAFT association model and Wilson equation shows that the former is better for dealing with aqueous solutions. Finally, the specialties of both models are discussed.

  6. 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 th...

  7. Detection of fat in lipomatous tumors of the myometrium by means of computed tomography and chemical shift magnetic resonance imaging; Deteccion de grasa en tumores lipomatosos del miometrio mediante TC y RM con tecnica de Desplazamiento Quimico

    Energy Technology Data Exchange (ETDEWEB)

    Costa, S.; Marti-Bonmati, L.; Delgado, F.; Ripolles, T. [Hospital Universitario Doctor Peset. Valencia (Spain)

    2000-07-01

    Lipomatous tumors of the myometrium are rare lesions composed of varying amounts of mature fatty tissue. Our objective was to assess the computed tomography (CT) and magnetic resonance MR findings associated with these tumors and determine the utility of the chemical shift imaging technique in the detection of fact within these focal uterine masses. Lipomatous focal uterine lesions were detected in three women by means of ultrasound. The patients underwent CT and MR using the chemical shift imaging technique and in-phase and opposed phase T1-weighted gradient-echo images. Qualitative and quantitative analyses of the results were carried out, based on the attenuations and relations of signal intensity. The tumors were hypoattenuated in CT seans and hyperintense in T1-weighted images, showing a decreased signal in opposed phase T1-weighted images when compared with in-phase images. The percentage change (between 2% and 3%) is probably proportional to the differing proportions of fact and muscle elements present in these lipoleiomyomas. Lipomatous tumors of the myometrium are uterine lesions with a varying proportion of fact. Their fat composition can be detected by CT and MR. The chemical shift imaging technique reveals the variations in the proportions of fat in these tumors. Since the presence of fat within uterine lesions is virtually diagnostic of the myometrial lipomatous tumor, the chemical shift imaging technique contributes to the characterization of these lesions. (Author) 11 refs.

  8. 13C chemical shift anisotropies for carbonate ions in cement minerals and the use of 13C, 27Al and 29Si MAS NMR in studies of Portland cement including limestone additions

    International Nuclear Information System (INIS)

    13C isotropic chemical shifts and chemical shift anisotropy parameters have been determined for a number of inorganic carbonates relevant in cement chemistry from slow-speed 13C MAS or 13C(1H) CP/MAS NMR spectra (9.4 T or 14.1 T) for 13C in natural abundance. The variation in the 13C chemical shift parameters is relatively small, raising some doubts that different carbonate species in Portland cement-based materials may not be sufficiently resolved in 13C MAS NMR spectra. However, it is shown that by combining 13C MAS and 13C(1H) CP/MAS NMR carbonate anions in anhydrous and hydrated phases can be distinguished, thereby providing valuable information about the reactivity of limestone in cement blends. This is illustrated for three cement pastes prepared from an ordinary Portland cement, including 0, 16, and 25 wt.% limestone, and following the hydration for up to one year. For these blends 29Si MAS NMR reveals that the limestone filler accelerates the hydration for alite and also results in a smaller fraction of tetrahedrally coordinated Al incorporated in the C-S-H phase. The latter result is more clearly observed in 27Al MAS NMR spectra of the cement–limestone blends and suggests that dissolved aluminate species in the cement–limestone blends readily react with carbonate ions from the limestone filler, forming calcium monocarboaluminate hydrate. -- Highlights: •13C chemical shift anisotropies for inorganic carbonates from 13C MAS NMR. •Narrow 13C NMR chemical shift range (163–171 ppm) for inorganic carbonates. •Anhydrous and hydrated carbonate species by 13C MAS and 13C(1H) CP/MAS NMR. •Limestone accelerates the hydration for alite in Portland – limestone cements. •Limestone reduces the amount of aluminium incorporated in the C-S-H phase

  9. Highly automated protein backbone resonance assignment within a few hours: the strategy and software package

    International Nuclear Information System (INIS)

    Sequential resonance assignment represents an essential step towards the investigation of protein structure, dynamics, and interaction surfaces. Although the experimental sensitivity has significantly increased in recent years, with the availability of high field magnets and cryogenically cooled probes, resonance assignment, even of small globular proteins, still generally requires several days of data collection and analysis using standard protocols. Here we introduce the BATCH strategy for fast and highly automated backbone resonance assignment of 13C, 15N-labelled proteins. BATCH makes use of the fast data acquisition and analysis tools BEST, ASCOM, COBRA, and HADAMAC, recently developed in our laboratory. An improved Hadamard encoding scheme, presented here, further increases the performance of the HADAMAC experiment. A new software platform, interfaced to the NMRView software package, has been developed that enables highly automated NMR data processing and analysis, sequential resonance assignment, and 13C chemical shift extraction. We demonstrate for four small globular proteins that sequential resonance assignment can be routinely obtained within a few hours, or less, in a highly automated and robust way

  10. {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

  11. Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

    International Nuclear Information System (INIS)

    The solution structure of d(CGCGAATTCGCG)2 has been determined on the basis of an exceptionally large set of residual dipolar couplings. In addition to the heteronuclear 13C-1H and 15N-1H and qualitative homonuclear 1H-1H dipolar couplings, previously measured in bicelle medium, more than 300 quantitative 1H-1H and 22 31P-1H dipolar restraints were obtained in liquid crystalline Pf1 medium, and 22 31P chemical shift anisotropy restraints. High quality DNA structures can be obtained solely on the basis of these new restraints, and these structures are in close agreement with those calculated previously on the basis of 13C-1H and 15N-1H dipolar couplings. In the newly calculated structures, 31P-1H dipolar and 3JsubH3'Psub couplings and 31P CSA data restrain the phosphodiester backbone torsion angles. The final structure represents a quite regular B-form helix with a modest bending of ∼10 deg., which is essentially independent of whether or not electrostatic terms are used in the calculation. Combined, the number of homo- and heteronuclear dipolar couplings significantly exceeds the number of degrees of freedom in the system. Results indicate that the dipolar coupling data cannot be fit by a single structure, but are compatible with the presence of rapid equilibria between C2'-endo and C3'-endo deoxyribose puckers (sugar switching). The C2'-H2'/H2'' dipolar couplings in B-form DNA are particularly sensitive to sugar pucker and yield the largest discrepancies when fit to a single structure. To resolve these discrepancies, we suggest a simplified dipolar coupling analysis that yields N/S equilibria for the ribose sugar puckers, which are in good agreement with previous analyses of NMR JHH couplings, with a population of the minor C3'-endo form higher for pyrimidines than for purines

  12. Utility of chemical-shift MR imaging in detecting small amounts of fat in extrahepatic abdominal tumors; Utilidad de la tecnica de desplazamiento quimico den RM para la deteccion de pequenas cantidades de grasa en tumores abdominales extrahepaticos

    Energy Technology Data Exchange (ETDEWEB)

    Martin, J.; Falco, J.; Puig, J.; Donoso, L. [Unidad de Diagnostico por Imagen de Alta Tecnologia (UDIAT). Sabadell (Spain)

    1999-07-01

    To determine the utility of the chemical shift technique in magnetic resonance imaging (MRI) to confirm small amounts of fat in extrahepatic intraabdominal tumours. 7 extrahepatic abdominal tumours that are suspected to have fat as seen in the axial computed tomography (TC) are analysed retrospectively. In order to confirm the fat content, the chemical displacement technique with gradient echo sequences (GE) in phase (P) and in opposite phase (OP) was used with MRI 1 T equipment. The tumours corresponded to renal angiomyolipoma (AML) (n=4), intraperitoneal liposarcoma (n=1), retroperitoneal liposarcoma (n=1) and intraabdominal extramedular hematopoiesis (n=1). To confirm the existence of fat in the tumours, we used a quantitative percentage variation parameter of the intensity of the signals (VIS) between the images in P and OP, according to the formula: IS{sub (}p)-IS({sub o}p)x100/IS{sub (}op), where IS is the intensity of the signal. The chemical shift technique showed fat in the seven tumours. Upon visual inspection, all the tumoral areas that were suspected to have fat showed a notable difference in the signal intensity, being hypointense in OP and hyperintense in P. In these areas the average VIS percentage was 170% while in the rest of the tumour the average VIS percentage was 3%. The chemical shift technique with RG sequences can be easily used in MRI equipment and allows us to confirm if a specific abdominal tumour has fat, even if there is only a small quantity. (Author) 13 refs.

  13. Double-echo gradient chemical shift MR imaging fails to differentiate minimal fat renal angiomyolipomas from other homogeneous solid renal tumors

    International Nuclear Information System (INIS)

    Highlights: •Diagnosis of AMLs with minimal fat (mfAMLs) is still challenging with MRI. •Drop of signal on opposed-phase MR imaging is not specific of mfAMLs. •Double-echo gradient-echo sequences cannot accurately differentiate renal mfAMLs from other renal tumors. -- Abstract: Objectives: The purpose of this retrospective study was to evaluate the diagnostic performance of double-echo gradient chemical shift (GRE) magnetic resonance (MR) imaging for the differentiation of angiomyolipomas with minimal fat (mfAML) from other homogeneous solid renal tumors. Methods: Between 2005 and 2010 in two institutions, all histologically proven homogenous solid renal tumors imaged with computed tomography and MR imaging, including GRE sequences, have been retrospectively selected. A total of 118 patients (mean age: 61 years; range: 20–87) with 119 tumors were included. Two readers measured independently the signal intensity (SI) on GRE images and calculated SI index (SII) and tumor-to-spleen ratio (TSR) on in-phase and opposed-phase images. Intra- and interreader agreement was obtained. Cut-off values were derived from the receiver operating characteristic (ROC) curve analysis. Results: Twelve mfAMLs in 11 patients were identified (mean size: 2.8 cm; range: 1.2–3.5), and 107 non-AML tumors (3.2 cm; 1–7.8) in 107 patients. The intraobserver reproducibility of SII and TSR was excellent with an intraclass correlation coefficient equal to 0.99 [0.98–0.99]. The coefficient of correlation between the readers was 0.99. The mean values of TSR for mfAMLs and non-mfAMLs were −7.0 ± 22.8 versus −8.2 ± 21.2 for reader 1 and −6.7 ± 22.8 versus −8.4 ± 20.9 for reader 2 respectively. No significant difference was noticed between the two groups for SII (p = 0.98) and TSR (p = 0.86). Only 1 out of 12 mfAMLs and 11 of 107 non-AML tumors presented with a TSR inferior to −30% (p = 0.83). Conclusion: In a routine practice, GRE sequences cannot be a confident tool to

  14. Double-echo gradient chemical shift MR imaging fails to differentiate minimal fat renal angiomyolipomas from other homogeneous solid renal tumors

    Energy Technology Data Exchange (ETDEWEB)

    Ferré, R., E-mail: kn638@yahoo.fr [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Cornelis, F. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Verkarre, V. [Department of Pathology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Eiss, D.; Correas, J.M. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Grenier, N. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Hélénon, O. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France)

    2015-03-15

    Highlights: •Diagnosis of AMLs with minimal fat (mfAMLs) is still challenging with MRI. •Drop of signal on opposed-phase MR imaging is not specific of mfAMLs. •Double-echo gradient-echo sequences cannot accurately differentiate renal mfAMLs from other renal tumors. -- Abstract: Objectives: The purpose of this retrospective study was to evaluate the diagnostic performance of double-echo gradient chemical shift (GRE) magnetic resonance (MR) imaging for the differentiation of angiomyolipomas with minimal fat (mfAML) from other homogeneous solid renal tumors. Methods: Between 2005 and 2010 in two institutions, all histologically proven homogenous solid renal tumors imaged with computed tomography and MR imaging, including GRE sequences, have been retrospectively selected. A total of 118 patients (mean age: 61 years; range: 20–87) with 119 tumors were included. Two readers measured independently the signal intensity (SI) on GRE images and calculated SI index (SII) and tumor-to-spleen ratio (TSR) on in-phase and opposed-phase images. Intra- and interreader agreement was obtained. Cut-off values were derived from the receiver operating characteristic (ROC) curve analysis. Results: Twelve mfAMLs in 11 patients were identified (mean size: 2.8 cm; range: 1.2–3.5), and 107 non-AML tumors (3.2 cm; 1–7.8) in 107 patients. The intraobserver reproducibility of SII and TSR was excellent with an intraclass correlation coefficient equal to 0.99 [0.98–0.99]. The coefficient of correlation between the readers was 0.99. The mean values of TSR for mfAMLs and non-mfAMLs were −7.0 ± 22.8 versus −8.2 ± 21.2 for reader 1 and −6.7 ± 22.8 versus −8.4 ± 20.9 for reader 2 respectively. No significant difference was noticed between the two groups for SII (p = 0.98) and TSR (p = 0.86). Only 1 out of 12 mfAMLs and 11 of 107 non-AML tumors presented with a TSR inferior to −30% (p = 0.83). Conclusion: In a routine practice, GRE sequences cannot be a confident tool to

  15. 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...... integrating real-world resource use into a game....

  16. Fluid Shifts

    Science.gov (United States)

    Stenger, M.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Lauriie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Ribeiro, L.; Lui, J.; Macias, B.; Arbeille, P.; Danielson, R.; Chang, D.; Johnston, S.; Ploutz-Snyder, R.; Smith, S.

    2016-01-01

    NASA is focusing on long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low-Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but more than 50% of ISS astronauts experienced more profound, chronic changes with objective structural and functional findings such as papilledema and choroidal folds. Globe flattening, optic nerve sheath dilation, and optic nerve tortuosity also are apparent. This pattern is referred to as the visual impairment and intracranial pressure (VIIP) syndrome. VIIP signs and symptoms, as well as postflight lumbar puncture data, suggest that elevated intracranial pressure (ICP) may be associated with the spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight, and to correlate these findings with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, is predicted by the crewmember's preflight conditions and responses to acute hemodynamic manipulations (such as head-down tilt). Lastly, we will evaluate the patterns of fluid distribution in ISS astronauts during acute reversal of fluid shifts through application of lower body negative pressure (LBNP) interventions to characterize and explain general and individual responses. METHODS: We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the Figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, calcaneus tissue thickness (by

  17. Oxygen 17 NMR in the evaluation of oxygen bounding with central ion using hydrolysis products of niobium, tantalum, arsenic, antimony pentafluorides as an example. Symbasis in the change of 17O and 19F chemical shifts

    International Nuclear Information System (INIS)

    Hydrolysis products of niobium, tantalum, antimony and arsenic pentafluorides in acetonitrile solution were studied by the methods of 17O and 19F NMR. In 17O NMR spectra of niobium and tantalum pentafluorides hydrolysis products resonance signals of oxo-, hydroxo- and aquafluorocomplexes were defined. Considerable shift of 17O NMR resonance signals towards weak field making up about 300 m.p., may indicate a higher covalency (Π-character) of Nb-O bond compared to Ta-O one. Symbasis in the change of chemical shifts in 17O NMR and 19F NMR of the relevant hexafluorides and hydrolysis products was detected implying similarity of chemical bond nature in oxygen and fluorine

  18. Further exploration of the conformational space of α-synuclein fibrils: solid-state NMR assignment of a high-pH polymorph.

    Science.gov (United States)

    Verasdonck, Joeri; Bousset, Luc; Gath, Julia; Melki, Ronald; Böckmann, Anja; Meier, Beat H

    2016-04-01

    Polymorphism is a common and important phenomenon for protein fibrils which has been linked to the appearance of strains in prion and other neurodegenerative diseases. Parkinson disease is a frequently occurring neurodegenerative pathology, tightly associated with the formation of Lewy bodies. These deposits mainly consist of α-synuclein in fibrillar, β-sheet-rich form. α-synuclein is known to form numerous different polymorphs, which show distinct structural features. Here, we describe the chemical shift assignments, and derive the secondary structure, of a polymorph that was fibrillized at higher-than-physiological pH conditions. The fibrillar core contains residues 40-95, with both the C- and N-terminus not showing any ordered, rigid parts. The chemical shifts are similar to those recorded previously for an assigned polymorph that was fibrillized at neutral pH. PMID:26318307

  19. 129Xe NMR of xenon adsorbed on the molecular sieves AlPO 4-11 and SAPO-11. Chemical shift anisotropy related to the asymmetry of the adsorption zones

    Science.gov (United States)

    Springuel-Huet, M. A.; Fraissard, J.

    1989-01-01

    The form of the 129Xe NMR signal of xenon adsorbed at low concentration on the molecular sieves SAPO-11 and AlPO 4-11 corresponds to a highly anisotropic chemical shift which expresses the asymmetry of the channels in which the xenon is located. To the asymmetry of the xenon-wall interaction is added that of the xenon-xenon interaction when the channels are largely filled.

  20. 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

  1. A Series of Diamagnetic Pyridine Monoimine Rhenium Complexes with Different Degrees of Metal-to-Ligand Charge Transfer: Correlating (13) C NMR Chemical Shifts with Bond Lengths in Redox-Active Ligands.

    Science.gov (United States)

    Sieh, Daniel; Kubiak, Clifford P

    2016-07-18

    A set of pyridine monoimine (PMI) rhenium(I) tricarbonyl chlorido complexes with substituents of different steric and electronic properties was synthesized and fully characterized. Spectroscopic (NMR and IR) and single-crystal X-ray diffraction analyses of these complexes showed that the redox-active PMI ligands are neutral and that the overall electronic structure is little affected by the choices of the substituent at the ligand backbone. One- and two-electron reduction products were prepared from selected starting compounds and could also be characterized by multiple spectroscopic methods and X-ray diffraction. The final product of a one-electron reduction in THF is a diamagnetic metal-metal-bonded dimer after loss of the chlorido ligand. Bond lengths in and NMR chemical shifts of the PMI ligand backbone indicate partial electron transfer to the ligand. Two-electron reduction in THF also leads to the loss of the chlorido ligand and a pentacoordinate complex is obtained. The comparison with reported bond lengths and (13) C NMR chemical shifts of doubly reduced free pyridine monoaldimine ligands indicates that both redox equivalents in the doubly reduced rhenium complex investigated here are located in the PMI ligand. With diamagnetic complexes varying over three formal reduction stages at the PMI ligand we were, for the first time, able to establish correlations of the (13) C NMR chemical shifts with the relevant bond lengths in redox-active ligands over a full redox series. PMID:27319753

  2. Interactive Assignments for Online Students

    Directory of Open Access Journals (Sweden)

    Pam Lowry

    2009-04-01

    Full Text Available Students can experience first hand through interactive assignments what is involved in teaching an online course. Most students develop a whole new appreciation for the student learning process. Faculty are beginning to realize that online instruction is more than a series of readings posted to a course management system. This paper summarizes the faculty member's instructional strategies involved when creating student interaction assignments. The paper also summarizes the assignments, discussion board, and trends in education from the student's perspective. In summary, it concludes with the faculty's overall perspective concerning these assignments and how the assignments could be more effective for the student.

  3. NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase.

    Science.gov (United States)

    Polshakov, Vladimir I; Petrova, Olga A; Parfenova, Yulia Yu; Efimov, Sergey V; Klochkov, Vladimir V; Zvereva, Maria I; Dontsova, Olga A

    2016-04-01

    Telomerase is a ribonucleoprotein enzyme that adds telomeric DNA fragments to the ends of chromosomes. This enzyme is the focus of substantial attention, both because its structure and mechanism of action are still poorly studied, and because of its pivotal roles in aging and cellular proliferation. The use of telomerase as a potential target for the design of new anticancer drugs is also of great interest. The catalytic protein subunit of telomerase (TERT) contains an N-terminal domain (TEN) that is essential for activity and processivity. Elucidation of the structure and dynamics of TEN in solution is important for understanding the molecular mechanism of telomerase activity and for the design of new telomerase inhibitors. To approach this problem, in this study we report the (1)H, (13)C, and (15)N chemical shift assignments of TEN from Ogataea polymorpha. Analysis of the assigned chemical shifts allowed us to identify secondary structures and protein regions potentially involved in interaction with other participants of the telomerase catalytic cycle. PMID:26721464

  4. Assigning large proteins in the solid state: a MAS NMR resonance assignment strategy using selectively and extensively 13C-labelled proteins

    International Nuclear Information System (INIS)

    In recent years, solid-state magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR) has been growing into an important technique to study the structure of membrane proteins, amyloid fibrils and other protein preparations which do not form crystals or are insoluble. Currently, a key bottleneck is the assignment process due to the absence of the resolving power of proton chemical shifts. Particularly for large proteins (approximately >150 residues) it is difficult to obtain a full set of resonance assignments. In order to address this problem, we present an assignment method based upon samples prepared using [1,3-13C]- and [2-13C]-glycerol as the sole carbon source in the bacterial growth medium (so-called selectively and extensively labelled protein). Such samples give rise to higher quality spectra than uniformly [13C]-labelled protein samples, and have previously been used to obtain long-range restraints for use in structure calculations. Our method exploits the characteristic cross-peak patterns observed for the different amino acid types in 13C-13C correlation and 3D NCACX and NCOCX spectra. An in-depth analysis of the patterns and how they can be used to aid assignment is presented, using spectra of the chicken α-spectrin SH3 domain (62 residues), αB-crystallin (175 residues) and outer membrane protein G (OmpG, 281 residues) as examples. Using this procedure, over 90% of the Cα, Cβ, C' and N resonances in the core domain of αB-crystallin and around 73% in the flanking domains could be assigned (excluding 24 residues at the extreme termini of the protein)

  5. Assigning large proteins in the solid state: a MAS NMR resonance assignment strategy using selectively and extensively {sup 13}C-labelled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Higman, Victoria A. [Leibniz-Institut fuer Molekulare Pharmakologie (Germany); Flinders, Jeremy [Genentech, Inc., Structural Biology Department (United States); Hiller, Matthias; Jehle, Stefan; Markovic, Stefan; Fiedler, Sebastian; Rossum, Barth-Jan van; Oschkinat, Hartmut [Leibniz-Institut fuer Molekulare Pharmakologie (Germany)], E-mail: oschkinat@fmp-berlin.de

    2009-08-15

    In recent years, solid-state magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR) has been growing into an important technique to study the structure of membrane proteins, amyloid fibrils and other protein preparations which do not form crystals or are insoluble. Currently, a key bottleneck is the assignment process due to the absence of the resolving power of proton chemical shifts. Particularly for large proteins (approximately >150 residues) it is difficult to obtain a full set of resonance assignments. In order to address this problem, we present an assignment method based upon samples prepared using [1,3-{sup 13}C]- and [2-{sup 13}C]-glycerol as the sole carbon source in the bacterial growth medium (so-called selectively and extensively labelled protein). Such samples give rise to higher quality spectra than uniformly [{sup 13}C]-labelled protein samples, and have previously been used to obtain long-range restraints for use in structure calculations. Our method exploits the characteristic cross-peak patterns observed for the different amino acid types in {sup 13}C-{sup 13}C correlation and 3D NCACX and NCOCX spectra. An in-depth analysis of the patterns and how they can be used to aid assignment is presented, using spectra of the chicken {alpha}-spectrin SH3 domain (62 residues), {alpha}B-crystallin (175 residues) and outer membrane protein G (OmpG, 281 residues) as examples. Using this procedure, over 90% of the C{alpha}, C{beta}, C' and N resonances in the core domain of {alpha}B-crystallin and around 73% in the flanking domains could be assigned (excluding 24 residues at the extreme termini of the protein)

  6. Shifting densities

    OpenAIRE

    Mille, Matthieu

    2000-01-01

    In this paper, the author adopt a time-geography approach to examine the temporal variation of urban density by analysing spatial load changes at different times of the day at the communal and community level. The evolution of means of transport coupled with the abandon of the notion of direct proximity to the urban dwelling place provide the basis for this new approach to the study of urban densities. The shift towards spatial specialisation within cities has lead to radical changes in the f...

