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Sample records for specific resonance assignment

  1. Assignment of methyl NMR resonances of a 52 kDa protein with residue-specific 4D correlation maps

    International Nuclear Information System (INIS)

    Mishra, Subrata H.; Frueh, Dominique P.

    2015-01-01

    Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method that facilitates assignment of methyl resonances from assigned amide groups. Calculating the covariance between sensitive methyl and amide 3D spectra, each providing correlations to C α and C β separately, produces 4D correlation maps directly correlating methyl groups to amide groups. Optimal correlation maps are obtained by extracting residue-specific regions, applying derivative to the dimensions subject to covariance, and multiplying 4D maps stemming from different 3D spectra. The latter procedure rescues weak signals that may be missed in traditional assignment procedures. Using these covariance correlation maps, nearly all assigned isoleucine, leucine, and valine amide resonances of a 52 kDa nonribosomal peptide synthetase cyclization domain were paired with their corresponding methyl groups

  2. Contact replacement for NMR resonance assignment.

    Science.gov (United States)

    Xiong, Fei; Pandurangan, Gopal; Bailey-Kellogg, Chris

    2008-07-01

    Complementing its traditional role in structural studies of proteins, nuclear magnetic resonance (NMR) spectroscopy is playing an increasingly important role in functional studies. NMR dynamics experiments characterize motions involved in target recognition, ligand binding, etc., while NMR chemical shift perturbation experiments identify and localize protein-protein and protein-ligand interactions. The key bottleneck in these studies is to determine the backbone resonance assignment, which allows spectral peaks to be mapped to specific atoms. This article develops a novel approach to address that bottleneck, exploiting an available X-ray structure or homology model to assign the entire backbone from a set of relatively fast and cheap NMR experiments. We formulate contact replacement for resonance assignment as the problem of computing correspondences between a contact graph representing the structure and an NMR graph representing the data; the NMR graph is a significantly corrupted, ambiguous version of the contact graph. We first show that by combining connectivity and amino acid type information, and exploiting the random structure of the noise, one can provably determine unique correspondences in polynomial time with high probability, even in the presence of significant noise (a constant number of noisy edges per vertex). We then detail an efficient randomized algorithm and show that, over a variety of experimental and synthetic datasets, it is robust to typical levels of structural variation (1-2 AA), noise (250-600%) and missings (10-40%). Our algorithm achieves very good overall assignment accuracy, above 80% in alpha-helices, 70% in beta-sheets and 60% in loop