  7. High resolution 4D HPCH experiment for sequential assignment of 13C-labeled RNAs via phosphodiester backbone

    International Nuclear Information System (INIS)

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of 1H and 13C chemical shifts, especially of C4′/H4′. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4′–H4′ correlations are resolved along the 1H3′–31P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional 31P and 1H3′ dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic 13C-labeling with evolution of C4′ carbons. Band selective 13C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4′–C3′ and C4′–C5′ homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop

  8. High resolution 4D HPCH experiment for sequential assignment of {sup 13}C-labeled RNAs via phosphodiester backbone

    Energy Technology Data Exchange (ETDEWEB)

    Saxena, Saurabh; Stanek, Jan [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland); Cevec, Mirko; Plavec, Janez [National Institute of Chemistry, Slovenian NMR Centre (Slovenia); Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

    2015-11-15

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of {sup 1}H and {sup 13}C chemical shifts, especially of C4′/H4′. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4′–H4′ correlations are resolved along the {sup 1}H3′–{sup 31}P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional {sup 31}P and {sup 1}H3′ dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic {sup 13}C-labeling with evolution of C4′ carbons. Band selective {sup 13}C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4′–C3′ and C4′–C5′ homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.

  9. Balanced input-output assignment

    Science.gov (United States)

    Gawronski, W.; Hadaegh, F. Y.

    1989-01-01

    Actuator/sensor locations and balanced representations of linear systems are considered for a given set of controllability and observability grammians. The case of equally controlled and observed states is given special attention. The assignability of grammians is examined, and the conditions for their existence are presented, along with several algorithms for their determination. Although an arbitrary positive semidefinite matrix is not always assignable, the identity grammian is shown to be always assignable. The results are extended to the case of flexible structures.

  10. Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments

    International Nuclear Information System (INIS)

    A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, δ subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.

  11. 76 FR 55880 - Recording Assignments

    Science.gov (United States)

    2011-09-09

    ..., depending on the date they were recorded. The public may also search patent and trademark assignment... United States Patent and Trademark Office Recording Assignments ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office (USPTO), as part of its continuing...

  12. Halogen effect on structure and 13C NMR chemical shift of 3,6-disubstituted-N-alkyl carbazoles

    DEFF Research Database (Denmark)

    Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof; Daszkiewicz, Zdzislaw; Sauer, Stephan P. A.

    2013-01-01

    Structures of selected 3,6-dihalogeno-N-alkyl carbazole derivatives were calculated at the B3LYP/6-311++G(3df,2pd) level of theory and their 13C NMR isotropic nuclear shieldings were predicted using density functional theory (DFT). The model compounds contained 9H-, N-methyl and N-ethyl derivatives....... The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin-orbit ZORA method. Significant heavy atom shielding effects for the carbon atom directly bonded with bromine and iodine were observed (~ -10 and ~ -30 ppm while the other carbon shifts were practically...

  13. Complete 1H and 13C NMR assignments and anti fungal activity of two 8-hydroxy flavonoids in mixture

    International Nuclear Information System (INIS)

    A mixture of the two new flavonols 8-hydroxy-3, 4', 5, 6, 7-pentamethoxyflavone (1) and 8-hydroxy-3, 3', 4', 5, 6, 7-hexamethoxyflavone (2) was isolated from a commercial sample of Citrus aurantifolia. An array of one- (1H NMR, {1H} -13C NMR, and APT-13C NMR) and two-dimensional NMR techniques (COSY, NOESY, HMQC and HMBC) was used to achieve the structural elucidation and the complete 1H and 13C chemical shift assignments of these natural compounds. In addition, the antifungal activity of these compounds against phytopathogenic and human pathogenic fungi was investigated. (author)

  14. A spectroscopic assignment technique for membrane proteins reconstituted in magnetically aligned bicelles

    International Nuclear Information System (INIS)

    Oriented-sample NMR (OS-NMR) has emerged as a powerful tool for the structure determination of membrane proteins in their physiological environments. However, the traditional spectroscopic assignment method in OS NMR that uses the “shotgun” approach, though effective, is quite labor- and time-consuming as it is based on the preparation of multiple selectively labeled samples. Here we demonstrate that, by using a combination of the spin exchange under mismatched Hartmann-Hahn conditions and a recent sensitivity-enhancement REP-CP sequence, spectroscopic assignment of solid-state NMR spectra of Pf1 coat protein reconstituted in magnetically aligned bicelles can be significantly improved. This method yields a two-dimensional spin-exchanged version of the SAMPI4 spectrum correlating the 15N chemical shift and 15N–1H dipolar couplings, as well as spin-correlations between the (i, i ± 1) amide sites. Combining the spin-exchanged SAMPI4 spectrum with the original SAMPI4 experiment makes it possible to establish sequential assignments, and this technique is generally applicable to other uniaxially aligned membrane proteins. Inclusion of an 15N–15N correlation spectrum into the assignment process helps establish correlations between the peaks in crowded or ambiguous spectral regions of the spin-exchanged SAMPI4 experiment. Notably, unlike the traditional method, only a uniformly labeled protein sample is required for spectroscopic assignment with perhaps only a few selectively labeled “seed” spectra. Simulations for the magnetization transfer between the dilute spins under mismatched Hartmann Hahn conditions for various B1 fields have also been performed. The results adequately describe the optimal conditions for establishing the cross peaks, thus eliminating the need for lengthy experimental optimizations.

  15. Assignment of the vibrations of the S0, S1, and D0 (+) states of perhydrogenated and perdeuterated isotopologues of chlorobenzene.

    Science.gov (United States)

    Andrejeva, Anna; Tuttle, William D; Harris, Joe P; Wright, Timothy G

    2015-09-14

    We report vibrationally resolved spectra of the S1←S0 transition of chlorobenzene using resonance-enhanced multiphoton ionization spectroscopy. We study chlorobenzene-h5 as well as its perdeuterated isotopologue, chlorobenzene-d5. Changes in the form of the vibrational modes between the isotopologues and also between the S0 and S1 electronic states are discussed for each species. Vibrational bands are assigned utilizing quantum chemical calculations, previous experimental results, and isotopic shifts, including those between the (35)Cl and (37)Cl isotopologues. Previous work and assignments of the S1 spectra are discussed. Additionally, the vibrations in the ground state cation, D0 (+), are considered, since these have also been used by previous workers in assigning the excited neutral state spectra. PMID:26374040

  16. Influence of Chemical Effect on the Kβ/Kα Intensity Ratios and Kβ Energy Shift of Co, Ni, Cu, and Zn Complexes

    Institute of Scientific and Technical Information of China (English)

    G. Apaydma, V. Ayhkg; Z. Biyiklioglu; E. Tirasoglu; H. Kantekin

    2008-01-01

    Chemical effects on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes were investigated. The samples were excited by 59.5 keV γ-rays from a 241 Am annular radioactive source. K X-rays emitted by samples were counted by an Ultra-LEGe detector with a resolution of 150 eV at 5.9 keV. We observed the effects of different ligands on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes. We tried to investigate chemical effects on central atoms using the behaviors of different ligands in these complexes. The experimental values of Kβ/Kα were compared with the theoretical and other experimental values of pure Co, Ni, Cu, and Zn.

  17. Determination of the configuration in six-membered saturated heterocycles (N, P, S, Se) and their oxidation products using experimental and calculated NMR chemical shifts

    Czech Academy of Sciences Publication Activity Database

    Buděšínský, Miloš; Vaněk, Václav; Dračínský, Martin; Pohl, Radek; Poštová Slavětínská, Lenka; Sychrovský, Vladimír; Pícha, Jan; Císařová, I.

    2014-01-01

    Roč. 70, č. 25 (2014), s. 3871-3886. ISSN 0040-4020 R&D Projects: GA ČR GA203/09/1919; GA ČR GA13-24880S Institutional support: RVO:61388963 Keywords : six-membered saturated heterocycles (N, P, S, Se) * oxidation products * configuration * NMR * quantum chemical calculations * X-ray structures Subject RIV: CC - Organic Chemistry Impact factor: 2.641, year: 2014

  18. Job Assignment with Multivariate Skills

    OpenAIRE

    Brilon, Stefanie

    2010-01-01

    This paper analyzes the job assignment problem faced by a firm when workers' skills are distributed along several dimensions and jobs require different skills to varying extent. I derive optimal assignment rules with and without slot constraints, and show that under certain circumstances workers may get promoted although in their new job they are expected to be less productive than in their old job. This can be interpreted as a version of the Peter Principle which states that workers get prom...

  19. 4D experiments measured with APSY for automated backbone resonance assignments of large proteins

    International Nuclear Information System (INIS)

    Detailed structural and functional characterization of proteins by solution NMR requires sequence-specific resonance assignment. We present a set of transverse relaxation optimization (TROSY) based four-dimensional automated projection spectroscopy (APSY) experiments which are designed for resonance assignments of proteins with a size up to 40 kDa, namely HNCACO, HNCOCA, HNCACB and HN(CO)CACB. These higher-dimensional experiments include several sensitivity-optimizing features such as multiple quantum parallel evolution in a ‘just-in-time’ manner, aliased off-resonance evolution, evolution-time optimized APSY acquisition, selective water-handling and TROSY. The experiments were acquired within the concept of APSY, but they can also be used within the framework of sparsely sampled experiments. The multidimensional peak lists derived with APSY provided chemical shifts with an approximately 20 times higher precision than conventional methods usually do, and allowed the assignment of 90 % of the backbone resonances of the perdeuterated primase-polymerase ORF904, which contains 331 amino acid residues and has a molecular weight of 38.4 kDa.

  20. Assignment of the side-chain 1H and 13C resonances of interleukin-1β using double- and triple-resonance heteronuclear three-dimensional NMR spectroscopy

    International Nuclear Information System (INIS)

    The assignment of the aliphatic 1H and 13C resonances of IL-1β, a protein of 153 residues and molecular mass 17.4 kDa, is presented by use of a number of novel three-dimensional (3D) heteronuclear NMR experiments which rely on large heteronuclear one-bond J couplings to transfer magnetization and establish through-bond connectivities. These 3D NMR experiments circumvent problems traditionally associated with the application of conventional 2D 1H-1H correlation experiments to proteins of this size, in particular the extensive chemical shift overlap which precludes the interpretation of the spectra and the reduced sensitivity arising from 1H line widths that are often significantly larger than the 1H-1H J couplings. The assignment proceeds in two stages. In the first step the 13Cα chemical shifts are correlated with the NH and 15N chemical shifts by a 3D triple-resonance NH-15N-13Cα (HNCA) correlation experiment which reveals both intraresidue NH(i)-15N(i)-13Cα(i) and some weaker interresidue NH(i)-15N(i)-Cα(i-1) correlations, the former via intraresidue one-bond 1JNCα and the latter via interresidue two-bond 2HNCα couplings. The second step involves the identification of side-chain spin systems by 3D 1H-13C-13C-1H correlated (HCCH-COSY) and 3D 1H-13C-13C-1H total correlated (HCCH-TOCSY) spectroscopy, the latter making use of isotropic mixing of 13C magnetization to obtain relayed connectivities along the side chains. The authors were able to obtain complete 1H and 13C side-chain assignments for all residues, with the exception of 4 (out of a total of 15) lysine residues for which partial assignments were obtained

  1. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2012-03-21

    Background: Chemical shift mapping is an important technique in NMR-based 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, which is not efficient for high-throughput drug screening.Results: 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-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

  2. Synthesis, antimicrobial evaluation and theoretical prediction of NMR chemical shifts of thiazole and selenazole derivatives with high antifungal activity against Candida spp.

    Science.gov (United States)

    Łączkowski, Krzysztof Z.; Motylewska, Katarzyna; Baranowska-Łączkowska, Angelika; Biernasiuk, Anna; Misiura, Konrad; Malm, Anna; Fernández, Berta

    2016-03-01

    Synthesis and investigation of antimicrobial activities of novel thiazoles and selenazoles is presented. Their structures were determined using NMR, FAB(+)-MS, HRMS and elemental analyses. To support the experiment, theoretical calculations of the 1H NMR shifts were carried out for representative systems within the DFT B3LYP/6-311++G** approximation which additionally confirmed the structure of investigated compounds. Among the derivatives, compounds 4b, 4h, 4j and 4l had very strong activity against reference strains of Candida albicans ATCC and Candida parapsilosis ATCC 22019 with MIC = 0.49-7.81 μg/ml. In the case of compounds 4b, 4c, 4h - 4j and 4l, the activity was very strong against of Candida spp. isolated from clinical materials, i.e. C. albicans, Candida krusei, Candida inconspicua, Candida famata, Candida lusitaniae, Candida sake, C. parapsilosis and Candida dubliniensis with MIC = 0.24-15.62 μg/ml. The activity of several of these was similar to the activity of commonly used antifungal agent fluconazole. Additionally, compounds 4m - 4s were found to be active against Gram-positive bacteria, both pathogenic staphylococci Staphylococcus aureus ATCC with MIC = 31.25-125 μg/ml and opportunistic bacteria, such as Staphylococcus epidermidis ATCC 12228 and Micrococcus luteus ATCC 10240 with MIC = 7.81-31.25 μg/ml.

  3. Triple-Resonance Methods for Complete Resonance Assignment of Aromatic Protons and Directly Bound Heteronuclei in Histidine and Tryptophan Residues

    International Nuclear Information System (INIS)

    A set of three experiments is described which correlate aromatic resonances of histidine and tryptophan residues with amide resonances in 13C/15N-labelled proteins. Provided that backbone 1H and 15N positions of the sequentially following residues are known, this results in sequence-specific assignment of histidine chemical shifts. In the reverse situation, these residues can be located in the 1H-15N correlation map to facilitate backbone assignments. It may be chosen between selective versions for either of the two amino acid types or simultaneous detection of both with complete discrimination against phenylalanine or tyrosine residues in each case. The linkages between δ-proton/carbon and the remaining aromatic as well as backbone resonances do not rely on through-space interactions, which may be ambiguous, but exclusively employ one-bond scalar couplings for magnetization transfer instead. Knowledge of these aromatic chemical shifts is the prerequisite for the analysis of NOESY spectra, the study of protein-ligand interactions involving histidine and tryptophan residues and the monitoring of imidazole protonation states during pH titrations. The new methods are demonstrated with five different proteins with molecular weights ranging from 11 to 28 kDa

  4. The Tactical Berth Allocation Problem with QC Assignment and Transshipment Costs

    OpenAIRE

    Giallombardo, Giovanni; Moccia, Luigi; Salani, Matteo; Vacca, Ilaria

    2009-01-01

    In this work we integrate at the tactical level two decision problems arising in container terminals: the berth allocation problem, which consists of assigning and scheduling incoming ships to berthing positions, and the quay crane assignment problem, which assigns to incoming ships a certain QC profile (i.e. number of quay cranes per working shift). We present two formulations: a mixed integer quadratic program and a linearization which reduces to a mixed integer linear program. The objectiv...

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

    International Nuclear Information System (INIS)

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

  6. Hard X-ray photoelectron spectra (HXPES) of bulk non-conductor vitreous SiO2: Minimum linewidths and surface chemical shifts

    International Nuclear Information System (INIS)

    Highlights: • Electronic structure of non-conducting glass studied by hard X-ray photoelectron spectroscopy. • A thin film of Cr was deposited on the vitreous SiO2 glass to overcome the sample charging. • Excellent O 1s and Si 1s linewidths were obtained, matching those reported using the laboratory based Kratos Axis Ultra spectrometer equipped with a magnetic compensation system. • The bulk and interface states of non-conducting samples are studied as a function of photon energy. - Abstract: Hard X-ray photoelectron spectra (2200 eV to 5000 eV photon energies) have been obtained for the first time on a bulk non-conductor, vitreous SiO2, on a high resolution (E/ΔE of 10,000) synchrotron beamline at the Canadian Light Source (CLS). To minimize charging and differential charging, the SiO2 was coated with very thin layers (0.5 to 1.5 nm) of Cr metal. The O 1s linewidth obtained at 2500 eV photon energy was 1.26 eV—the minimum linewidth for SiO2—and in good agreement with that obtained at 1486 eV on a Kratos Axis Ultra spectrometer equipped with a magnetic charge compensation system. The Si 1s linewidth of 1.5 eV, somewhat broader than that previously obtained at 1486 eV on the Si 2p3/2 line of 1.16 eV, is mainly due to the much larger inherent Si 1s linewidth (0.5 eV) compared to the inherent Si 2p linewidth (<0.1 eV). Both linewidths are dominated by the large final state vibrational broadening previously described. The Cr coating produces surface monolayers of interfacial Cr “suboxide” (Cr-subox), Cr metal, and a surface Cr oxide (Cr-surfox). Cr-subox (Si−O−Cr) gives rise to the weak near-surface Si 1s peak, while both oxides give rise to both the weak surface O 1s peak and the Cr 2p oxide peak. Both the O 1s and Si 1s surface peaks are shifted by ∼2 eV relative to the large bulk Si 1s and O 1s peaks. The weak Si 1s and O 1s surface peaks along with the Cr 2p oxide peak decrease in intensity greatly as the photon energy increases, due to an

  7. Using NMR chemical shift imaging to monitor swelling and molecular transport in drug-loaded tablets of hydrophobically modified poly(acrylic acid): methodology and effects of polymer (in)solubility.

    Science.gov (United States)

    Knöös, Patrik; Topgaard, Daniel; Wahlgren, Marie; Ulvenlund, Stefan; Piculell, Lennart

    2013-11-12

    A new technique has been developed using NMR chemical shift imaging (CSI) to monitor water penetration and molecular transport in initially dry polymer tablets that also contain small low-molecular weight compounds to be released from the tablets. Concentration profiles of components contained in the swelling tablets could be extracted via the intensities and chemical shift changes of peaks corresponding to protons of the components. The studied tablets contained hydrophobically modified poly(acrylic acid) (HMPAA) as the polymer component and griseofulvin and ethanol as hydrophobic and hydrophilic, respectively, low-molecular weight model compounds. The water solubility of HMPAA could be altered by titration with NaOH. In the pure acid form, HMPAA tablets only underwent a finite swelling until the maximum water content of the polymer-rich phase, as confirmed by independent phase studies, had been reached. By contrast, after partial neutralization with NaOH, the polyacid became fully miscible with water. The solubility of the polymer affected the water penetration, the polymer release, and the releases of both ethanol and griseofulvin. The detailed NMR CSI concentration profiles obtained highlighted the clear differences in the disintegration/dissolution/release behavior for the two types of tablet and provided insights into their molecular origin. The study illustrates the potential of the NMR CSI technique to give information of importance for the development of pharmaceutical tablets and, more broadly, for the general understanding of any operation that involves the immersion and ultimate disintegration of a dry polymer matrix in a solvent. PMID:24106807

  8. Who Benefits from Homework Assignments?

    Science.gov (United States)

    Ronning, Marte

    2011-01-01

    Using Dutch data on pupils in elementary school this paper is the first empirical study to analyze whether assigning homework has a heterogeneous impact on pupil achievement. Addressing potential biases by using a difference-in-difference approach, I find that the test score gap is larger in classes where everybody gets homework than in classes…

  9. Assigning agents to a line

    DEFF Research Database (Denmark)

    Hougaard, Jens Leth; Moreno-Ternero, Juan D.; Østerdal, Lars Peter Raahave

    2014-01-01

    minimizing modification of the classic random priority method to solve this class of problems. We also provide some logical relations in our setting among standard axioms in the literature on assignment problems, and explore the robustness of our results to several extensions of our setting....

  10. Probabilistic analysis of power assignments

    NARCIS (Netherlands)

    Graaf, de Maurits; Manthey, Bodo

    2014-01-01

    A fundamental problem for wireless ad hoc networks is the assignment of suitable transmission powers to the wireless devices such that the resulting communication graph is connected. The goal is to minimize the total transmit power in order to maximize the life-time of the network. Our aim is a prob

  11. Resonance assignments, secondary structure and topology of leukaemia inhibitory factor in solution

    International Nuclear Information System (INIS)

    The chemical shift assignments and secondary structure of a murine-human chimera,MH35, of leukaemia inhibitory factor (LIF), a 180-residue protein of molecular mass 20 kDa,have been determined from multidimensional heteronuclear NMR spectra acquired on a uniformly 13C,15N-labelled sample. Secondary structure elements were defined on the basis of chemical shifts, NH-CαH coupling constants, medium-range NOEs and the location of slowly exchanging amide protons. The protein contains four α-helices, the relative orientations of which were determined on the basis of long-range, interhelical NOEs. The four helices are arranged in an up-up-down-down orientation, as found in other four-helical bundle cytokines. The overall topology of MH35-LIF is similar to that of the X-ray crystallographic structure for murine LIF [Robinson et al. (1994) Cell, 77, 1101-1116]. Differences between the X-ray structure and the solution structure are evident in the N-terminal tail, where the solution structure has a trans-Pro17 compared with the cis-Pro17 found in the crystal structure and the small antiparallel β-sheet encompassing residues in the N-terminus and CD loop in the crystal structure is less stable

  12. Special training of shift personnel

    International Nuclear Information System (INIS)

    The first step of on-the-job training is practical observation phase in an operating Nuclear Plant, where the participants are assigned to shift work. The simulator training for operating personnel, for key personnel and, to some extent, also for maintenance personnel and specialists give the practical feeling for Nuclear Power Plant behaviour during normal and abnormal conditions. During the commissioning phase of the own Nuclear Power Plant, which is the most important practical training, the participants are integrated into the commissioning staff and assisted during their process of practical learning by special instructors. The preparation for the licensing exams is vitally important for shift personnel and special courses are provided after the first non-nuclear trial operation of the plant. Personnel training also includes performance of programmes and material for retraining, training of instructors and assistance in building up special training programmes and material as well as training centers. (orig./RW)

  13. 1H, 15N and 13C NMR resonance assignment, secondary structure and global fold of the FMN-binding domain of human cytochrome P450

    International Nuclear Information System (INIS)

    The FMN-binding domain of human NADPH-cytochrome P450 reductase,corresponding to exons 3-;7, has been expressed at high level in an active form and labelled with 13C and 15N. Most of the backbone and aliphatic side-chain 1H, 15Nand 13C resonances have been assigned using heteronuclear double- and triple-resonance methods, together with a semiautomatic assignment strategy. The secondary structure as estimated from the chemical shift index and NOE connectivities consists of six α-helices and fiveβ-strands. The global fold was deduced from the long-range NOE sun ambiguously assigned in a 4D 13C-resolved HMQC-NOESY-HMQC spectrum. The fold is of the alternating α/β type, with the fiveβ-strands arranged into a parallel β-sheet. The secondary structure and global fold are very similar to those of the bacterial flavodoxins, but the FMN-binding domain has an extra short helix in place of a loop, and an extra helix at the N-terminus (leading to the membrane anchordomain in the intact P450 reductase). The experimental constraints were combined with homology modelling to obtain a structure of the FMN-bindingdomain satisfying the observed NOE constraints. Chemical shift comparisons showed that the effects of FMN binding and of FMN reduction are largely localised at the binding site

  14. Reduced Dimensionality tailored HN(C)N Pulse Sequences for Efficient Backbone Resonance Assignment of Proteins through Rapid Identification of Sequential HSQC peaks

    CERN Document Server

    Kumar, Dinesh

    2013-01-01

    Two novel reduced dimensionality (RD) experiments -(4,3)D-hNCOcaNH and (4,3)D-hNcoCANH- have been presented here to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. The experiments basically represent an improvisation of previously reported HN(C)N experiment [Panchal et. al., J. Biomol. NMR. (2002), 20 (2), 135-147] and exploit the simple reduced dimensionality NMR concept [Szyperski et. al. (2002), Proc. Natl. Acad. Sci. U.S.A. 99(12), 8009-8014] to achieve (a) higher dispersion and resolution along the co-evolved F1 dimension and (b) rapid identification of sequential HSQC peaks on its F2(15N)- F3(1H) planes. The current implementation is based on the fact that the linear combination of 15N and 13CO/13Ca chemical shifts offers relatively better dispersion and randomness compared to the individual chemical shifts; thus enables the assignment of crowded HSQC spectra by resolving the ambiguities generally encountered in HNCN based assignment protocol because of ...

  15. 78 FR 70047 - Request for the Technical Review of 25 Draft Skin Notation Assignments and Skin Notation Profiles

    Science.gov (United States)

    2013-11-22

    ... Skin Notation Assignments and Skin Notation Profiles AGENCY: National Institute for Occupational Safety... Human Services (HHS). ACTION: Request for comments. SUMMARY: The National Institute for Occupational..., such as airway hyper reactivity (asthma). Candidate chemicals may be assigned more than one...

  16. Structure-based predictions of 13C-NMR chemical shifts for a series of 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indoles derivatives using GA-based MLR method

    Science.gov (United States)

    Ghavami, Raouf; Sadeghi, Faridoon; Rasouli, Zolikha; Djannati, Farhad

    2012-12-01

    Experimental values for the 13C NMR chemical shifts (ppm, TMS = 0) at 300 K ranging from 96.28 ppm (C4' of indole derivative 17) to 159.93 ppm (C4' of indole derivative 23) relative to deuteride chloroform (CDCl3, 77.0 ppm) or dimethylsulfoxide (DMSO, 39.50 ppm) as internal reference in CDCl3 or DMSO-d6 solutions have been collected from literature for thirty 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indole derivatives containing different substituted groups. An effective quantitative structure-property relationship (QSPR) models were built using hybrid method combining genetic algorithm (GA) based on stepwise selection multiple linear regression (SWS-MLR) as feature-selection tools and correlation models between each carbon atom of indole derivative and calculated descriptors. Each compound was depicted by molecular structural descriptors that encode constitutional, topological, geometrical, electrostatic, and quantum chemical features. The accuracy of all developed models were confirmed using different types of internal and external procedures and various statistical tests. Furthermore, the domain of applicability for each model which indicates the area of reliable predictions was defined.

  17. Solution behavior and complete 1H and 13C NMR assignments of the coenzyme B12 derivative (5'-deoxyadenosyl)cobinamide using modern 2D NMR experiments, including 600-MHz 1H NMR data

    International Nuclear Information System (INIS)

    Two-dimensional (2D) NMR methods have been used to assign completely the 1H and 13C NMR spectra of the (5'-deoxyadenosyl)cobinamide cation (AdoCbi+) in D2O. Most of the 1H spectral assignments were made by using 2D homonuclear shift correlation spectroscopy (COSY), homonuclear Hartmann-Hahn spectroscopy (HOHAHA), absorption-mode (phase sensitive) 2D nuclear Overhauser effect (NOE) spectroscopy, and spin-locked NOE spectroscopy (also called ROESY, for rotating-frame Overhauser enhancement spectroscopy). Most of the protonated carbon resonances were assigned by using 1H-detected heteronuclear multiple-quantum coherence (HMQC) spectroscopy. The nonprotonated carbon resonances, as well as the remaining unassigned 1H and 13C NMR signals, were assigned from long-range 1H-13C connectivities determined from 1H-detected multiple-bond heteronuclear multiple-quantum coherence spectroscopy (HMBC). Comparison of the 13C chemical shifts and 1H NOEs of AdoCbi+ with those of coenzyme B12 ((5'-deoxyadenosyl)cobalamin) and its benzimidazole-protonated, base-off form indicates that the electronic properties and structure of AdoCbi+ are similar to that of coenzyme B12 in the protonated, base-off form. The 13C chemical shifts of most of the carbons of AdoCbi+ do not vary significantly from those of base-off, benzimidazole-protonated coenzyme B12, indicating that the electronic environment of the corrin ring is also similar in both compounds. However, significant differences in the chemical shifts of some of the corresponding carbons of the b, d, e, and f corrin side chains in AdoCbi+ and in base-off, benzimidazole-protonated coenzyme B12 indicate that the positions of these side chains may be different in AdoCbi+ compared to base-off coenzyme B12

  18. Fleet Assignment Using Collective Intelligence

    Science.gov (United States)

    Antoine, Nicolas E.; Bieniawski, Stefan R.; Kroo, Ilan M.; Wolpert, David H.

    2004-01-01

    Product distribution theory is a new collective intelligence-based framework for analyzing and controlling distributed systems. Its usefulness in distributed stochastic optimization is illustrated here through an airline fleet assignment problem. This problem involves the allocation of aircraft to a set of flights legs in order to meet passenger demand, while satisfying a variety of linear and non-linear constraints. Over the course of the day, the routing of each aircraft is determined in order to minimize the number of required flights for a given fleet. The associated flow continuity and aircraft count constraints have led researchers to focus on obtaining quasi-optimal solutions, especially at larger scales. In this paper, the authors propose the application of this new stochastic optimization algorithm to a non-linear objective cold start fleet assignment problem. Results show that the optimizer can successfully solve such highly-constrained problems (130 variables, 184 constraints).

  19. Who benefits from homework assignments?

    OpenAIRE

    Rønning, Marte

    2008-01-01

    Abstract: Using Dutch data on pupils in elementary school this paper is the first empirical study that analyzes whether assigning homework has an heterogeneous impact on pupil achievement. Addressing potential biases that arise from unobserved school quality, pupil selection by exploiting different methods, I find that the test score gap is larger in classes where everybody gets homework than in classes where nobody gets homework. More precisely pupils belonging to the upper part of the so...

  20. Relevant Explanations: Allowing Disjunctive Assignments

    OpenAIRE

    Shimony, Solomon Eyal

    2013-01-01

    Relevance-based explanation is a scheme in which partial assignments to Bayesian belief network variables are explanations (abductive conclusions). We allow variables to remain unassigned in explanations as long as they are irrelevant to the explanation, where irrelevance is defined in terms of statistical independence. When multiple-valued variables exist in the system, especially when subsets of values correspond to natural types of events, the over specification problem, alleviated by inde...

  1. On the calculation of Mossbauer isomer shift

    NARCIS (Netherlands)

    Filatov, Michael

    2007-01-01

    A quantum chemical computational scheme for the calculation of isomer shift in Mossbauer spectroscopy is suggested. Within the described scheme, the isomer shift is treated as a derivative of the total electronic energy with respect to the radius of a finite nucleus. The explicit use of a finite nuc

  2. A Statistical Programme Assignment Model

    DEFF Research Database (Denmark)

    Rosholm, Michael; Staghøj, Jonas; Svarer, Michael

    When treatment effects of active labour market programmes are heterogeneous in an observable way  across the population, the allocation of the unemployed into different programmes becomes a particularly  important issue. In this paper, we present a statistical model designed to improve the present...... duration of unemployment spells may result if a statistical programme assignment model is introduced. We discuss several issues regarding the  plementation of such a system, especially the interplay between the statistical model and  case workers....

  3. A comparative quantitative analysis of the IDEAL (iterative decomposition of water and fat with echo asymmetry and least-squares estimation) and the CHESS (chemical shift selection suppression) techniques in 3.0 T L-spine MRI

    Science.gov (United States)

    Kim, Eng-Chan; Cho, Jae-Hwan; Kim, Min-Hye; Kim, Ki-Hong; Choi, Cheon-Woong; Seok, Jong-min; Na, Kil-Ju; Han, Man-Seok

    2013-03-01

    This study was conducted on 20 patients who had undergone pedicle screw fixation between March and December 2010 to quantitatively compare a conventional fat suppression technique, CHESS (chemical shift selection suppression), and a new technique, IDEAL (iterative decomposition of water and fat with echo asymmetry and least squares estimation). The general efficacy and usefulness of the IDEAL technique was also evaluated. Fat-suppressed transverse-relaxation-weighed images and longitudinal-relaxation-weighted images were obtained before and after contrast injection by using these two techniques with a 1.5T MR (magnetic resonance) scanner. The obtained images were analyzed for image distortion, susceptibility artifacts and homogenous fat removal in the target region. The results showed that the image distortion due to the susceptibility artifacts caused by implanted metal was lower in the images obtained using the IDEAL technique compared to those obtained using the CHESS technique. The results of a qualitative analysis also showed that compared to the CHESS technique, fewer susceptibility artifacts and more homogenous fat removal were found in the images obtained using the IDEAL technique in a comparative image evaluation of the axial plane images before and after contrast injection. In summary, compared to the CHESS technique, the IDEAL technique showed a lower occurrence of susceptibility artifacts caused by metal and lower image distortion. In addition, more homogenous fat removal was shown in the IDEAL technique.

  4. Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women

    Energy Technology Data Exchange (ETDEWEB)

    Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C.; Joseph, Gabby B.; Yap, Samuel P.; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M. [University of California, San Francisco, Musculoskeletal and Quantitative Imaging Research Group, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States)

    2012-07-15

    The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 {+-} 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P < 0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0-4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. (orig.)

  5. Sofic Tree-Shifts

    OpenAIRE

    Aubrun, Nathalie; Béal, Marie-Pierre

    2013-01-01

    We introduce the notion of sofic tree-shifts which corresponds to symbolic dynamical systems of infinite ranked trees accepted by finite tree automata. We show that, contrary to shifts of infinite sequences, there is no unique reduced deterministic irreducible tree automaton accepting an irreducible sofic tree-shift, but that there is a unique synchronized one, called the Fischer automaton of the tree-shift. We define the notion of almost of finite type tree-shift which are sofic tree-shifts accepted...

  6. Heterologous Expression of Hen Egg White Lysozyme and Resonance Assignment of Tryptophan Side Chains in its Non-native States

    International Nuclear Information System (INIS)

    A new protocol is described for the isotope (15N and 13C,15N) enrichment of hen egg white lysozyme. Hen egg white lysozyme and an all-Ala-mutant of this protein have been expressed in E. coli. They formed inclusion bodies from which mg quantities of the proteins were purified and prepared for NMR spectroscopic investigations. 1H,13C and 15N main chain resonances of disulfide reduced and S-methylated lysozyme were assigned and its residual structure in water pH 2 was characterized by chemical shift perturbation analysis. A new NMR experiment has been developed to assign tryptophan side chain indole resonances by correlation of side chain and backbone NH resonances with the Cγ resonances of these residues. Assignment of tryptophan side chains enables further residue specific investigations on structural and dynamical properties, which are of significant interest for the understanding of non-natives states of lysozyme stabilized by hydrophobic interactions between clusters of tryptophan residues

  7. ADAPT-NMR 3.0: utilization of BEST-type triple-resonance NMR experiments to accelerate the process of data collection and assignment

    International Nuclear Information System (INIS)

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) is a software package whose Bayesian core uses on-the-fly chemical shift assignments to guide data acquisition by non-uniform sampling from a panel of through-bond NMR experiments. The new version of ADAPT-NMR (ADAPT-NMR v3.0) has the option of utilizing 2D tilted-plane versions of 3D fast spectral acquisition with BEST-type pulse sequences, while also retaining the capability of acquiring and processing data from tilted-plane versions of conventional sensitivity-enhanced experiments. The use of BEST experiments significantly reduces data collection times and leads to enhanced performance by ADAPT-NMR

  8. Assignment Choice, Effort, and Assignment Completion: Does Work Ethic Predict Those Who Choose Higher-Effort Assignments?

    Science.gov (United States)

    Parkhurst, John T.; Fleisher, Matthew S.; Skinner, Christopher H.; Woehr, David J.; Hawthorn-Embree, Meredith L.

    2011-01-01

    After completing the Multidimensional Work-Ethic Profile (MWEP), 98 college students were given a 20-problem math computation assignment and instructed to stop working on the assignment after completing 10 problems. Next, they were allowed to choose to finish either the partially completed assignment that had 10 problems remaining or a new…

  9. Resonance-enhanced multiphoton ionization (REMPI) spectroscopy of bromobenzene and its perdeuterated isotopologue: Assignment of the vibrations of the S(0), S(1), and D(0)(+) states of bromobenzene and the S(0) and D(0)(+) states of iodobenzene.

    Science.gov (United States)

    Andrejeva, Anna; Tuttle, William D; Harris, Joe P; Wright, Timothy G

    2015-12-28

    We report vibrationally resolved spectra of the S1←S0 transition of bromobenzene using resonance-enhanced multiphoton ionization spectroscopy. We study bromobenzene-h5 as well as its perdeuterated isotopologue, bromobenzene-d5. The form of the vibrational modes between the isotopologues and also between the S0 and S1 electronic states is discussed for each species, allowing assignment of the bands to be achieved and the activity between states and isotopologues to be established. Vibrational bands are assigned utilizing quantum chemical calculations, previous experimental results, and isotopic shifts. Previous work and assignments of the S1 spectra are discussed. Additionally, the vibrations in the ground state cation, D0 (+), are considered, since these have also been used by previous workers in assigning the excited neutral state spectra. We also examine the vibrations of iodobenzene in the S0 and D0 (+) states and comment on the previous assignments of these. In summary, we have been able to assign the corresponding vibrations across the whole monohalobenzene series of molecules, in the S0, S1, and D0 (+) states, gaining insight into vibrational activity and vibrational couplings. PMID:26723684

  10. Resonance-enhanced multiphoton ionization (REMPI) spectroscopy of bromobenzene and its perdeuterated isotopologue: Assignment of the vibrations of the S0, S1, and D0+ states of bromobenzene and the S0 and D0+ states of iodobenzene

    International Nuclear Information System (INIS)

    We report vibrationally resolved spectra of the S1←S0 transition of bromobenzene using resonance-enhanced multiphoton ionization spectroscopy. We study bromobenzene-h5 as well as its perdeuterated isotopologue, bromobenzene-d5. The form of the vibrational modes between the isotopologues and also between the S0 and S1 electronic states is discussed for each species, allowing assignment of the bands to be achieved and the activity between states and isotopologues to be established. Vibrational bands are assigned utilizing quantum chemical calculations, previous experimental results, and isotopic shifts. Previous work and assignments of the S1 spectra are discussed. Additionally, the vibrations in the ground state cation, D0+, are considered, since these have also been used by previous workers in assigning the excited neutral state spectra. We also examine the vibrations of iodobenzene in the S0 and D0+ states and comment on the previous assignments of these. In summary, we have been able to assign the corresponding vibrations across the whole monohalobenzene series of molecules, in the S0, S1, and D0+ states, gaining insight into vibrational activity and vibrational couplings

  11. Influence of substituents on chemical shift of {delta}({sup 13}C) in the series of 5-methyl-5H-indole [2,3-b]quinoline derivatives; Wplyw podstawnikow na przesuniecie chemiczne {sigma}({sup 13}C) w serii pochodnych 5-metylo-5H-indolo-[2,3-b]chinoliny

    Energy Technology Data Exchange (ETDEWEB)

    Kamienska-Trela, K.; Kania, L.; Kaczmarek, L. [Inst. Chemii Organicznej, Polska Akademia Nauk, Warsaw (Poland)

    1994-12-31

    {sup 13}C NMR spectra of series of 5-methyl-5H-indole quinoline substituted with different groups and their number have been measured. The influence of steric and electronic properties of substituents on observed chemical shifts of {sup 13}C nuclei have been discussed. 1 fig., 1 tab.

  12. 7 CFR 1437.104 - Assigned production.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Assigned production. 1437.104 Section 1437.104... Determining Yield Coverage Using Actual Production History § 1437.104 Assigned production. (a) When determining losses under this section, assigned production will be used to offset the loss of production...

  13. Lexical Stress Assignment in Italian Developmental Dyslexia

    Science.gov (United States)

    Paizi, Despina; Zoccolotti, Pierluigi; Burani, Cristina

    2011-01-01

    Stress assignment to Italian polysyllabic words is unpredictable, because stress is neither marked nor predicted by rule. Stress assignment, especially to low frequency words, has been reported to be a function of stress dominance and stress neighbourhood. Two experiments investigate stress assignment in sixth-grade, skilled and dyslexic, readers.…

  14. Chemical characteristics assigned to trajectory clusters during the MINOS campaign

    Directory of Open Access Journals (Sweden)

    M. Traub

    2003-01-01

    Full Text Available During the Mediterranean Intensive Oxidant Study (MINOS in August 2001 a total of 14 measurement flights were performed with the DLR Falcon jet aircraft from Heraklion, Crete. One objective of this campaign was to investigate the role of long-range transport of pollutants into the Mediterranean area. An analysis of 5-day back trajectories indicates that in the lower troposphere (0-4 km air masses originated from eastern and western Europe, in the mid-troposphere (4-8 km from the North Atlantic Ocean region and in the upper troposphere (8-14 km from North Atlantic Ocean/North America (NANA as well as South Asia. We allocated all back trajectories to clusters based on their ending height and source region. The mixing ratios of ozone, nitrogen oxide, total reactive oxidized nitrogen (NOy, formaldehyde, methanol, acetonitrile, acetone, peroxyacetyl nitrate (PAN, carbon dioxide, carbon monoxide and methane measured along the flight tracks are examined in relation to the different cluster trajectories. In the lower troposphere the mean trace gas mixing ratios of the eastern Europe cluster trajectories were significantly higher than those from western Europe. In the upper troposphere air from the NANA region seems to be influenced by the stratosphere, in addition, air masses were transported from South Asia, being influenced by strong convection in the Indian monsoon.

  15. 磁共振化学位移成像评估椎体骨髓脂肪含量的应用%Application of assessing fat content of vertebral bone marrow with chemical-shift MRI

    Institute of Scientific and Technical Information of China (English)

    雷立存; 任庆云; 母建奎; 祁宇轩; 何丽; 刘斋

    2015-01-01

    目的:探讨磁共振化学位移成像技术评估绝经后女性椎体骨髓脂肪含量的可行性。方法选取56例绝经后女性患者的腰椎1~4椎体(共计224个椎体),所有患者均行磁共振化学位移成像和双能X线吸收法骨密度测定,得出每个椎体信号下降指数和骨密度值,按照骨密度T分数分为骨量正常组,骨量减少组和骨质疏松组,分析三组椎体信号下降指数的差异,探讨不同骨密度组椎体信号下降指数的变化规律。结果56例患者224个椎体按照T分数进行分组,骨量正常组68个,骨量减少组72个,骨质疏松组84个,骨量正常组,骨量减少组和骨质疏松组椎体信号下降指数的中位数分别是60.57%(67.86%~45.34%),58.22%(69.29%~49.49%),56.80%(67.52%~36.00%),骨质疏松组同正常组、骨量减少组比较具有统计学差异(P<0.05),正常组、骨量减少组比较无统计学差异(P>0.05)。结论磁共振化学位移成像通过测定椎体下降指数可以反映椎体脂肪含量的变化,对骨质疏松做出诊断,具有较高的应用价值。%Objective To investigate the feasibility for assessing the fat content of vertebral bone marrow in postmenopausal women with chemical-shift MRI technique..Methods Lumbar vertebral body.(L1-L4)(224 vertebral body) of 56 cases of postmeno-pausal women were selected and all patients were performed with chemical-shift MRI and dual-energy X-ray absorptiometry (DXA).to obtain signal decline index and bone density..The patients were divided into normal group,.osteopenia group and osteoporosis group according to DXA results,.and the difference of signal decline index among three groups was analyzed so as to investigate the law of signal decline index of vertebrae of groups with different bone density. Results 68 subjects in normal group,.72 subjects with osteopenia and 84 subjects with

  16. An Investigation of the Partial-Assignment Completion Effect on Students' Assignment Choice Behavior

    Science.gov (United States)

    Hawthorn-Embree, Meredith L.; Skinner, Christopher H.; Parkhurst, John; Conley, Elisha

    2011-01-01

    This study was designed to investigate the partial assignment completion effect. Seventh-grade students were given a math assignment. After working for 5 min, they were interrupted and their partially completed assignments were collected. About 20 min later, students were given their partially completed assignment and a new, control assignment…

  17. Models and Heuristics for the Tactical Berth Allocation Problem with Quay-Crane Assignment and Transshipment Costs

    OpenAIRE

    Giallombardo, Giovanni; Moccia, Luigi; Salani, Matteo; Vacca, Ilaria

    2009-01-01

    In the context of international sea-freight container transport, we study an integrated decision problem arising in container terminal management. We consider the integration of the Berth Allocation Problem (BAP), which consists of assigning and scheduling incoming ships to berthing positions, and the Quay Crane Assignment Problem (QCAP), which assigns to incoming ships a certain QC profile (i.e. number of quay cranes per working shift). BAP and QCAP are strictly correlated, since the QC prof...

  18. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    1969-01-01

    High Resolution NMR: Theory and Chemical Applications focuses on the applications of nuclear magnetic resonance (NMR), as well as chemical shifts, lattices, and couplings. The book first offers information on the theory of NMR, including nuclear spin and magnetic moment, spin lattice relaxation, line widths, saturation, quantum mechanical description of NMR, and ringing. The text then ponders on instrumentation and techniques and chemical shifts. Discussions focus on the origin of chemical shifts, reference compounds, empirical correlations of chemical shifts, modulation and phase detection,

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

    International Nuclear Information System (INIS)

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

  20. Implementing OpenShift

    CERN Document Server

    Miller, Adam

    2013-01-01

    A standard tutorial-based approach to using OpenShift and deploying custom or pre-built web applications to the OpenShift Online cloud.This book is for software developers and DevOps alike who are interested in learning how to use the OpenShift Platform-as-a-Service for developing and deploying applications, how the environment works on the back end, and how to deploy their very own open source Platform-as-a-Service based on the upstream OpenShift Origin project.

  1. Quantized beam shifts

    CERN Document Server

    Kort-Kamp, W J M; Dalvit, D A R

    2015-01-01

    We predict quantized Imbert-Fedorov, Goos-H\\"anchen, and photonic spin Hall shifts for light beams impinging on a graphene-on-substrate system in an external magnetic field. In the quantum Hall regime the Imbert-Fedorov and photonic spin Hall shifts are quantized in integer multiples of the fine structure constant $\\alpha$, while the Goos- H\\"anchen ones in multiples of $\\alpha^2$. We investigate the influence on these shifts of magnetic field, temperature, and material dispersion and dissipation. An experimental demonstration of quantized beam shifts could be achieved at terahertz frequencies for moderate values of the magnetic field.

  2. Unambiguous assigning of the signals of the nuclear magnetic resonance spectra of {sup 1} H and {sup 13} C of monoterpenes using computational methods; Asignacion inequivoca de las senales del espectro de resonancia magnetica nuclear de {sup 1} H y {sup 13} C de monoterpenos empleando metodos computacionales

    Energy Technology Data Exchange (ETDEWEB)

    Cortes, F.; Cuevas, G.; Tenorio, J.; Rochin, A.L. [Universidad Nacional Autonoma de Mexico, Instituto de Quimica, A.P. 70213, 04510 Mexico D.F. (Mexico)

    2000-07-01

    Ab initio calculations, within the frame of Density Functional Theory were carried out on camphene and {alpha}-pinene. The {sup 1} H and {sup 13} C shifts were estimated according to the recently developed Sum-Over-States Density Functional Perturbation Theory (SOS-DFPT) as implemented in a modified deMon-KS program. The calculations not only reproduced the observed NMR chemical shifts, quantitatively in the case of {sup 1} H nuclei and qualitatively in the case of {sup 13} C nuclei, but also allow assigning unambiguously the signal on these spectra. (Author)

  3. Out-and-back {sup 13}C-{sup 13}C scalar transfers in protein resonance assignment by proton-detected solid-state NMR under ultra-fast MAS

    Energy Technology Data Exchange (ETDEWEB)

    Barbet-Massin, Emeline; Pell, Andrew J. [University of Lyon, CNRS/ENS Lyon/UCB Lyon 1, Centre de RMN a Tres Hauts Champs (France); Jaudzems, Kristaps [Latvian Institute of Organic Synthesis (Latvia); Franks, W. Trent; Retel, Joren S. [Leibniz-Institut fuer Molekulare Pharmakologie (Germany); Kotelovica, Svetlana; Akopjana, Inara; Tars, Kaspars [Biomedical Research and Study Center (Latvia); Emsley, Lyndon [University of Lyon, CNRS/ENS Lyon/UCB Lyon 1, Centre de RMN a Tres Hauts Champs (France); Oschkinat, Hartmut [Leibniz-Institut fuer Molekulare Pharmakologie (Germany); Lesage, Anne; Pintacuda, Guido, E-mail: guido.pintacuda@ens-lyon.fr [University of Lyon, CNRS/ENS Lyon/UCB Lyon 1, Centre de RMN a Tres Hauts Champs (France)

    2013-08-15

    We present here {sup 1}H-detected triple-resonance H/N/C experiments that incorporate CO-CA and CA-CB out-and-back scalar-transfer blocks optimized for robust resonance assignment in biosolids under ultra-fast magic-angle spinning (MAS). The first experiment, (H)(CO)CA(CO)NH, yields {sup 1}H-detected inter-residue correlations, in which we record the chemical shifts of the CA spins in the first indirect dimension while during the scalar-transfer delays the coherences are present only on the longer-lived CO spins. The second experiment, (H)(CA)CB(CA)NH, correlates the side-chain CB chemical shifts with the NH of the same residue. These high sensitivity experiments are demonstrated on both fully-protonated and 100 %-H{sup N} back-protonated perdeuterated microcrystalline samples of Acinetobacter phage 205 (AP205) capsids at 60 kHz MAS.

  4. The Mechanism Design Approach to Student Assignment

    OpenAIRE

    Pathak, Parag A.

    2011-01-01

    The mechanism design approach to student assignment involves the theoretical, empirical, and experimental study of systems used to allocate students into schools around the world. Recent practical experience designing systems for student assignment has raised new theoretical questions for the theory of matching and assignment. This article reviews some of this recent literature, highlighting how issues from the field motivated theoretical developments and emphasizing how the dialogue may be a...

  5. Job Assignments, Intrinsic Motivation and Explicit Incentives

    OpenAIRE

    Nafziger, Julia

    2008-01-01

    This paper considers the interplay of job assignments with the intrinsic and extrinsic motivation of an agent. Job assignments influence the self confidence of the agent, and thereby his intrinsic motivation. Monetary reward allow the principal to complement intrinsic motivation with extrinsic incentives. The main result is that the principal chooses an inefficient job assignment rule to enhance the agent's intrinsic motivation even though she can motivate him with monetary rewards. This show...

  6. Assigning proctors to exams with scatter search

    OpenAIRE

    Ramalhinho-Louren??o, Helena; Mart??, Rafael; Laguna, Manuel

    2001-01-01

    In this paper we present an algorithm to assign proctors to exams. This NP-hard problem is related to the generalized assignment problem with multiple objectives. The problem consists of assigning teaching assistants to proctor final exams at a university. We formulate this problem as a multiobjective integer program (IP) with a preference function and a workload-fairness function. We then consider also a weighted objective that combines both functions. We develop a scatter ...

  7. An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments

    Energy Technology Data Exchange (ETDEWEB)

    Langmead, Christopher James [Dartmouth Computer Science Department (United States); Donald, Bruce Randall [Dartmouth Center for Structural Biology and Computational Chemistry (United States)], E-mail: brd@cs.dartmouth.edu

    2004-06-15

    We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of an homologous structure. Our algorithm performs Nuclear Vector Replacement (NVR) by Expectation/Maximization (EM) to compute assignments. NVR correlates experimentally-measured NH residual dipolar couplings (RDCs) and chemical shifts to a given a priori whole-protein 3D structural model. The algorithm requires only uniform {sup 15}N-labelling of the protein, and processes unassigned H{sup N}-{sup 15}N HSQC spectra, H{sup N}-{sup 15}N RDCs, and sparse H{sup N}-H{sup N} NOE's (d{sub NN}s). NVR runs in minutes and efficiently assigns the (H{sup N},{sup 15}N) backbone resonances as well as the sparse d{sub NN}s from the 3D {sup 15}N-NOESY spectrum, in O(n{sup 3}) time. The algorithm is demonstrated on NMR data from a 76-residue protein, human ubiquitin, matched to four structures, including one mutant (homolog), determined either by X-ray crystallography or by different NMR experiments (without RDCs). NVR achieves an average assignment accuracy of over 99%. We further demonstrate the feasibility of our algorithm for different and larger proteins, using different combinations of real and simulated NMR data for hen lysozyme (129 residues) and streptococcal protein G (56 residues), matched to a variety of 3D structural models. Abbreviations: NMR, nuclear magnetic resonance; NVR, nuclear vector replacement; RDC, residual dipolar coupling; 3D, three-dimensional; HSQC, heteronuclear single-quantum coherence; H{sup N}, amide proton; NOE, nuclear Overhauser effect; NOESY, nuclear Overhauser effect spectroscopy; d{sub NN}, nuclear Overhauser effect between two amide protons; MR, molecular replacement; SAR, structure activity relation; DOF, degrees of freedom; nt., nucleotides; SPG, Streptococcal protein G; SO(3), special orthogonal (rotation) group in 3D; EM, Expectation/Maximization; SVD, singular value decomposition.

  8. Sequence-Specific Assignment and Secondary Structure of the Catalytic Domain of Protein from Ubiquitination Pathway

    International Nuclear Information System (INIS)

    Ubiquitination is a post-translational protein modification which plays an important role in a wide variety of cellular processes including cell cycle, DNA repair and cell apoptosis. It is well known, that the ubiquitination requires sequential activity of three enzymes with different functions: activation, conjugation and ligation. Unfortunately, the three-dimensional structures of all three proteins responsible for these processes are not available at present and the process of proteins ubiquitination still is not understood in detail. In our communication, we present first, preliminary NMR data for the sequence-specific assignments for 112 amino acid residues long domain of one of the proteins from the ubiquitination pathway. The NMR samples were prepared by dissolving 1 mm either 15N-labeled or 15N, 13C-double labeled protein in 90%/10% H2O/D2O, 50 mm TRIS buffer, and 50 mm NaCl. The ph was adjusted to 6.5 (uncorrected value). All NMR measurements were performed on the Varian Unity+ 500 NMR spectrometer (11.7 T) equipped with three channels, Performa II PFG unit and 5 mm 1H, 13C, 15N-triple resonance pro behead. The 1H, 15N, and 13C backbone resonances were assigned by standard methods using 3D heteronuclear HNCACB, CBCA(CO)NH, HNCA, HN(CO)CA, HNCO, (HCA)CO(CA)NH NMR spectra collected at 303 K. The aliphatic 1H and 13C resonances were assigned on the basis of C(CO)NH, HBHA(CO)NH, and H(CO)NH experiments. After finishing of assignment procedure, solution of secondary structure in studied protein has been performed. The exact position of the α-helices and β-strands were solved on base analysis of cross-peaks between HN and Hα protons in 3D 15N-edited NOESY-HSQC spectrum, 3JNHα coupling constants evaluated from 3D HNHA experiment, and chemical shifts of backbone nuclei (TALOS software). Obtained results will be used in future for solution of three-dimensional structure of catalytic domain with high resolution by means NMR methods. (author)

  9. Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks

    Science.gov (United States)

    Kumar, Dinesh

    2013-12-01

    Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone 15N and 13C‧/13Cα chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone 15N(i) chemical shifts with that of 13C‧ (i - 1)/13Cα (i - 1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate 15N chemical shifts and (ii) reduces the signal overlap in F2(15N)-F3(1H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.

  10. Rest requirements and rest management of personnel in shift work

    Energy Technology Data Exchange (ETDEWEB)

    Hammell, B.D. [PDG Environmental, Melbourne, FL (United States); Scheuerle, A. [Univ. of Texas, Houston, TX (United States)

    1995-12-31

    A difficulty-weighted shift assignment scheme is proposed for use in prolonged and strenuous field operations such as emergency response, site testing, and short term hazardous waste remediation projects. The purpose of the work rotation plan is to increase productivity, safety, and moral of workers. Job weighting is accomplished by assigning adjustments to the mental and physical intensity of the task, the protective equipment worn, and the climatic conditions. The plan is based on medical studies of sleep deprivation, the effects of rest adjustments, and programs to reduce sleep deprivation and normalize shift schedules.

  11. Shifted Independent Component Analysis

    DEFF Research Database (Denmark)

    Mørup, Morten; Madsen, Kristoffer Hougaard; Hansen, Lars Kai

    2007-01-01

    Delayed mixing is a problem of theoretical interest and practical importance, e.g., in speech processing, bio-medical signal analysis and financial data modelling. Most previous analyses have been based on models with integer shifts, i.e., shifts by a number of samples, and have often been carried...

  12. OpenShift cookbook

    CERN Document Server

    Gulati, Shekhar

    2014-01-01

    If you are a web application developer who wants to use the OpenShift platform to host your next big idea but are looking for guidance on how to achieve this, then this book is the first step you need to take. This is a very accessible cookbook where no previous knowledge of OpenShift is needed.

  13. Detecting Plagiarism in MS Access Assignments

    Science.gov (United States)

    Singh, Anil

    2013-01-01

    Assurance of individual effort from students in computer-based assignments is a challenge. Due to digitization, students can easily use a copy of their friend's work and submit it as their own. Plagiarism in assignments puts students who cheat at par with those who work honestly and this compromises the learning evaluation process. Using a…

  14. 12 CFR 25.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... DEPOSIT PRODUCTION REGULATIONS Regulations Standards for Assessing Performance § 25.28 Assigned ratings... a rating of “outstanding,” “satisfactory,” “needs to improve,” or “substantial noncompliance” based... 12 Banks and Banking 1 2010-01-01 2010-01-01 false Assigned ratings. 25.28 Section 25.28 Banks...

  15. Online Discussion Assignments Improve Students' Class Preparation

    Science.gov (United States)

    Lineweaver, Tara T.

    2010-01-01

    To increase the number of students who read the text before class and to promote student interaction centering on text material, I developed an online discussion assignment as a required component of a cognitive psychology course. Across 2 studies, this assignment had a limited effect on examination performance, but students completing online…

  16. Protein secondary structure: category assignment and predictability

    DEFF Research Database (Denmark)

    Andersen, Claus A.; Bohr, Henrik; Brunak, Søren

    2001-01-01

    structures. Single sequence prediction of the new three category assignment gives an overall prediction improvement of 3.1% and 5.1%, compared to the DSSP assignment and schemes where the helix category consists of a-helix and 3(10)-helix, respectively. These results were achieved using a standard feed...

  17. Stress Assignment in Reading Italian Polysyllabic Pseudowords

    Science.gov (United States)

    Sulpizio, Simone; Arduino, Lisa S.; Paizi, Despina; Burani, Cristina

    2013-01-01

    In 4 naming experiments we investigated how Italian readers assign stress to pseudowords. We assessed whether participants assign stress following distributional information such as stress neighborhood (the proportion and number of existent words sharing orthographic ending and stress pattern) and whether such distributional information affects…

  18. Individualized Assignments in an Experimental Psychology Course.

    Science.gov (United States)

    Hovancik, John R.

    1984-01-01

    A computer is used to individualize student assignments in statistics. The principal benefit of individualized activities is that they emphasize decision-making processes rather than correct answers. Students in an individualized assignment group scored higher on an examination than those in a comparison group. (RM)

  19. Assignments and structure determination of the catalytic domain of human fibroblast collagenase using 3D double and triple resonance NMR spectroscopy

    International Nuclear Information System (INIS)

    We report here the backbone 1HN, 15N, 13Cα, 13CO, and 1Hα NMR assignments for the catalytic domain of human fibroblast collagenase (HFC). Three independent assignment pathways (matching 1H, 13Cα, and 13CO resonances) were used to establish sequential connections. The connections using 13Cα resonances were obtained from HNCOCA and HNCA experiments; 13CO connections were obtained from HNCO and HNCACO experiments. The sequential proton assignment pathway was established from a 3D(1H/15N) NOESY-HSQC experiment. Amino acid typing was accomplished using 13C and 15N chemical shifts, specific labeling of 15N-Leu, and spin pattern recognition from DQF-COSY. The secondary structure was determined by analyzing the 3D (1H/15N) NOESY-HSQC. A preliminary NMR structure calculation of HFC was found to be in agreement with recent X-ray structures of human fibroblast collagenase and human neutrophil collagenase as well as similar to recent NMR structures of a highly homologous protein, stromelysin. All three helices were located; a five-stranded β-sheet (four parallel strands, one antiparallel strand) was also determined. β-Sheet regions were identified by cross-strand dαN and dNN connections and by strong intraresidue dαN correlations, and were corroborated by observing slow amide proton exchange. Chemical shift changes in a selectively 15N-labeled sample suggest that substantial structural changes occur in the active site cleft on the binding of an inhibitor

  20. Airport Gate Assignment: New Model and Implementation

    CERN Document Server

    Li, Chendong

    2008-01-01

    Airport gate assignment is of great importance in airport operations. In this paper, we study the Airport Gate Assignment Problem (AGAP), propose a new model and implement the model with Optimization Programming language (OPL). With the objective to minimize the number of conflicts of any two adjacent aircrafts assigned to the same gate, we build a mathematical model with logical constraints and the binary constraints, which can provide an efficient evaluation criterion for the Airlines to estimate the current gate assignment. To illustrate the feasibility of the model we construct experiments with the data obtained from Continental Airlines, Houston Gorge Bush Intercontinental Airport IAH, which indicate that our model is both energetic and effective. Moreover, we interpret experimental results, which further demonstrate that our proposed model can provide a powerful tool for airline companies to estimate the efficiency of their current work of gate assignment.

  1. Nitrogen-detected CAN and CON experiments as alternative experiments for main chain NMR resonance assignments

    International Nuclear Information System (INIS)

    Heteronuclear direct-detection experiments, which utilize the slower relaxation properties of low γ nuclei, such as 13C have recently been proposed for sequence-specific assignment and structural analyses of large, unstructured, and/or paramagnetic proteins. Here we present two novel 15N direct-detection experiments. The CAN experiment sequentially connects amide 15N resonances using 13Cα chemical shift matching, and the CON experiment connects the preceding 13C' nuclei. When starting from the same carbon polarization, the intensities of nitrogen signals detected in the CAN or CON experiments would be expected four times lower than those of carbon resonances observed in the corresponding 13C-detecting experiment, NCA-DIPAP or NCO-IPAP (Bermel et al. 2006b; Takeuchi et al. 2008). However, the disadvantage due to the lower γ is counteracted by the slower 15N transverse relaxation during detection, the possibility for more efficient decoupling in both dimensions, and relaxation optimized properties of the pulse sequences. As a result, the median S/N in the 15N observe CAN experiment is 16% higher than in the 13C observe NCA-DIPAP experiment. In addition, significantly higher sensitivity was observed for those residues that are hard to detect in the NCA-DIPAP experiment, such as Gly, Ser and residues with high-field Cα resonances. Both CAN and CON experiments are able to detect Pro resonances that would not be observed in conventional proton-detected experiments. In addition, those experiments are free from problems of incomplete deuterium-to-proton back exchange in amide positions of perdeuterated proteins expressed in D2O. Thus, these features and the superior resolution of 15N-detected experiments provide an attractive alternative for main chain assignments. The experiments are demonstrated with the small model protein GB1 at conditions simulating a 150 kDa protein, and the 52 kDa glutathione S-transferase dimer, GST.

  2. Academic Peer Effects with Different Group Assignment Policies : Residential Tracking versus Random Assignment

    OpenAIRE

    Garlick, Robert

    2014-01-01

    This paper studies the relative academic performance of students tracked or randomly assigned to South African university dormitories. Tracked or streamed assignment creates dormitories where all students obtained similar scores on high school graduation examinations. Random assignment creates dormitories that are approximately representative of the population of students. Tracking lowers ...

  3. Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment.

    Science.gov (United States)

    Ovchinnikova, Tatyana V; Shenkarev, Zakhar O; Yakimenko, Zoya A; Svishcheva, Natalia V; Tagaev, Andrey A; Skladnev, Dmitry A; Arseniev, Alexander S

    2003-01-01

    Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution. PMID:14658801

  4. Computational Chemistry-based Acute Aquatic Toxicity Mode of Action Assignment

    Science.gov (United States)

    The ability to determine the mode of action (MOA) for a diverse group of chemicals is a critical part of ecological risk assessment and chemical regulation. However, existing MOA assignment approaches in ecotoxicology have been limited to a relatively few MOAs, have high uncertai...

  5. Discrepancy and Disliking Do Not Induce Negative Opinion Shifts

    NARCIS (Netherlands)

    Takacs, Karoly; Flache, Andreas; Maes, Michael

    2016-01-01

    Both classical social psychological theories and recent formal models of opinion differentiation and bi-polarization assign a prominent role to negative social influence. Negative influence is defined as shifts away from the opinion of others and hypothesized to be induced by discrepancy with or dis

  6. Reading assignment 10 - Linguistics 8806 (group 3)

    OpenAIRE

    Muñoz Baell, Irma María

    2010-01-01

    Reading assignment 10 - PART II. AN INTRODUCTION TO THE HISTORY OF LINGUISTICS. Key topic: Nineteenth-century linguistics: Historical linguistics. Academic year 2009-2010 (Course credits: 12 (15 ECTS)).

  7. Quantum probability assignment limited by relativistic causality.

    Science.gov (United States)

    Han, Yeong Deok; Choi, Taeseung

    2016-01-01

    Quantum theory has nonlocal correlations, which bothered Einstein, but found to satisfy relativistic causality. Correlation for a shared quantum state manifests itself, in the standard quantum framework, by joint probability distributions that can be obtained by applying state reduction and probability assignment that is called Born rule. Quantum correlations, which show nonlocality when the shared state has an entanglement, can be changed if we apply different probability assignment rule. As a result, the amount of nonlocality in quantum correlation will be changed. The issue is whether the change of the rule of quantum probability assignment breaks relativistic causality. We have shown that Born rule on quantum measurement is derived by requiring relativistic causality condition. This shows how the relativistic causality limits the upper bound of quantum nonlocality through quantum probability assignment. PMID:26971717

  8. Diagnosis code assignment: models and evaluation metrics

    OpenAIRE

    Perotte, Adler; Pivovarov, Rimma; Natarajan, Karthik; Weiskopf, Nicole; Wood, Frank; Elhadad, Noémie

    2013-01-01

    Background and objective The volume of healthcare data is growing rapidly with the adoption of health information technology. We focus on automated ICD9 code assignment from discharge summary content and methods for evaluating such assignments. Methods We study ICD9 diagnosis codes and discharge summaries from the publicly available Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC II) repository. We experiment with two coding approaches: one that treats each ICD9 code indepen...

  9. On pole structure assignment in linear systems

    Czech Academy of Sciences Publication Activity Database

    Loiseau, J.-J.; Zagalak, Petr

    2009-01-01

    Roč. 82, č. 7 (2009), s. 1179-1192. ISSN 0020-7179 R&D Projects: GA ČR(CZ) GA102/07/1596 Institutional research plan: CEZ:AV0Z10750506 Keywords : linear systems * linear state feedback * pole structure assignment Subject RIV: BC - Control Systems Theory Impact factor: 1.124, year: 2009 http://library.utia.cas.cz/separaty/2009/AS/zagalak-on pole structure assignment in linear systems.pdf

  10. Absorption driven focus shift

    Science.gov (United States)

    Harrop, N.; Wolf, S.; Maerten, O.; Dudek, K.; Ballach, S.; Kramer, R.

    2016-03-01

    Modern high brilliance near infrared lasers have seen a tremendous growth in applications throughout the world. Increased productivity has been achieved by higher laser power and increased brilliance of lasers. Positive impacts on the performance and costs of parts are opposed to threats on process stability and quality, namely shift of focus position over time. A high initial process quality will be reduced by contamination of optics, eventually leading to a focus shift or even destruction of the optics. Focus analysis at full power of multi-kilowatt high brilliance lasers is a very demanding task because of high power densities in the spot and the high power load on optical elements. With the newly developed high power projection optics, the High-Power Micro-Spot Monitor High Brilliance (HP-MSM-HB) is able to measure focus diameter as low as 20 μm at power levels up to 10 kW at very low internal focus shift. A main driving factor behind thermally induced focus shift is the absorption level of the optical element. A newly developed measuring system is designed to determine the relative absorption level in reference to a gold standard. Test results presented show a direct correlation between absorption levels and focus shift. The ability to determine the absorption level of optical elements as well as their performance at full processing power before they are put to use, enables a high level of quality assurance for optics manufacturers and processing head manufacturers alike.

  11. Competitive Traffic Assignment in Road Networks

    Directory of Open Access Journals (Sweden)

    Krylatov Alexander Y.

    2016-09-01

    Full Text Available Recently in-vehicle route guidance and information systems are rapidly developing. Such systems are expected to reduce congestion in an urban traffic area. This social benefit is believed to be reached by imposing the route choices on the network users that lead to the system optimum traffic assignment. However, guidance service could be offered by different competitive business companies. Then route choices of different mutually independent groups of users may reject traffic assignment from the system optimum state. In this paper, a game theoretic approach is shown to be very efficient to formalize competitive traffic assignment problem with various groups of users in the form of non-cooperative network game with the Nash equilibrium search. The relationships between the Wardrop’s system optimum associated with the traffic assignment problem and the Nash equilibrium associated with the competitive traffic assignment problem are investigated. Moreover, some related aspects of the Nash equilibrium and the Wardrop’s user equilibrium assignments are also discussed.

  12. Resonance-enhanced multiphoton ionization (REMPI) spectroscopy of bromobenzene and its perdeuterated isotopologue: Assignment of the vibrations of the S{sub 0}, S{sub 1}, and D{sub 0}{sup +} states of bromobenzene and the S{sub 0} and D{sub 0}{sup +} states of iodobenzene

    Energy Technology Data Exchange (ETDEWEB)

    Andrejeva, Anna; Tuttle, William D.; Harris, Joe P.; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk [School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)

    2015-12-28

    We report vibrationally resolved spectra of the S{sub 1}←S{sub 0} transition of bromobenzene using resonance-enhanced multiphoton ionization spectroscopy. We study bromobenzene-h{sub 5} as well as its perdeuterated isotopologue, bromobenzene-d{sub 5}. The form of the vibrational modes between the isotopologues and also between the S{sub 0} and S{sub 1} electronic states is discussed for each species, allowing assignment of the bands to be achieved and the activity between states and isotopologues to be established. Vibrational bands are assigned utilizing quantum chemical calculations, previous experimental results, and isotopic shifts. Previous work and assignments of the S{sub 1} spectra are discussed. Additionally, the vibrations in the ground state cation, D{sub 0}{sup +}, are considered, since these have also been used by previous workers in assigning the excited neutral state spectra. We also examine the vibrations of iodobenzene in the S{sub 0} and D{sub 0}{sup +} states and comment on the previous assignments of these. In summary, we have been able to assign the corresponding vibrations across the whole monohalobenzene series of molecules, in the S{sub 0}, S{sub 1}, and D{sub 0}{sup +} states, gaining insight into vibrational activity and vibrational couplings.

  13. Flexible taxonomic assignment of ambiguous sequencing reads

    Directory of Open Access Journals (Sweden)

    Jansson Jesper

    2011-01-01

    Full Text Available Abstract Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results.

  14. A Shift of Power

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Administrative reforms are shifting prefecture government powers to the county level in an effort to boost local economies on July 8, the government of China’s southernmost Hainan Province announced that it was to hand over 177 of its administrative powers to county-level governments. The move practically dismantled the powers of the

  15. Nitrogen Band Assignments for Presolar and Carbonado Diamonds

    CERN Document Server

    Garai, Jozsef; Chen, Jiuhua

    2010-01-01

    Presolar and carbonado diamonds formed in hydrogen rich environment and received severe radiation dose. It is suggested that these environmental affects altered the Substitutional N0 defect to Substitutional N+H defect by ionizing the nitrogen due to irradiation and by hydrogenating the ionized nitrogen. The bands of the substitutional N+H defect are deduced by red shifting the irradiation induced N+ bands due to the mass of the additional Hydrogen. The identified six bands induced by the N+H defects are present in both the presolar and the carbonado diamond spectra. The assignment of the substitutional N+H bands identifies all of the nitrogen related bands in the spectra, which shows that presolar and carbonado diamonds contain almost exclusively single nitrogen impurities. Thus these diamonds can be classified as type Ib. The substitutional N+H induced bands can be used to identify diamonds in space.

  16. THE EVOLUTION OF GARNISHMENT AND WAGE ASSIGNMENT LAW IN ILLINOIS

    Directory of Open Access Journals (Sweden)

    Bradley A. Hansen

    2014-07-01

    Full Text Available Recent research shows that, despite high interest rates, wage earners in the early twentieth century frequently obtained credit from retail shops, from loan sharks, and from the emerging formal consumer credit market. When wage earners defaulted, the options for collection available to their creditors were governed by state laws on garnishment and wage assignment. These important laws varied widely from state to state, and little is known about their origins or evolution. In Illinois, the law put significant restrictions on creditors in the late nineteenth century, but the restrictions were removed in the first quarter of the twentieth century. This article shows how this dramatic shift resulted from the interaction of legislative and judicial activity and was driven by both interest group politics and judicial action.

  17. Protein secondary structure assignment revisited: a detailed analysis of different assignment methods

    Directory of Open Access Journals (Sweden)

    de Brevern Alexandre G

    2005-09-01

    Full Text Available Abstract Background A number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure. Methods To address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures. Results A detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior. Conclusion Our method provides valuable assignments which favor the regularity of secondary structure segments.

  18. Unifying Temporal and Structural Credit Assignment Problems

    Science.gov (United States)

    Agogino, Adrian K.; Tumer, Kagan

    2004-01-01

    Single-agent reinforcement learners in time-extended domains and multi-agent systems share a common dilemma known as the credit assignment problem. Multi-agent systems have the structural credit assignment problem of determining the contributions of a particular agent to a common task. Instead, time-extended single-agent systems have the temporal credit assignment problem of determining the contribution of a particular action to the quality of the full sequence of actions. Traditionally these two problems are considered different and are handled in separate ways. In this article we show how these two forms of the credit assignment problem are equivalent. In this unified frame-work, a single-agent Markov decision process can be broken down into a single-time-step multi-agent process. Furthermore we show that Monte-Carlo estimation or Q-learning (depending on whether the values of resulting actions in the episode are known at the time of learning) are equivalent to different agent utility functions in a multi-agent system. This equivalence shows how an often neglected issue in multi-agent systems is equivalent to a well-known deficiency in multi-time-step learning and lays the basis for solving time-extended multi-agent problems, where both credit assignment problems are present.

  19. 75 FR 22148 - Request for the Technical Review of 22 Draft Skin Notation Assignments and Skin Notation Profiles

    Science.gov (United States)

    2010-04-27

    ... Skin Notation Assignments and Skin Notation Profiles AGENCY: National Institute for Occupational Safety... Occupational Safety and Health (NIOSH) of the Centers for Disease Control and Prevention (CDC) is conducting a...-mediated responses, such as airway hyper reactivity (asthma). Candidate chemicals may be assigned more...

  20. Writing Assignments that Promote Active Learning

    Science.gov (United States)

    Narayanan, M.

    2014-12-01

    Encourage students to write a detailed, analytical report correlating classroom discussions to an important historical event or a current event. Motivate students interview an expert from industry on a topic that was discussed in class. Ask the students to submit a report with supporting sketches, drawings, circuit diagrams and graphs. Propose that the students generate a complete a set of reading responses pertaining to an assigned topic. Require each student to bring in one comment or one question about an assigned reading. The assignment should be a recent publication in an appropriate journal. Have the students conduct a web search on an assigned topic. Ask them to generate a set of ideas that can relate to classroom discussions. Provide the students with a study guide. The study guide should provide about 10 or 15 short topics. Quiz the students on one or two of the topics. Encourage the students to design or develop some creative real-world examples based on a chapter discussed or a topic of interest. Require that students originate, develop, support and defend a viewpoint using a specifically assigned material. Make the students practice using or utilizing a set of new technical terms they have encountered in an assigned chapter. Have students develop original examples explaining the different terms. Ask the students to select one important terminology from the previous classroom discussions. Encourage the students to explain why they selected that particular word. Ask them to talk about the importance of the terminology from the point of view of their educational objectives and future career. Angelo, T. A. (1991). Ten easy pieces: Assessing higher learning in four dimensions. In T. A. Angelo (Ed.), Classroom research: Early lessons from success (pp. 17-31). New Directions for Teaching and Learning, No. 46. San Francisco: Jossey-Bass.

  1. Radio labeling with pre-assigned frequencies

    OpenAIRE

    Bodlaender, H.L.; Broersma, H.J.; Fomin, F.V.; Pyatkin, A.V.; Woeginer, G.J.

    2007-01-01

    A radio labeling of a graph G is an assignment of pairwise distinct, positive integer labels to the vertices of G such that labels of adjacent vertices differ by at least 2. The radio labeling problem (RL) consists in determining a radio labeling that minimizes the maximum label that is used (the so-called span of the labeling). RL is a well-studied problem, mainly motivated by frequency assignment problems in which transmitters are not allowed to operate on the same frequency channel. We con...

  2. Radio labeling with pre-assigned frequencies

    OpenAIRE

    Bodlaender, H.L.; Broersma, H.J.; Fomin, F.V.; Pyatkin, A.V.; Woeginger, G.J.

    2002-01-01

    A radio labeling of a graph $G$ is an assignment of pairwise distinct, positive integer labels to the vertices of $G$ such that labels of adjacent vertices differ by at least $2$. The radio labeling problem (\\mbox{\\sc RL}) consists in determining a radio labeling that minimizes the maximum label that is used (the so-called span of the labeling). \\mbox{\\sc RL} is a well-studied problem, mainly motivated by frequency assignment problems in which transmitters are not allowed to operate on the sa...

  3. Evolving Networks with Nonlinear Assignment of Weight

    Institute of Scientific and Technical Information of China (English)

    TANG Chao; TANG Yi

    2006-01-01

    We propose a weighted evolving network model in which the underlying topological structure is still driven by the degree according to the preferential attachment rule while the weight assigned to the newly established edges is dependent on the degree in a nonlinear form. By varying the parameter α that controls the function determining the assignment of weight, a wide variety of power-law behaviours of the total weight distributions as well as the diversity of the weight distributions of edges are displayed. Variation of correlation and heterogeneity in the network is illustrated as well.

  4. Shifts that divide population

    Science.gov (United States)

    Muneepeerakul, Rachata; Qubbaj, Murad; Aggarwal, Rimjhim; Anderies, John M.; Janssen, Marco

    2014-05-01

    How does a population of organisms in an ecosystem or of people in a society respond to rapid shifts in the environment? Answers to this question are critical to our ability to anticipate and cope with a changing ecohydrological system. We have developed a generic model of adaptation mechanisms, based on replicator dynamics, in which we derive a simple and insightful threshold condition that separates two important types of responses: 'cohesive transition' in which the whole population changes gradually together, and 'population-dividing transition' in which the population splits into two groups with one eventually dominating the other. The threshold depends on the magnitude of the shift and the shape of the fitness landscape. Division in populations can fundamentally alter the functioning of and induce subsequent feedbacks within the system; knowing the condition that gives rise to such division is thus fundamentally important.

  5. Toward the solution structure of human insulin: Sequential 2D 1H NMR assignment of a des-pentapeptide analogue and comparison with crystal structure

    International Nuclear Information System (INIS)

    2D 1H NMR studies are presented of des-pentapeptide-insulin, an analogue of human insulin lacking the C-terminal five residues of the B chain. Removal of these residues, which are not required for function, is shown to reduce conformational broadening previously described in the spectrum of intact insulin. This difference presumably reflects more rapid internal motions in the fragment, which lead to more complete averaging of chemical shifts on the NMR time scale. Sequential 1H NMR assignment and preliminary structural analysis demonstrate retention in solution of the three α-helices observed in the crystal state and the relative orientation of the receptor-binding surfaces. These studies provide a foundation for determining the solution structure of insulin

  6. Toward the solution structure of human insulin: Sequential 2D sup 1 H NMR assignment of a des-pentapeptide analogue and comparison with crystal structure

    Energy Technology Data Exchange (ETDEWEB)

    Hua, Q.; Weiss, M.A. (Harvard Medical School, Boston, MA (USA) Massachusetts Institute of Technology, Cambridge (USA))

    1990-11-01

    2D {sup 1}H NMR studies are presented of des-pentapeptide-insulin, an analogue of human insulin lacking the C-terminal five residues of the B chain. Removal of these residues, which are not required for function, is shown to reduce conformational broadening previously described in the spectrum of intact insulin. This difference presumably reflects more rapid internal motions in the fragment, which lead to more complete averaging of chemical shifts on the NMR time scale. Sequential {sup 1}H NMR assignment and preliminary structural analysis demonstrate retention in solution of the three {alpha}-helices observed in the crystal state and the relative orientation of the receptor-binding surfaces. These studies provide a foundation for determining the solution structure of insulin.

  7. New shifted hybrid inflation

    International Nuclear Information System (INIS)

    A new shifted hybrid inflationary scenario is introduced which, in contrast to the older one, relies only on renormalizable superpotential terms. This scenario is automatically realized in a concrete extension of the 'minimal' supersymmetric Pati-Salam model which naturally leads to a moderate violation of Yukawa unification so that, for μ>0, the predicted b-quark mass is acceptable even with universal boundary conditions. It is shown that this extended model possesses a classically flat 'shifted' trajectory which acquires a slope via one-loop radiative corrections and can be used as inflationary path. The constraints from the cosmic background explorer can be met with natural values of the relevant parameters. Also, there is no disastrous production of magnetic monopoles after inflation since the Pati-Salam gauge group is already broken on the 'shifted' path. The relevant part of inflation takes place at values of the inflaton field which are not much smaller than the 'reduced' Planck scale and, thus, supergravity corrections could easily invalidate inflation. It is, however, shown that inflation can be kept intact provided that an extra gauge singlet with a superheavy vacuum expectation value, which originates from D-terms, is introduced and a specific form of the Kaehler potential is used. Moreover, it is found that, although the supergravity corrections are sizable, the constraints from the cosmic background explorer can again be met by readjusting the values of the parameters which were obtained with global supersymmetry. (author)

  8. 75 FR 55352 - Delegation of Authorities and Assignment of Responsibilities

    Science.gov (United States)

    2010-09-10

    ... of the Secretary Delegation of Authorities and Assignment of Responsibilities Secretary's Order 5-2010 Subject: Delegation of Authorities and Assignment of Responsibilities to the Administrator, Wage and Hour Division. 1. Purpose. To delegate authorities and assign responsibilities to...

  9. Tabu search for target-radar assignment

    DEFF Research Database (Denmark)

    Hindsberger, Magnus; Vidal, Rene Victor Valqui

    2000-01-01

    In the paper the problem of assigning air-defense illumination radars to enemy targets is presented. A tabu search metaheuristic solution is described and the results achieved are compared to those of other heuristic approaches, implementation and experimental aspects are discussed. It is argued...... that tabu search could be used in near real-time decision making systems...

  10. Teaching Historical Analysis through Creative Writing Assignments

    Science.gov (United States)

    Peterson, Janine Larmon; Graham, Lea

    2015-01-01

    Incorporating creative writing exercises in history courses can heighten students' critical reading and analytical skills in an active learning model. We identify and define two types of possible assignments that use model texts as their locus: centripetal, which focuses on specific context and disciplinary terms, and centrifugal, which address…

  11. 24 CFR 221.255 - Assignment option.

    Science.gov (United States)

    2010-04-01

    ... DEVELOPMENT MORTGAGE AND LOAN INSURANCE PROGRAMS UNDER NATIONAL HOUSING ACT AND OTHER AUTHORITIES LOW COST AND MODERATE INCOME MORTGAGE INSURANCE-SAVINGS CLAUSE Contract Rights and Obligations-Low Cost Homes § 221.255... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Assignment option. 221.255...

  12. 24 CFR 221.770 - Assignment option.

    Science.gov (United States)

    2010-04-01

    ... DEVELOPMENT MORTGAGE AND LOAN INSURANCE PROGRAMS UNDER NATIONAL HOUSING ACT AND OTHER AUTHORITIES LOW COST AND... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Assignment option. 221.770 Section 221.770 Housing and Urban Development Regulations Relating to Housing and Urban Development...

  13. Experimental results on quadratic assignment problem

    Directory of Open Access Journals (Sweden)

    N.P. Nikolov

    1999-08-01

    Full Text Available The paper presents experimental results on quadratic assignment problem. The "scanning area" method formulated for radioelectronic equipment design is applied. For all more complex tests ours results are better or coincident with the ones known in literature. Conclusion concerning the effectiveness of method are given.

  14. 12 CFR 345.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ...,” “satisfactory,” “needs to improve,” or “substantial noncompliance” based on the bank's performance under the... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Assigned ratings. 345.28 Section 345.28 Banks and Banking FEDERAL DEPOSIT INSURANCE CORPORATION REGULATIONS AND STATEMENTS OF GENERAL...

  15. Incentivized optimal advert assignment via utility decomposition

    NARCIS (Netherlands)

    F. Kelly; P. Key; N. Walton

    2014-01-01

    We consider a large-scale Ad-auction where adverts are assigned over a potentially infinite number of searches. We capture the intrinsic asymmetries in information between advertisers, the advert platform and the space of searches: advertisers know and can optimize the average performance of their a

  16. Tabu search for target-radar assignment

    DEFF Research Database (Denmark)

    Hindsberger, Magnus; Vidal, Rene Victor Valqui

    2000-01-01

    In the paper the problem of assigning air-defense illumination radars to enemy targets is presented. A tabu search metaheuristic solution is described and the results achieved are compared to those of other heuristic approaches, implementation and experimental aspects are discussed. It is argued...

  17. Strategy-Proof Assignment Of Multiple Resources

    DEFF Research Database (Denmark)

    Erlanson, Albin; Szwagrzak, Karol

    2015-01-01

    We examine the strategy-proof allocation of multiple resources; an application is the assignment of packages of tasks, workloads, and compensations among the members of an organization. In the domain of multidimensional single-peaked preferences, we find that any allocation mechanism obtained by ......), some of which date back to the Babylonian Talmud....

  18. On Online Assignments in a Calculus Class

    Science.gov (United States)

    Jungic, Veselin; Kent, Deborah; Menz, Petra

    2012-01-01

    In this paper, we describe our experience with the creation and utilization of online assignments for several calculus classes at Simon Fraser University (SFU). We present our findings regarding available software by considering the needs and perspectives of the instructors, students, and administrators. We provide a list of questions that guide…

  19. Systematic Sorting: Teacher Characteristics and Class Assignments

    Science.gov (United States)

    Kalogrides, Demetra; Loeb, Susanna; Beteille, Tara

    2013-01-01

    Although prior research has documented differences in the distribution of teacher characteristics across schools serving different student populations, few studies have examined the extent to which teacher sorting occurs within schools. This study uses data from one large urban school district and compares the class assignments of teachers who…

  20. Generalised Assignment Matrix Methodology in Linear Programming

    Science.gov (United States)

    Jerome, Lawrence

    2012-01-01

    Discrete Mathematics instructors and students have long been struggling with various labelling and scanning algorithms for solving many important problems. This paper shows how to solve a wide variety of Discrete Mathematics and OR problems using assignment matrices and linear programming, specifically using Excel Solvers although the same…

  1. Variability in automated assignment of NOESY spectra and three-dimensional structure determination: A test case on three small disulfide-bonded proteins

    Energy Technology Data Exchange (ETDEWEB)

    Savarin, Philippe; Zinn-Justin, Sophie; Gilquin, Bernard [CEA-Saclay, Departement d' Ingenierie et d' Etudes des Proteines (Bat. 152) (France)

    2001-01-15

    Three independent runs of automatic assignment and structure calculations were performed on three small proteins, calcicludine from the venom of the green mamba Dendroaspis angusticeps, {kappa}-conotoxin PVIIA from the purple cone Conus purpurascens and HsTX1, a short scorpion toxin from the venom of Heterometrus spinnifer. At the end of all the runs, the number of cross peaks which remained unassigned (0.6%, 1.4% and 2% for calcicludine, {kappa}-conotoxin and HsTX1, respectively), as well as the number of constraints which were rejected as producing systematic violations (2.7%, 1.0%, and 1.4% for calcicludine, {kappa}-conotoxin and HsTX1, respectively) were low. The conformation of the initial model used in the procedure (linear model or constructed by homology) has no influence on the final structures. Mainly two parameters control the procedure: the chemical shift tolerance and the cut-off distance. Independent runs of structure calculations, using the same parameters, yield structures for which the rmsd between averaged structures and the rmsd around each averaged structure were of the same order of magnitude. A different cut-off distance and a different chemical shift tolerance yield rmsd values on final average structures which did not differ more than 0.5 A compared to the rmsd obtained around the averaged structure for each calculation. These results show that the procedure is robust when applied to such a small disulfide-bonded protein.

  2. CO{sub H}(N)CACB experiments for assigning backbone resonances in {sup 13}C/{sup 15}N-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Astrof, Nathan; Bracken, Clay; Cavanagh, John; Palmer, Arthur G

    1998-05-15

    A triple resonance NMR experiment, denoted CO{sub H}(N)CACB, correlates{sup 1}H{sup N} and {sup 13}CO spins with the{sup 13}C{sup {alpha}} and{sup 13}C{sup {beta}} spins of adjacent amino acids. The pulse sequence is an 'out-and-back' design that starts with{sup 1}H{sup N} magnetization and transfers coherence via the {sup 15}N spin simultaneously to the {sup 13}CO and{sup 13}C{sup {alpha}} spins, followed by transfer to the{sup 13}C{sup {beta}} spin. Two versions of the sequence are presented: one in which the {sup 13}CO spins are frequency labeled during an incremented t{sub 1} evolution period prior to transfer of magnetization from the {sup 13}C{sup {alpha}} to the{sup 13}C{sup {beta}} resonances, and one in which the{sup 13}CO spins are frequency labeled in a constant-time manner during the coherence transfer to and from the{sup 13}C{sup {beta}} resonances. Because {sup 13}COand {sup 15}N chemical shifts are largely uncorrelated, the technique will be especially useful when degeneracy in the{sup 1}H{sup N}-{sup 15}N chemical shifts hinders resonance assignment. The CO{sub H}(N)CACB experiment is demonstrated using uniformly {sup 13}C/{sup 15}N-labeled ubiquitin.

  3. Variability in automated assignment of NOESY spectra and three-dimensional structure determination: A test case on three small disulfide-bonded proteins

    International Nuclear Information System (INIS)

    Three independent runs of automatic assignment and structure calculations were performed on three small proteins, calcicludine from the venom of the green mamba Dendroaspis angusticeps, κ-conotoxin PVIIA from the purple cone Conus purpurascens and HsTX1, a short scorpion toxin from the venom of Heterometrus spinnifer. At the end of all the runs, the number of cross peaks which remained unassigned (0.6%, 1.4% and 2% for calcicludine, κ-conotoxin and HsTX1, respectively), as well as the number of constraints which were rejected as producing systematic violations (2.7%, 1.0%, and 1.4% for calcicludine, κ-conotoxin and HsTX1, respectively) were low. The conformation of the initial model used in the procedure (linear model or constructed by homology) has no influence on the final structures. Mainly two parameters control the procedure: the chemical shift tolerance and the cut-off distance. Independent runs of structure calculations, using the same parameters, yield structures for which the rmsd between averaged structures and the rmsd around each averaged structure were of the same order of magnitude. A different cut-off distance and a different chemical shift tolerance yield rmsd values on final average structures which did not differ more than 0.5 A compared to the rmsd obtained around the averaged structure for each calculation. These results show that the procedure is robust when applied to such a small disulfide-bonded protein

  4. Assignment and Correspondence Tracking System - Tactical / Operational Reporting

    Data.gov (United States)

    Social Security Administration — Reporting data store for the Assignment and Correspondence Tracking System (ACT). ACT automates the assignment and tracking of correspondence processing within the...

  5. Discrepancy and Disliking Do Not Induce Negative Opinion Shifts

    Science.gov (United States)

    Flache, Andreas; Mäs, Michael

    2016-01-01

    Both classical social psychological theories and recent formal models of opinion differentiation and bi-polarization assign a prominent role to negative social influence. Negative influence is defined as shifts away from the opinion of others and hypothesized to be induced by discrepancy with or disliking of the source of influence. There is strong empirical support for the presence of positive social influence (a shift towards the opinion of others), but evidence that large opinion differences or disliking could trigger negative shifts is mixed. We examine positive and negative influence with controlled exposure to opinions of other individuals in one experiment and with opinion exchange in another study. Results confirm that similarities induce attraction, but results do not support that discrepancy or disliking entails negative influence. Instead, our findings suggest a robust positive linear relationship between opinion distance and opinion shifts. PMID:27333160

  6. Shifted genus expanded W ∞ algebra and shifted Hurwitz numbers

    Science.gov (United States)

    Zheng, Quan

    2016-05-01

    We construct the shifted genus expanded W ∞ algebra, which is isomorphic to the central subalgebra A ∞ of infinite symmetric group algebra and to the shifted Schur symmetrical function algebra Λ* defined by Okounkov and Olshanskii. As an application, we get some differential equations for the generating functions of the shifted Hurwitz numbers; thus, we can express the generating functions in terms of the shifted genus expanded cut-and-join operators.

  7. Repetition and Translation Shifts

    Directory of Open Access Journals (Sweden)

    Simon Zupan

    2006-06-01

    Full Text Available Repetition manifests itself in different ways and at different levels of the text. The first basic type of repetition involves complete recurrences; in which a particular textual feature repeats in its entirety. The second type involves partial recurrences; in which the second repetition of the same textual feature includes certain modifications to the first occurrence. In the article; repetitive patterns in Edgar Allan Poe’s short story “The Fall of the House of Usher” and its Slovene translation; “Konec Usherjeve hiše”; are compared. The author examines different kinds of repetitive patterns. Repetitions are compared at both the micro- and macrostructural levels. As detailed analyses have shown; considerable microstructural translation shifts occur in certain types of repetitive patterns. Since these are not only occasional; sporadic phenomena; but are of a relatively high frequency; they reduce the translated text’s potential for achieving some of the gothic effects. The macrostructural textual property particularly affected by these shifts is the narrator’s experience as described by the narrative; which suffers a reduction in intensity.

  8. Weapon Target Assignment with Combinatorial Optimization Techniques

    Directory of Open Access Journals (Sweden)

    Asim Tokgöz

    2013-07-01

    Full Text Available Weapon Target Assignment (WTA is the assignment of friendly weapons to the hostile targets in order to protect friendly assets or destroy the hostile targets and considered as a NP-complete problem. Thus, it is very hard to solve it for real time or near-real time operational needs. In this study, genetic algorithm (GA, tabu search (TS, simulated annealing (SA and Variable Neighborhood Search (VNS combinatorial optimization techniques are applied to the WTA problem and their results are compared with each other and also with the optimized GAMS solutions. Algorithms are tested on the large scale problem instances. It is found that all the algorithms effectively converge to the near global optimum point(s (a good quality and the efficiency of the solutions (speed of solution might be improved according to the operational needs. VNS and SA solution qualities are better than both GA and TS.

  9. Weekly Fleet Assignment Model and Algorithm

    Institute of Scientific and Technical Information of China (English)

    ZHU Xing-hui; ZHU Jin-fu; GONG Zai-wu

    2007-01-01

    A 0-1 integer programming model for weekly fleet assignment was put forward based on linear network and weekly flight scheduling in China. In this model, the objective function is to maximize the total profit of fleet assignment, subject to the constraints of coverage, aircraft flow balance, fleet size, aircraft availability, aircraft usage, flight restriction, aircraft seat capacity,and stopover. Then the branch-and-bound algorithm based on special ordered set was applied to solve the model. At last, a realworld case study on an airline with 5 fleets, 48 aircrafts and 1 786 flight legs indicated that the profit increase was $1591276 one week and the running time was no more than 4 min, which shows that the model and algorithm are fairly good for domestic airline.

  10. Optimization and visualization of the edge weights in optimal assignment methods for virtual screening

    Science.gov (United States)

    2013-01-01

    Background Ligand‐based virtual screening plays a fundamental part in the early drug discovery stage. In a virtual screening, a chemical library is searched for molecules with similar properties to a query molecule by means of a similarity function. The optimal assignment of chemical graphs has proven to be a valuable similarity function for many cheminformatic tasks, such as virtual screening. The optimal assignment assumes all atoms of a query molecule to be equally important, which is not realistic depending on the binding mode of a ligand. The importance of a query molecule’s atoms can be integrated in the optimal assignment by weighting the assignment edges. We optimized the edge weights with respect to the virtual screening performance by means of evolutionary algorithms. Furthermore, we propose a visualization approach for the interpretation of the edge weights. Results We evaluated two different evolutionary algorithms, differential evolution and particle swarm optimization, for their suitability for optimizing the assignment edge weights. The results showed that both optimization methods are suited to optimize the edge weights. Furthermore, we compared our approach to the optimal assignment with equal edge weights and two literature similarity functions on a subset of the Directory of Useful Decoys using sophisticated virtual screening performance metrics. Our approach achieved a considerably better overall and early enrichment performance. The visualization of the edge weights enables the identification of substructures that are important for a good retrieval of ligands and for the binding to the protein target. Conclusions The optimization of the edge weights in optimal assignment methods is a valuable approach for ligand‐based virtual screening experiments. The approach can be applied to any similarity function that employs the optimal assignment method, which includes a variety of similarity measures that have proven to be valuable in various

  11. Capacity constrained assignment in spatial databases

    DEFF Research Database (Denmark)

    U, Leong Hou; Yiu, Man Lung; Mouratidis, Kyriakos;

    2008-01-01

    Given a point set P of customers (e.g., WiFi receivers) and a point set Q of service providers (e.g., wireless access points), where each q 2 Q has a capacity q.k, the capacity constrained assignment (CCA) is a matching M Q × P such that (i) each point q 2 Q (p 2 P) appears at most k times (at most...

  12. Total Synthesis and Stereochemical Assignment of Callyspongiolide.

    Science.gov (United States)

    Zhou, Jingjing; Gao, Bowen; Xu, Zhengshuang; Ye, Tao

    2016-06-01

    Total synthesis of four callyspongiolide stereoisomers led to unambiguous assignment of relative and absolute stereochemistry of the natural product. Key features of the convergent, fully stereocontrolled route include the use of Krische allylation, Kiyooka Aldol reaction, Kociénski-Julia olefination, Still-Gennari olefination, Yamaguchi macrocyclization, and Sonogashira coupling reaction. Biological evaluation of the synthesized compounds against an array of cancer cells revealed that the stereochemistry of the macrolactone core played an important role. PMID:27227371

  13. Online Ad Assignment with an Ad Exchange

    OpenAIRE

    Dvořák, Wolfgang; Henzinger, Monika

    2016-01-01

    Ad exchanges are becoming an increasingly popular way to sell advertisement slots on the internet. An ad exchange is basically a spot market for ad impressions. A publisher who has already signed contracts reserving advertisement impressions on his pages can choose between assigning a new ad impression for a new page view to a contracted advertiser or to sell it at an ad exchange. This leads to an online revenue maximization problem for the publisher. Given a new impression to sell decide whe...

  14. Incentivized optimal advert assignment via utility decomposition

    OpenAIRE

    Kelly, F.; Key, P.; Walton, N.

    2014-01-01

    We consider a large-scale Ad-auction where adverts are assigned over a potentially infinite number of searches. We capture the intrinsic asymmetries in information between advertisers, the advert platform and the space of searches: advertisers know and can optimize the average performance of their advertisement campaign; the platform knows and can optimize on each search instance; and, neither party knows the distribution of the infinite number of searches that can occur. We look at maximizin...

  15. Autocorrelation Measures for the Quadratic Assignment Problem

    OpenAIRE

    Chicano, Francisco; Luque, Gabriel; Alba, Enrique

    2012-01-01

    In this article we provide an exact expression for computing the autocorrelation coefficient $\\xi$ and the autocorrelation length $\\ell$ of any arbitrary instance of the Quadratic Assignment Problem (QAP) in polynomial time using its elementary landscape decomposition. We also provide empirical evidence of the autocorrelation length conjecture in QAP and compute the parameters $\\xi$ and $\\ell$ for the 137 instances of the QAPLIB. Our goal is to better characterize the difficulty of this impor...

  16. Automated feedback generation for introductory programming assignments

    OpenAIRE

    Singh, Rishabh; Gulwani, Sumit; Solar-Lezama, Armando

    2013-01-01

    We present a new method for automatically providing feedback for introductory programming problems. In order to use this method, we need a reference implementation of the assignment, and an error model consisting of potential corrections to errors that students might make. Using this information, the system automatically derives minimal corrections to student's incorrect solutions, providing them with a measure of exactly how incorrect a given solution was, as well as feedback about what they...

  17. Optimal State Assignment for Finite State Machines

    OpenAIRE

    Micheli, Giovanni De; Brayton, Robert K.; Sangiovanni-Vincentelli, Alberto

    1985-01-01

    Computer-Aided synthesis of sequential functions of VLSI systems, such as microprocessor control units, must include design optimization procedures to yield area-effective circuits. We model sequential functions as deterministic synchronous Finite State Machines (FSM's), and we consider a regular and structured implementation by means of Programmable Logic Arrays (PLA's) and feedback registers. State assignment, i.e., binary encoding of the internal states of the finite state machine, affects...

  18. File Assignment Policy in Network Storage System

    Institute of Scientific and Technical Information of China (English)

    Cao Qiang; Xie Chang-sheng

    2003-01-01

    Network storage increase capacity and scalability of storage system, data availability and enables the sharing of data among clients. When the developing network technology reduce performance gap between disk and network, however, mismatched policies and access pattern can significantly reduce network storage performance. So the strategy of data placement in system is an important factor that impacts the performance of overall system. In this paper, the two algorithms of file assignment are presented. One is Greed partition that aims at the load balance across all NADs (Network Attached Disk). The other is Sort partition that tries to minimize variance of service time in each NAD. Moreover, we also compare the performance of our two algorithms in practical environment. Our experimental results show that when the size distribution (load characters) of all assigning files is closer and larger, Sort partition provides consistently better response times than Greedy algorithm. However, when the range of all assigning files is wider, there are more small files and access rate is higher, the Greedy algorithm has superior performance in compared with the Sort partition in off-line.

  19. The double-assignment method for the exponential chaotic tabu search in quadratic assignment problems

    Science.gov (United States)

    Shibata, Kazuaki; Horio, Yoshihiko; Aihara, Kazuyuki

    The quadratic assignment problem (QAP) is one of the NP-hard combinatorial optimization problems. An exponential chaotic tabu search using a 2-opt algorithm driven by chaotic neuro-dynamics has been proposed as one heuristic method for solving QAPs. In this paper we first propose a new local search, the double-assignment method, suitable for the exponential chaotic tabu search, which adopts features of the Lin-Kernighan algorithm. We then introduce chaotic neuro-dynamics into the double-assignment method to propose a novel exponential chaotic tabu search. We further improve the proposed exponential chaotic tabu search with the double-assignment method by enhancing the effect of chaotic neuro-dynamics.

  20. 28 CFR 301.103 - Inmate work assignments.

    Science.gov (United States)

    2010-07-01

    ... COMPENSATION General § 301.103 Inmate work assignments. The unit team of each inmate, which ordinarily designates work assignments, or whoever makes work assignments, shall review appropriate medical records... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Inmate work assignments. 301.103...

  1. 49 CFR 821.35 - Assignment, duties and powers.

    Science.gov (United States)

    2010-10-01

    ... SAFETY BOARD RULES OF PRACTICE IN AIR SAFETY PROCEEDINGS Law Judges § 821.35 Assignment, duties and powers. (a) Assignment of law judge and duration of assignment. The chief law judge shall assign a law... addressed to the Case Manager for handling by the chief law judge, who may handle these matters...

  2. Chemical recycling of carbon dioxide emissions from a cement plant into dimethyl ether, a case study of an integrated process in France using a Reverse Water Gas Shift (RWGS) step

    International Nuclear Information System (INIS)

    Recycling of carbon dioxide (CO2) and hydrogen (H2) into liquid fuel technology has recently gained wide public interest since it is a potential pathway to increase the liquid fuel supply and to mitigate CO2 emissions simultaneously. In France, the majority of the electricity production is derived from nuclear and renewable energy which have a low CO2 footprint. This electricity power enables a potential for massive hydrogen production with low carbon emissions. We studied the possibility to develop this technology at an industrial scale in the French context on a typical industrial example of a cement manufacture in the south of France. An integrated process is proposed, which enables the use of the heat released by the CO2 to fuel process to help to capture the CO2 released by the cement manufacture. Some technological issues are discussed, and a potential solution is proposed for the catalyst used in the critical step of the Reverse Water Gas-Shift reaction (RWGS) of the process. (authors)

  3. Student Perceptions of the Benefits of a Learner-Based Writing Assignment in Organic Chemistry

    Science.gov (United States)

    Ablin, Lois

    2008-01-01

    A writing assignment to increase student understanding of and interest in practical applications of organic chemistry is described. Students were required to study a pharmaceutical or other organic compound and perform a qualitative risk assessment on the chemical. Student perceptions of the benefits of the paper were generally positive. (Contains…

  4. Phase shifting interferometer

    Science.gov (United States)

    Sommargren, Gary E.

    1999-01-01

    An interferometer which has the capability of measuring optical elements and systems with an accuracy of .lambda./1000 where .lambda. is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about .lambda./50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. Whereas current interferometers illuminate the optic to be tested with an aberrated wavefront which also limits the accuracy of the measurement, this interferometer uses an essentially perfect spherical measurement wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms.

  5. Replicating and Extending Research on the Partial Assignment Completion Effect: Is Sunk Cost Related to Partial Assignment Completion Strength?

    Science.gov (United States)

    Hawthorn-Embree, Meredith L.; Taylor, Emily P.; Skinner, Christopher H.; Parkhurst, John; Nalls, Meagan L.

    2014-01-01

    After students acquire a skill, mastery often requires them to choose to engage in assigned academic activities (e.g., independent seatwork, and homework). Although students may be more likely to choose to work on partially completed assignments than on new assignments, the partial assignment completion (PAC) effect may not be very powerful. The…

  6. Isotope Shifts and Isomer Shifts in Muonic Atoms

    International Nuclear Information System (INIS)

    Recent results on isotope shifts (142-146,148,150 Nd, 92,95-97 Mo, 50,52-54Cr) and isomer shifts (182,184,186W) are summarized in this paper. First, the merits and disadvantages of the three different isotope shift methods (optical h.f.s. spectra, electronic X-rays and muonic X-rays) are briefly outlined. The sensitivities of model dependence of the observed isotope shifts by these three methods are also introduced and discussed. The main emphasis of the paper is to show and to explain how the muonic isotope shift results may be used to normalize the optical isotope shift results and obtain the specific mass corrections occurring in optical results. The energy shifts of nuclear gamma rays as the result of the dynamic E2 interactions in several deformed nuclei have been precisely measured. The calculated shifts of the centre of gravity of the unresolved magnetic doublet are first applied to the observed shifts. The remaining shifts may be interpreted as the isomer effects, i.e. the effect of charge distribution on the transition energy, A comparison of the isomer effects by the muonic atom method and by the Mössbauer technique is included. (author)

  7. An Eigenstructure Assignment for a Static Synchronous Compensator

    Directory of Open Access Journals (Sweden)

    Ahmad N. Al-Husban

    2009-01-01

    Full Text Available Problem statement: Power flow through an AC transmission line is influenced by three basic electrical parameters, which are line impedance, magnitudes and phase-shift angle between the sending and receiving voltages. Therefore, the change in any of the three basic parameters means a change in the power flow through the transmission line. The aims of this research paper are: increase the power transfer capability of transmission systems, minimize the transmission losses, support a good voltage profile and retain system stability under large disturbances. Study the use of eigenstructure techniques for state feedback control of the power system static compensator. Therefore, the mathematical analysis was performed for eigenvector assignment, power flow transmission line and for the static compensator analysis based on the transformation of the three-phase into d-q frame. Approach: A novel control method for regulating the power system in case of abnormal conditions was carried out. The system considered is a static synchronous compensator. The study includes a detailed mathematical analysis of the impact of the shunt compensator on the power flow; investigation of the system constraints and their effects on the static compensator control; in addition simulation of static compensator to control a transmitted active power flow on the transmission line. The conducted method provides a way of constructing the state feedback gain matrix to satisfy a certain prescribed performance. Results: The solutions of the obtained equation were conducted using the computer simulation method for both open-loop and static compensator techniques. The result shows fast tracking of the power flow transient response when using the static compensator technique comparing with open-loop technique. However, the same trend of the behavior was observed for all cases. Conclusion: A new method for developing a parameterized feedback matrix that assigns a closed-loop prespecified

  8. Shift work in a security environment

    International Nuclear Information System (INIS)

    Human beings are diurnal species, normally active by day and asleep by night. Yet over thirty million Americans struggle with work schedules that include an off-normal work effort. The railroads, law enforcement, health services, Department of Defense, factory workers, chemical plants and public services, communications and utility workers must provide some form of around-the-clock effort. Shift work has been around since the advent of recorded history. There has always been a need for some type of off-normal service and assistance. The impact of shift work is replete with tales and factual evidence of an increased personnel error rate; disorders, both personal and family, and of course, increased accident events. In recent memory, the Three Mile Island Nuclear Plant incident, Union Carbide's explosion in Bhopal, and the Chernobyl Nuclear Plant catastrophe all occurred during off-normal working hours. Yet management overall has done little to correct the production-driven twelve hour, seven day week shift mentality of the nineteenth century. Most schedules in use today are nothing more than cosmetic variations of the old production schedules. This could be driven by a management consideration of the worker's response to change coupled with a reluctant buy-in of responsibility for the effects of change. Florida Power Corporation has developed for its nuclear security force, a unique work schedule which attempts to employ the sound principles of circadian rhythms coupled with a comprehensive training program to counter the problems associated with shift work. The results over the last four years have seen a marked reduction in the generic problems of personnel errors, absenteeism, unscheduled overtime and turnover rates. Utilization and understanding of this scheduling process for rotational shift work needs to be assessed to determine if the benefits are site specific or provide an expected response to the problems of shift work

  9. An assignment based distributed resource manager

    Science.gov (United States)

    Poore, Aubrey B.; Danford, Scott; Hilt, Matthew J.

    2010-04-01

    The goal of this paper is to demonstrate the coordination in real-time of the operation of multiple sensors in such a way that those best-equipped for certain missions should perform those missions for the entire network, while other sensors fill in the gaps with their capabilities. The networked system of sensors must search, detect, track, classify, and engage targets of high value in a timely fashion. The information transmitted should be that which contributes the most toward achieving the performance goals (e.g., track accuracy, track completeness, and a consistent operational picture or single integrated air picture (SIAP)) subject to the network bandwidth constraints and the capabilities of the sensors. We present an overview of an assignment based sensor resource manager, a distributed algorithm for coordinating the assignment problem, and simulation results that validate this approach. While the assignment formulation and algorithms could include both sensor resource and bandwidth constraints with versions for single and multiple time periods, i.e., myopic and non-myopic, the distributed prototype formulation and algorithms developed for these experiments were restricted to the tasking of certain sensors to make measurements and transmit them over the network based on the current air picture. The number of measurements put on the network was controlled by limiting the number of sensors that could transmit measurements on each target. The communication loading was then measured to demonstrate that indeed one can design a distributed sensor resource manager capable of achieving the objectives of significantly reducing the communication loading and maintaining SIAP.

  10. Colony location algorithm for assignment problems

    Institute of Scientific and Technical Information of China (English)

    Dingwei WANG

    2004-01-01

    A novel algorithm called Colony Location Algorithm (CLA) is proposed. It mimics the phenomena in biotic conmunity that colonies of species could be located in the places most suitable to their growth. The factors working on the species location such as the nutrient of soil, resource competition between species, growth and decline process, and effect on environment were considered in CLA via the nutrient function, growth and decline rates, environment evaluation and fertilization strategy.CLA was applied to solve the classical assignment problems. The computation results show that CLA can achieve the optimal solution with higher possibility and shorter running time.

  11. Genetic spectrum assignment model with constraints in cognitive radio networks

    Directory of Open Access Journals (Sweden)

    Fang Ye

    2011-06-01

    Full Text Available The interference constraints of genetic spectrum assignment model in cognitive radio networks are analyzed in this paper. An improved genetic spectrum assignment model is proposed. The population of genetic algorithm is divided into two sets, the feasible spectrum assignment strategies and the randomly updated spectrum assignment strategies. The penalty function is added to the utility function to achieve the spectrum assignment strategy that satisfies the interference constraints and has better fitness. The proposed method is applicable in both the genetic spectrum assignment model and the quantum genetic spectrum assignment mode. It can ensure the randomness of partial chromosomes in the population to some extent, and reduce the computational complexity caused by the constraints-free procedure after the update of population. Simulation results show that the proposed method can achieve better performance than the conventional genetic spectrum assignment model and quantum genetic spectrum assignment model

  12. Antiretroviral therapy: Shifting sands.

    Science.gov (United States)

    Sashindran, V K; Chauhan, Rajeev

    2016-01-01

    HIV/AIDS has been an extremely difficult pandemic to control. However, with the advent of antiretroviral therapy (ART), HIV has now been transformed into a chronic illness in patients who have continued treatment access and excellent long-term adherence. Existing indications for ART initiation in asymptomatic patients were based on CD4 levels; however, recent evidence has broken the shackles of CD4 levels. Early initiation of ART in HIV patients irrespective of CD4 counts can have profound positive impact on morbidity and mortality. Early initiation of ART has been found not only beneficial for patients but also to community as it reduces the risk of transmission. There have been few financial concerns about providing ART to all HIV-positive people but various studies have proven that early initiation of ART not only proves to be cost-effective but also contributes to economic and social growth of community. A novel multidisciplinary approach with early initiation and availability of ART at its heart can turn the tide in our favor in future. Effective preexposure prophylaxis and postexposure prophylaxis can also lower transmission risk of HIV in community. New understanding of HIV pathogenesis is opening new vistas to cure and prevention. Various promising candidate vaccines and drugs are undergoing aggressive clinical trials, raising optimism for an ever-elusive cure for HIV. This review describes various facets of tectonic shift in management of HIV. PMID:26900224

  13. 1H-MAS-NMR Chemical Shifts in Hydrogen-Bonded Complexes of Chlorophenols (Pentachlorophenol, 2,4,6-Trichlorophenol, 2,6-Dichlorophenol, 3,5-Dichlorophenol, and p-Chlorophenol) and Amine, and H/D Isotope Effects on 1H-MAS-NMR Spectra

    OpenAIRE

    Hisashi Honda

    2013-01-01

    Chemical shifts (CS) of the 1H nucleus in N···H···O type hydrogen bonds (H-bond) were observed in some complexes between chlorophenols [pentachlorophenol (PCP), 2,4,6-tricholorophenol (TCP), 2,6-dichlorophenol (26DCP), 3,5-dichlorophenol (35DCP), and p-chlorophenol (pCP)] and nitrogen-base (N-Base) by solid-state high-resolution 1H-NMR with the magic-angle-spinning (MAS) method. Employing N-Bases with a wide range of pKa values (0.65–10.75), 1H-MAS-NMR CS values of bridging H atoms in H-bonds...

  14. Portable shift register

    International Nuclear Information System (INIS)

    An electronics package for a small, battery-operated, self-contained, neutron coincidence counter based on a portable shift-register (PSR) has been developed. The counter was developed for applications not adequately addressed by commercial packages, including in-plant measurements to demonstrate compliance with regulations (domestic and international), in-plant process control, and in-field measurements (environmental monitoring or safeguards). Our package's features, which address these applications, include the following: Small size for portability and ease of installation;battery or mains operation; a built-in battery to power the unit and a typical detector such as a small sample counter, for over 6 h if power lines are bad or noisy, if there is a temporary absence of power, or if portability is desired; complete support, including bias, for standard neutron detectors; a powerful communications package to easily facilitate robust external control over a serial port; and a C-library to simplify creating external control programs in computers or other controllers. Whereas the PSR specifically addresses the applications mentioned above, it also performs all the measurements made by previous electronics packages for neutron coincidence counters developed at Los Alamos and commercialized. The PSR electronics package, exclusive of carrying handle, is 8 by 10 by 20 cm; it contains the circuit boards, battery, and bias supply and weighs less than 2 kg. This instrument package is the second in an emerging family of portable measurement instruments being developed; the first was the Miniature and Modular Multichannel Analyzer (M3CA). The PSR makes extensive use of hardware and software developed for the M3CA; like the M3CA, it is intended primarily for use with an external controller interfaced over a serial channel

  15. Energy phase shift as mechanism for catalysis

    KAUST Repository

    Beke-Somfai, Tamás

    2012-05-01

    Catalysts are agents that by binding reactant molecules lower the energy barriers to chemical reaction. After reaction the catalyst is regenerated, its unbinding energy recruited from the environment, which is associated with an inevitable loss of energy. We show that combining several catalytic sites to become energetically and temporally phase-shifted relative to each other provides a possibility to sustain the overall reaction by internal \\'energy recycling\\', bypassing the need for thermal activation, and in principle allowing the system to work adiabatically. Using an analytical model for superimposed, phase-shifted potentials of F 1-ATP synthase provides a description integrating main characteristics of this rotary enzyme complex. © 2012 Elsevier B.V. All rights reserved.

  16. Shape-shifting colloids via stimulated dewetting.

    Science.gov (United States)

    Youssef, Mena; Hueckel, Theodore; Yi, Gi-Ra; Sacanna, Stefano

    2016-01-01

    The ability to reconfigure elementary building blocks from one structure to another is key to many biological systems. Bringing the intrinsic adaptability of biological systems to traditional synthetic materials is currently one of the biggest scientific challenges in material engineering. Here we introduce a new design concept for the experimental realization of self-assembling systems with built-in shape-shifting elements. We demonstrate that dewetting forces between an oil phase and solid colloidal substrates can be exploited to engineer shape-shifting particles whose geometry can be changed on demand by a chemical or optical signal. We find this approach to be quite general and applicable to a broad spectrum of materials, including polymers, semiconductors and magnetic materials. This synthetic methodology can be further adopted as a new experimental platform for designing and rapidly prototyping functional colloids, such as reconfigurable micro swimmers, colloidal surfactants and switchable building blocks for self-assembly. PMID:27426418

  17. Instrument Measures Shift In Focus

    Science.gov (United States)

    Steimle, Lawrence J.

    1992-01-01

    Optical components tested at wavelengths from ultraviolet to infrared. Focus-shift-measuring instrument easy to use. Operated in lighted room, without having to make delicate adjustments while peering through microscope. Measures distance along which focal point of converging beam of light shifted by introduction of nominally plane parallel optical component into beam. Intended primarily for measuring focus shifts produced by windows and filters at wavelengths from 120 to 1,100 nanometers. Portable, compact, and relatively inexpensive for degree of precision.

  18. Zero-shifted accelerometer outputs

    Science.gov (United States)

    Galef, Arnold

    1986-08-01

    It is claimed that the commonly appearing zero-shift in pyroshock data is usually a symptom of a malfunctioning measurement system, so that the data can not be repaired (by high-pass filtering or equivalent) unless tests can be devised that permit the demonstration that the system is operating in a linear mode in all respects other than the shift. The likely cause of the zero-shift and its prevention are discussed.

  19. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Jianyang [Duke University, Department of Computer Science (United States); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2011-08-15

    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called Nasca (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), Nasca extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that Nasca assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by Nasca have backbone RMSD 0

  20. 3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample

    Energy Technology Data Exchange (ETDEWEB)

    Krejcirikova, Anna; Tugarinov, Vitali, E-mail: vitali@umd.edu [University of Maryland, Department of Chemistry and Biochemistry (United States)

    2012-10-15

    The feasibility of practically complete backbone and ILV methyl chemical shift assignments from a single [U-{sup 2}H,{sup 15}N,{sup 13}C; Ile{delta}1-{l_brace}{sup 13}CH{sub 3}{r_brace}; Leu,Val-{l_brace}{sup 13}CH{sub 3}/{sup 12}CD{sub 3}{r_brace}]-labeled protein sample of the truncated form of ligand-free Bst-Tyrosyl tRNA Synthetase (Bst-{Delta}YRS), a 319-residue predominantly helical homodimer, is established. Protonation of ILV residues at methyl positions does not appreciably detract from the quality of TROSY triple resonance data. The assignments are performed at 40 Degree-Sign C to improve the sensitivity of the measurements and alleviate the overlap of {sup 1}H-{sup 15}N correlations in the abundant {alpha}-helical segments of the protein. A number of auxiliary approaches are used to assist in the assignment process: (1) selection of {sup 1}H-{sup 15}N amide correlations of certain residue types (Ala, Thr/Ser) that simplifies 2D {sup 1}H-{sup 15}N TROSY spectra, (2) straightforward identification of ILV residue types from the methyl-detected 'out-and-back' HMCM(CG)CBCA experiment, and (3) strong sequential HN-HN NOE connectivities in the helical regions. The two subunits of Bst-YRS were predicted earlier to exist in two different conformations in the absence of ligands. In agreement with our earlier findings (Godoy-Ruiz in J Am Chem Soc 133:19578-195781, 2011), no evidence of dimer asymmetry has been observed in either amide- or methyl-detected experiments.

  1. Quantized beam shifts in graphene

    Energy Technology Data Exchange (ETDEWEB)

    de Melo Kort-Kamp, Wilton Junior [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sinitsyn, Nikolai [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dalvit, Diego Alejandro Roberto [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-08

    We predict the existence of quantized Imbert-Fedorov, Goos-Hanchen, and photonic spin Hall shifts for light beams impinging on a graphene-on-substrate system in an external magnetic field. In the quantum Hall regime the Imbert-Fedorov and photonic spin Hall shifts are quantized in integer multiples of the fine structure constant α, while the Goos-Hanchen ones in multiples of α2. We investigate the influence on these shifts of magnetic field, temperature, and material dispersion and dissipation. An experimental demonstration of quantized beam shifts could be achieved at terahertz frequencies for moderate values of the magnetic field.

  2. Assignment of uncertainties to scientific data

    International Nuclear Information System (INIS)

    Long-standing problems of uncertainty assignment to scientific data came into a sharp focus in recent years when uncertainty information ('covariance files') had to be added to application-oriented large libraries of evaluated nuclear data such as ENDF and JEF. Question arouse about the best way to express uncertainties, the meaning of statistical and systematic errors, the origin of correlation and construction of covariance matrices, the combination of uncertain data from different sources, the general usefulness of results that are strictly valid only for Gaussian or only for linear statistical models, etc. Conventional statistical theory is often unable to give unambiguous answers, and tends to fail when statistics is bad so that prior information becomes crucial. Modern probability theory, on the other hand, incorporating decision information becomes group-theoretic results, is shown to provide straight and unique answers to such questions, and to deal easily with prior information and small samples. (author). 10 refs

  3. Characterization of Surface Chemical States of a Thick Insulator: Chemical State Imaging on MgO Surface

    Science.gov (United States)

    Yi, Yeonjin; Cho, Sangwan; Noh, Myungkeun; Whang, Chung-Nam; Jeong, Kwangho; Shin, Hyun-Joon

    2005-02-01

    We report a surface characterization tool that can be effectively used to investigate the chemical state and subtle radiation damage on a thick insulator surface. It has been used to examine the MgO surface of a plasma display panel (PDP) consisting of a stack of insulator layers of approximately 51 μm thickness on a 2-mm-thick glass plate. The scanning photoelectron microscopy (SPEM) image of the insulating MgO surface was obtained by using the difference in Au 4f peak shift due to the surface charging at each pixel, where a Au adlayer of approximately 15 {\\AA} thickness was formed on the surface to overcome the serious charging shift of the peak position and the spectral deterioration in the photoelectron spectra. The observed contrast in the SPEM image reveals the chemical modification of the underlying MgO surface induced by the plasma discharge damage. The chemical state analysis of the MgO surface was carried out by comparing the Mg 2p, C 1s and O 1s photoemission spectra collected at each pixel of the SPEM image. We assigned four suboxide phases, MgO, MgCO3, Mg(OH)2 and Mg1+, on the initial MgO surface, where the Mg(OH)2 and Mg1+ phases vanished rapidly as the discharge-induced surface damage began.

  4. Diagnosis code assignment: models and evaluation metrics

    Science.gov (United States)

    Perotte, Adler; Pivovarov, Rimma; Natarajan, Karthik; Weiskopf, Nicole; Wood, Frank; Elhadad, Noémie

    2014-01-01

    Background and objective The volume of healthcare data is growing rapidly with the adoption of health information technology. We focus on automated ICD9 code assignment from discharge summary content and methods for evaluating such assignments. Methods We study ICD9 diagnosis codes and discharge summaries from the publicly available Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC II) repository. We experiment with two coding approaches: one that treats each ICD9 code independently of each other (flat classifier), and one that leverages the hierarchical nature of ICD9 codes into its modeling (hierarchy-based classifier). We propose novel evaluation metrics, which reflect the distances among gold-standard and predicted codes and their locations in the ICD9 tree. Experimental setup, code for modeling, and evaluation scripts are made available to the research community. Results The hierarchy-based classifier outperforms the flat classifier with F-measures of 39.5% and 27.6%, respectively, when trained on 20 533 documents and tested on 2282 documents. While recall is improved at the expense of precision, our novel evaluation metrics show a more refined assessment: for instance, the hierarchy-based classifier identifies the correct sub-tree of gold-standard codes more often than the flat classifier. Error analysis reveals that gold-standard codes are not perfect, and as such the recall and precision are likely underestimated. Conclusions Hierarchy-based classification yields better ICD9 coding than flat classification for MIMIC patients. Automated ICD9 coding is an example of a task for which data and tools can be shared and for which the research community can work together to build on shared models and advance the state of the art. PMID:24296907

  5. Solving multiconstraint assignment problems using learning automata.

    Science.gov (United States)

    Horn, Geir; Oommen, B John

    2010-02-01

    This paper considers the NP-hard problem of object assignment with respect to multiple constraints: assigning a set of elements (or objects) into mutually exclusive classes (or groups), where the elements which are "similar" to each other are hopefully located in the same class. The literature reports solutions in which the similarity constraint consists of a single index that is inappropriate for the type of multiconstraint problems considered here and where the constraints could simultaneously be contradictory. This feature, where we permit possibly contradictory constraints, distinguishes this paper from the state of the art. Indeed, we are aware of no learning automata (or other heuristic) solutions which solve this problem in its most general setting. Such a scenario is illustrated with the static mapping problem, which consists of distributing the processes of a parallel application onto a set of computing nodes. This is a classical and yet very important problem within the areas of parallel computing, grid computing, and cloud computing. We have developed four learning-automata (LA)-based algorithms to solve this problem: First, a fixed-structure stochastic automata algorithm is presented, where the processes try to form pairs to go onto the same node. This algorithm solves the problem, although it requires some centralized coordination. As it is desirable to avoid centralized control, we subsequently present three different variable-structure stochastic automata (VSSA) algorithms, which have superior partitioning properties in certain settings, although they forfeit some of the scalability features of the fixed-structure algorithm. All three VSSA algorithms model the processes as automata having first the hosting nodes as possible actions; second, the processes as possible actions; and, third, attempting to estimate the process communication digraph prior to probabilistically mapping the processes. This paper, which, we believe, comprehensively reports the

  6. Improving load balance with flexibly assignable tasks

    Energy Technology Data Exchange (ETDEWEB)

    Pinar, Ali; Hendrickson, Bruce

    2003-09-09

    In many applications of parallel computing, distribution ofthe data unambiguously implies distribution of work among processors. Butthere are exceptions where some tasks can be assigned to one of severalprocessors without altering the total volume of communication. In thispaper, we study the problem of exploiting this flexibility in assignmentof tasks to improve load balance. We first model the problem in terms ofnetwork flow and use combinatorial techniques for its solution. Ourparametric search algorithms use maximum flow algorithms for probing on acandidate optimal solution value. We describe two algorithms to solve theassignment problem with \\logW_T and vbar P vbar probe calls, w here W_Tand vbar P vbar, respectively, denote the total workload and number ofproce ssors. We also define augmenting paths and cuts for this problem,and show that anyalgorithm based on augmenting paths can be used to findan optimal solution for the task assignment problem. We then consideracontinuous version of the problem, and formulate it as a linearlyconstrained optimization problem, i.e., \\min\\|Ax\\|_\\infty,\\; {\\rms.t.}\\;Bx=d. To avoid solving an intractable \\infty-norm optimization problem,we show that in this case minimizing the 2-norm is sufficient to minimizethe \\infty-norm, which reduces the problem to the well-studiedlinearly-constrained least squares problem. The continuous version of theproblem has the advantage of being easily amenable to parallelization.Our experiments with molecular dynamics and overlapped domaindecomposition applications proved the effectiveness of our methods withsignificant improvements in load balance. We also discuss how ourtechniques can be enhanced for heterogeneous systems.

  7. Assignment Choice: Do Students Choose Briefer Assignments or Finishing What They Started?

    Science.gov (United States)

    Hawthorn-Embree, Meredith L.; Skinner, Christopher H.; Parkhurst, John; O'Neil, Michael; Conley, Elisha

    2010-01-01

    Academic skill development requires engagement in effortful academic behaviors. Although students may be more likely to choose to engage in behaviors that require less effort, they also may be motivated to complete assignments that they have already begun. Seventh-grade students (N = 88) began a mathematics computation worksheet, but were stopped…

  8. System optimal traffic assignment with departure time choice

    OpenAIRE

    Chow, A. H. F.

    2007-01-01

    This thesis investigates analytical dynamic system optimal assignment with departure time choice in a rigorous and original way. Dynamic system optimal assignment is formulated here as a state-dependent optimal control problem. A fixed volume of traffic is assigned to departure times and routes such that the total system travel cost is minimized. Although the system optimal assignment is not a realistic representation of traffic, it provides a bound on performance and shows how...

  9. 24 CFR 255.2 - GNMA right to assignment.

    Science.gov (United States)

    2010-04-01

    ... will have the right to perfect an assignment of the mortgage to itself. However, before exercising this right, GNMA will attempt to have the Mortgage assigned to another eligible coinsuring lender (unless... defaulting lender-issuer, GNMA will have the right to perfect an assignment of the Coinsured...

  10. 24 CFR 252.2 - GNMA right to assignment.

    Science.gov (United States)

    2010-04-01

    ....2 GNMA right to assignment. If the lender-issuer defaults on its obligations under the GNMA Mortgage... defaulting lender-issuer, GNMA will have the right to perfect an assignment of the mortgage to itself. However, before exercising this right, GNMA will attempt to have the Mortgage assigned to another...

  11. 24 CFR 251.2 - GNMA right to assignment.

    Science.gov (United States)

    2010-04-01

    ... right to assignment. If the lender-issuer defaults on its obligations under the GNMA Mortgage-Backed...-issuer, GNMA will have the right to perfect an assignment of the mortgage to itself. However, before exercising this right, GNMA will attempt to have the Mortgage assigned to another eligible coinsuring...

  12. Solving the k-cardinality assignment problem by transformation

    NARCIS (Netherlands)

    A. Volgenant

    2004-01-01

    The k-cardinality Linear Assignment Problem (k-LAP) with k a given integer is a generalization of the linear assignment problem: one wants to assign k rows (a free choice out of more rows) to k columns (a free choice out of more columns) minimizing the sum of the corresponding costs. For this polyno

  13. 75 FR 55354 - Delegation of Authority and Assignment of Responsibilities

    Science.gov (United States)

    2010-09-10

    ... of the Secretary Delegation of Authority and Assignment of Responsibilities Secretary's Order 3-2010 Subject: Delegation of Authority and Assignment of Responsibilities to the Employee Benefits Security Administration. 1. Purpose. To delegate authority and assign responsibilities for the administration of...

  14. Optimal assignment of incoming flights to baggage carousels at airports

    DEFF Research Database (Denmark)

    Barth, Torben C.

    The problem considered in this report is an assignment problem occurring at airports. This problem concerns the assignment of baggage carousels in baggage claim halls to arriving aircraft (baggage carousel assignment problem). This is a highly dynamic problem since disruptions frequently occur du...

  15. Learning through Writing: Teaching Critical Thinking Skills in Writing Assignments

    Science.gov (United States)

    Cavdar, Gamze; Doe, Sue

    2012-01-01

    Traditional writing assignments often fall short in addressing problems in college students' writing as too often these assignments fail to help students develop critical thinking skills and comprehension of course content. This article reports the use of a two-part (staged) writing assignment with postscript as a strategy for improving critical…

  16. Assessment of a Diversity Assignment in a PR Principles Course

    Science.gov (United States)

    Gallicano, Tiffany Derville; Stansberry, Kathleen

    2012-01-01

    This study assesses an assignment for incorporating diversity into the principles of public relations course. The assignment is tailored to the challenges of using an active learning approach in a large lecture class. For the assignment, students write a goal, objectives, strategies, an identification of tactics, and evaluation plans for either…

  17. Flexible Schedules and Shift Work.

    Science.gov (United States)

    Beers, Thomas M.

    2000-01-01

    Flexible work hours have gained prominence, as more than 25 million workers (27.6% of all full-time workers) can now vary their schedules. However, there has been little change since the mid-1980s in the proportion who work a shift other than a regular daytime shift. (JOW)

  18. TIPS (trigger an IIF paradigm shift)

    International Nuclear Information System (INIS)

    5 had no severe (recordable) injuries -Biggest total injury type was ergonomic -Biggest recordable injury type (58%) was cuts/lacerations -Chemical exposure and inhalations resulted in no recordables - Biggest root cause category was behavioral -Biggest behavioral root cause was 'Failure to Evaluate Hazards' - Biggest administrative controls root cause was 'Inadequate Procedures' - Biggest engineering controls root cause was 'Unrecognized Workplace Hazard' - Majority of injuries occurred in Spring/Summer which accounted for 86% of recordables -Response was inadequate or poor for 25% of injuries - Number of injuries by workgroup were about equal -Work area injuries were mostly in the CUB and Subfab but CUB injuries favored cuts/lacerations while Subfab favored ergonomic injuries These learnings and gaps were used to develop our New Mexico Site Safety Action Plan for 2005. It has also been used by individual managers and supervisors in their day-to-day business meetings, activities, and communications, for a more focused IIF message and effort. Results: Conclusions/Recommendations: Challenges are different amongst shifts. Shift culture may be stronger than workgroup culture. Work areas pose different challenges that all should be aware of and prepared for. We should prepare ourselves for challenges posed by the Spring and Summer seasons as well. We should be aware of and prepare for the different challenges and cultures characteristic of each shift. Supervisors need to spend more time in the field with their people to help them address safety issues and help make IIF a more consistent component of daily workgroup culture. Each site should analyze their data and look for their unique safety challenges. This will allow customized, focused action plans that meet the unique needs of each site

  19. A Bayesian approach to simultaneously quantify assignments and linguistic uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Chavez, Gregory M [Los Alamos National Laboratory; Booker, Jane M [BOOKER SCIENTIFIC FREDERICKSBURG; Ross, Timothy J [UNM

    2010-10-07

    Subject matter expert assessments can include both assignment and linguistic uncertainty. This paper examines assessments containing linguistic uncertainty associated with a qualitative description of a specific state of interest and the assignment uncertainty associated with assigning a qualitative value to that state. A Bayesian approach is examined to simultaneously quantify both assignment and linguistic uncertainty in the posterior probability. The approach is applied to a simplified damage assessment model involving both assignment and linguistic uncertainty. The utility of the approach and the conditions under which the approach is feasible are examined and identified.

  20. Optimal Index Assignment for Multiple Description Scalar Quantization

    CERN Document Server

    Zhang, Guoqiang; Kleijn, W Bastiaan

    2011-01-01

    We provide a method for designing an optimal index assignment for scalar K-description coding. The method stems from a construction of translated scalar lattices, which provides a performance advantage by exploiting a so-called staggered gain. Interestingly, generation of the optimal index assignment is based on a lattice in K-1 dimensional space. The use of the K-1 dimensional lattice facilitates analytic insight into the performance and eliminates the need for a greedy optimization of the index assignment. It is shown that that the optimal index assignment is not unique. This is illustrated for the two-description case, where a periodic index assignment is selected from possible optimal assignments and described in detail. The new index assignment is applied to design of a K-description quantizer, which is found to outperform a reference K-description quantizer at high rates. The performance advantage due to the staggered gain increases with increasing redundancy among the descriptions.

  1. Is there a shift to 'active nanostructures'?

    International Nuclear Information System (INIS)

    It has been suggested that an important transition in the long-run trajectory of nanotechnology development is a shift from passive to active nanostructures. Such a shift could present different or increased societal impacts and require new approaches for risk assessment. An active nanostructure 'changes or evolves its state during its operation,' according to the National Science Foundation's (2006) Active Nanostructures and Nanosystems grant solicitation. Active nanostructure examples include nanoelectromechanical systems (NEMS), nanomachines, self-healing materials, targeted drugs and chemicals, energy storage devices, and sensors. This article considers two questions: (a) Is there a 'shift' to active nanostructures? (b) How can we characterize the prototypical areas into which active nanostructures may emerge? We build upon the NSF definition of active nanostructures to develop a research publication search strategy, with a particular intent to distinguish between passive and active nanotechnologies. We perform bibliometric analyses and describe the main publication trends from 1995 to 2008. We then describe the prototypes of research that emerge based on reading the abstracts and review papers encountered in our search. Preliminary results suggest that there is a sharp rise in active nanostructures publications in 2006, and this rise is maintained in 2007 and through to early 2008. We present a typology that can be used to describe the kind of active nanostructures that may be commercialized and regulated in the future.

  2. Efficient Credit Assignment through Evaluation Function Decomposition

    Science.gov (United States)

    Agogino, Adrian; Turner, Kagan; Mikkulainen, Risto

    2005-01-01

    Evolutionary methods are powerful tools in discovering solutions for difficult continuous tasks. When such a solution is encoded over multiple genes, a genetic algorithm faces the difficult credit assignment problem of evaluating how a single gene in a chromosome contributes to the full solution. Typically a single evaluation function is used for the entire chromosome, implicitly giving each gene in the chromosome the same evaluation. This method is inefficient because a gene will get credit for the contribution of all the other genes as well. Accurately measuring the fitness of individual genes in such a large search space requires many trials. This paper instead proposes turning this single complex search problem into a multi-agent search problem, where each agent has the simpler task of discovering a suitable gene. Gene-specific evaluation functions can then be created that have better theoretical properties than a single evaluation function over all genes. This method is tested in the difficult double-pole balancing problem, showing that agents using gene-specific evaluation functions can create a successful control policy in 20 percent fewer trials than the best existing genetic algorithms. The method is extended to more distributed problems, achieving 95 percent performance gains over tradition methods in the multi-rover domain.

  3. Regulatory focus and the assignment of punishment

    Directory of Open Access Journals (Sweden)

    Chloe Carmichael

    2007-06-01

    Full Text Available Regulatory Focus has been demonstrated to influence human behavior in a number of domains, such as object valuation and readiness to commit time or money to social projects. It has also been demonstrated to influence an individual’s approach to mistakes; and a person’s preference for global or local processing of information. The present work seeks to consider how regulatory focus might interact with punitive behaviors, specifically, the assignment of legal punishment. In this study, 240 undergraduates completed a series of written instruments that assessed their regulatory focus. They read a vignette that described a target that commits a crime, is detected by the police, and is arrested due to a careless mistake. Participants were asked what level of legal punishment they deemed appropriate. Participants’ punitive evaluations show that there are significant interactions a between the regulatory focus of the participant and the regulatory focus of the target and b between the regulatory focus of the participant and the level of detail used to describe the target and her behavior. In each case, when the regulatory foci matched, causing ‘fit,’ the participant was more lenient than in the non-fit condition.

  4. 1H-MAS-NMR Chemical Shifts in Hydrogen-Bonded Complexes of Chlorophenols (Pentachlorophenol, 2,4,6-Trichlorophenol, 2,6-Dichlorophenol, 3,5-Dichlorophenol, and p-Chlorophenol and Amine, and H/D Isotope Effects on 1H-MAS-NMR Spectra

    Directory of Open Access Journals (Sweden)

    Hisashi Honda

    2013-04-01

    Full Text Available Chemical shifts (CS of the 1H nucleus in N···H···O type hydrogen bonds (H-bond were observed in some complexes between chlorophenols [pentachlorophenol (PCP, 2,4,6-tricholorophenol (TCP, 2,6-dichlorophenol (26DCP, 3,5-dichlorophenol (35DCP, and p-chlorophenol (pCP] and nitrogen-base (N-Base by solid-state high-resolution 1H-NMR with the magic-angle-spinning (MAS method. Employing N-Bases with a wide range of pKa values (0.65–10.75, 1H-MAS-NMR CS values of bridging H atoms in H-bonds were obtained as a function of the N-Base’s pKa. The result showed that the CS values were increased with increasing pKa values in a range of DpKa 2: The maximum CS values was recorded in the PCP (pKa = 5.26–4-methylpyridine (6.03, TCP (6.59–imidazole (6.99, 26DCP (7.02–2-amino-4-methylpyridine (7.38, 35DCP (8.04–4-dimethylaminopyridine (9.61, and pCP (9.47–4-dimethylaminopyridine (9.61 complexes. The largest CS value of 18.6 ppm was recorded in TCP–imidazole crystals. In addition, H/D isotope effects on 1H-MAS-NMR spectra were observed in PCP–2-amino-3-methylpyridine. Based on the results of CS simulation using a B3LYP/6-311+G** function, it can be explained that a little changes of the N–H length in H-bond contribute to the H/D isotope shift of the 1H-MAS-NMR peaks.

  5. Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

    Science.gov (United States)

    Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

    2016-05-01

    Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes. PMID:27074500

  6. Conformational study of aromatic ketones: chemical shift reagents: uranium chelates

    International Nuclear Information System (INIS)

    A series of benzophenones, 2-benzoyl thiophenes and 2-benzoyl pyridines, all substituted at the benzene ring by an amino acid chain, have been synthesised with the object of examining to what extent the site of the aminoacid chain and the site and nature of the other substituents modify the electronic structure of the molecule and the orientation of each ring with respect to the plane of the carbonyl group. In the second part a study of paramagnetic cations, in particular of uranium, which is able to form stable chelates with beta-diketones was carried out to study their complexing power. The chelates studied are the (hexafluoropentanedionate)4U, the (heptafluorodimethyloctanedionate)4U and the (trifluorophenylbutanedionate)4U

  7. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts

    DEFF Research Database (Denmark)

    Eriksen, Janus Juul; Olsen, Jógvan Magnus Haugaard; Aidas, Kestutis; Ågren, Hans; Mikkelsen, Kurt V.; Kongsted, Jacob

    2011-01-01

    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 u...

  8. Chemical shift imprint of intersubunit communication in a symmetric homodimer.

    Science.gov (United States)

    Falk, Bradley T; Sapienza, Paul J; Lee, Andrew L

    2016-08-23

    Allosteric communication is critical for protein function and cellular homeostasis, and it can be exploited as a strategy for drug design. However, unlike many protein-ligand interactions, the structural basis for the long-range communication that underlies allostery is not well understood. This lack of understanding is most evident in the case of classical allostery, in which a binding event in one protomer is sensed by a second symmetric protomer. A primary reason why study of interdomain signaling is challenging in oligomeric proteins is the difficulty in characterizing intermediate, singly bound species. Here, we use an NMR approach to isolate and characterize a singly ligated state ("lig1") of a homodimeric enzyme that is otherwise obscured by rapid exchange with apo and saturated forms. Mixed labeled dimers were prepared that simultaneously permit full population of the lig1 state and isotopic labeling of either protomer. Direct visualization of peaks from lig1 yielded site-specific ligand-state multiplets that provide a convenient format for assessing mechanisms of intersubunit communication from a variety of NMR measurements. We demonstrate this approach on thymidylate synthase from Escherichia coli, a homodimeric enzyme known to be half-the-sites reactive. Resolving the dUMP1 state shows that active site communication occurs not upon the first dUMP binding, but upon the second. Surprisingly, for many sites, dUMP1 peaks are found beyond the limits set by apo and dUMP2 peaks, indicating that binding the first dUMP pushes the enzyme ensemble to further conformational extremes than the apo or saturated forms. The approach used here should be generally applicable to homodimers. PMID:27466406

  9. Ligand Binding Analysis and Screening by Chemical Denaturation Shift

    OpenAIRE

    Sch n, Arne; Brown, Richard K; Hutchins, Burleigh M.; Freire, Ernesto

    2013-01-01

    The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Towards this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Since ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization ef...

  10. Explaining (Missing) Regulator Paradigm Shifts

    DEFF Research Database (Denmark)

    Wigger, Angela; Buch-Hansen, Hubert

    2014-01-01

    regulation after the crisis in the 1970s, the paper argues that the preconditions for a fundamental shift in this issue area are not present this time around. Several reasons account for this: the current crisis has been construed by economic and political elites as a crisis within and not of neoliberal......The global financial and economic crisis has prompted some scholars to suggest that a fundamental regulatory shift away from neoliberalism will take place – both in general and in the field of EU competition regulation. This paper shows that so far no radical break with the neoliberal type of...... competition regulation is heaving into sight. It sets out to explain this from the vantage point of a critical political economy perspective, which identifies the circumstances under which a crisis can result in a regulatory paradigm shift. Contrasting the current situation with the shift in EC/EU competition...

  11. Asymmetric Synthesis and Absolute Configuration Assignment of a New Type of Bedaquiline Analogue

    OpenAIRE

    Chang-Jiang Qiao; Xiao-Kui Wang; Fei Xie; Wu Zhong; Song Li

    2015-01-01

    Bedaquiline is the first FDA-approved new chemical entity to fight multidrug-resistant tuberculosis in the last forty years. Our group replaced the quinoline ring with a naphthalene ring, leading to a new type of triarylbutanol skeleton. An asymmetric synthetic route was established for our bedaquiline analogues, and the goal of assigning their absolute configurations was achieved by comparison of experimental and calculated electronic circular dichroism spectra, and was confirmed by the comb...

  12. Towards Automated Structure-Based NMR Resonance Assignment

    Science.gov (United States)

    Jang, Richard; Gao, Xin; Li, Ming

    We propose a general framework for solving the structure-based NMR backbone resonance assignment problem. The core is a novel 0-1 integer programming model that can start from a complete or partial assignment, generate multiple assignments, and model not only the assignment of spins to residues, but also pairwise dependencies consisting of pairs of spins to pairs of residues. It is still a challenge for automated resonance assignment systems to perform the assignment directly from spectra without any manual intervention. To test the feasibility of this for structure-based assignment, we integrated our system with our automated peak picking and sequence-based resonance assignment system to obtain an assignment for the protein TM1112 with 91% recall and 99% precision without manual intervention. Since using a known structure has the potential to allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data, we work towards the goal of automated structure-based assignment using only such labeled data. Our system reduced the assignment error of Xiong-Pandurangan-Bailey-Kellogg's contact replacement (CR) method, which to our knowledge is the most error-tolerant method for this problem, by 5 folds on average. By using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for Ubiquitin, where the type prediction accuracy is 83%, we achieved 91% assignment accuracy, compared to the 59% accuracy that was obtained without correcting for typing errors.

  13. Semantic Shift in Plant Names

    OpenAIRE

    DOSKOČILOVÁ, Iveta

    2014-01-01

    The aim of the present work is to identify and list English plant names coined by semantic shift, namely by metaphor, metonymy or synecdoche, and to carry out a detailed categorisation of individual semantic categories based on different tendencies within them and interpretation of the results. The theoretical part of my work focuses on different approaches to semantic shift and its categories. It is followed by the practical part which deals individually with metaphor, metonymy and synecdoch...

  14. Unconventional treatment of focal shift

    OpenAIRE

    Vokinger, Urs; Dändliker, René; Blattner, Peter; Herzig, Hans-Peter

    2007-01-01

    We present an unconventional approach for the explanation of focal shift behind a lens. It is based on the fact that, within the approximation of Fresnel diffraction, the intensity distributions in the conjugate planes of a lens are equal to their geometrical images. We show that the focus (position of highest intensity) is always shifted towards the lens. The results for a Gaussian beam and a uniform converging spherical wave are presented.

  15. Assignment of 1HN, 15N, 13Cα, 13CO and 13Cβ resonances in a 67 kDa p53 dimer using 4D-TROSY NMR spectroscopy

    International Nuclear Information System (INIS)

    The p53 tumor suppressor is a transcription factor that plays a crucial role in the activation of genes in response to DNA damage. As a first step towards detailed structural studies of the molecule aimed at understanding its regulation, we have used 4D-TROSY triple resonance NMR spectroscopy to obtain nearly complete 1HN, 15N, 13Cα, 13CO and 13Cβ resonance assignments of a dimeric form of the protein comprising DNA-binding and oligomerization domains (67 kDa). A simple comparison of 4D spectra recorded on p53 molecules consisting of DNA-binding and oligomerization domains with and without the regulatory domain establishes that both constructs have essentially identical chemical shifts. Although the affinity of p53 for target DNA is decreased in constructs containing the regulatory domain, the chemical shift results reported here suggest that this decrease is not due to specific domain interactions involving the regulatory portion of the molecule, or alternatively, that such interactions require the presence of DNA

  16. A New Paradigm for Chemical Engineering?

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    system boundary under investigation? A fundamental rethinking of how to identify the needed chemicals based products and how to design, build and operate the corresponding production units, is necessary. Indeed, the chemical industry today is changed from the chemical industry of forty years ago. Clear...... evidence of this change comes from the jobs taken by graduating chemical engineering professionals in North America, Europe, and some of the Asian countries. In terms of where the graduating chemical engineers are going to work, a clear shift from the commodity chemical industry to the product oriented...... businesses has been observed. There is an increasing trend within the chemical industry to focus on products and the sustainable processes that can make them. Do these changes point to a paradigm shift in chemical engineering as a discipline? Historically, two previous paradigm shifts in chemical engineering...

  17. Electronic structures, vibrational spectra, and revised assignment of aniline and its radical cation: Theoretical study

    Science.gov (United States)

    Wojciechowski, Piotr M.; Zierkiewicz, Wiktor; Michalska, Danuta; Hobza, Pavel

    2003-06-01

    Comprehensive studies of the molecular and electronic structures, vibrational frequencies, and infrared and Raman intensities of the aniline radical cation, C6H5NH2+ have been performed by using the unrestricted density functional (UB3LYP) and second-order Møller-Plesset (UMP2) methods with the extended 6-311++G(df,pd) basis set. For comparison, analogous calculations were carried out for the closed-shell neutral aniline. The studies provided detailed insight into the bonding changes that take place in aniline upon ionization. The natural bond orbital (NBO) analysis has revealed that the pπ-radical conjugative interactions are of prime importance in stabilizing the planar, quinoid-type structure of the aniline radical cation. It is shown that the natural charges calculated for aniline are consistent with the chemical properties of this molecule (an ortho- and para-directing power of the NH2 group in electrophilic substitutions), whereas Mulliken charges are not reliable. The theoretical vibrational frequencies of aniline, calculated by the B3LYP method, show excellent agreement with the available experimental data. In contrast, the MP2 method is deficient in predicting the frequencies of several modes in aniline, despite the use of the extended basis set in calculations. The frequencies of aniline radical cation, calculated at the UB3LYP/6-311++G(df,pd) level, are in very good agreement with the recently reported experimental data from zero kinetic energy photoelectron and infrared depletion spectroscopic studies. The clear- cut assignment of the IR and Raman spectra of the investigated molecules has been made on the basis of the calculated potential energy distributions. Several bands in the spectra have been reassigned. It is shown that ionization of aniline can be easily identified by the appearance of the very strong band at about 1490 cm-1, in the Raman spectrum. The redshift of the N-H stretching frequencies and the blueshift of the C-H stretching

  18. Why the Rhetoric of CS Programming Assignments Matters

    Science.gov (United States)

    Wolfe, Joanna

    2004-06-01

    Despite the multiple potential benefits of asking students working on programming tasks to consider human factors, most programming assignments narrowly focus on technical details and requirements. Female students in particular may be attracted to assignments that emphasize human as well as technical factors. To assess how students respond to changes in the rhetorical presentation of programming instructions, 81 students completed questionnaires evaluating different assignment instructions. Students generally perceived assignments emphasizing real-world contexts and users as more motivating and enjoyable to program than those that did not emphasize human factors. Moreover, when asked what makes a "good" programming assignment, over half of the students volunteered that they looked for assignments stressing a real-world purpose, use or application.

  19. Quantum chemical and spectroscopic investigations of 5-aminoquinoline

    Science.gov (United States)

    Arjunan, V.; Mohan, S.; Balamourougane, P. S.; Ravindran, P.

    2009-12-01

    The Fourier transform infrared (FTIR) and FT-Raman spectra of 5-aminoquinoline (5AQ) have been recorded in the range 4000-400 and 3500-100 cm -1, respectively. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the observed FTIR and FT-Raman data. 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by using the gauge independent atomic orbital (GIAO) method. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The geometric parameters, chemical shifts and absorption wavelengths were compared with the experimental data of the molecule. The vibrational frequencies which were determined experimentally are compared with those obtained theoretically from ab initio HF and DFT-B3LYP gradient calculations employing the 6-31G** and 6-311++G** basis sets for optimized geometries of the compound. The interactions of NH-π and the influence of amino group on the skeletal modes are investigated.

  20. Variability of Cranial Nerve Assignment to Speech and Swallow Muscles

    OpenAIRE

    Morrey, Kristina

    2011-01-01

    The object of this study was to examine and document anatomical variability of cranial nerve assignment for muscles of the speech and swallow mechanism. Through means of textbook review, the study’s first purpose was to identify which cranial nerves were attributed to the innervation for muscles associated with the speech and swallow mechanism. The second purpose was to examine if cranial nerve assignment, field of study, or geographic region explained differences in cranial nerve assignment ...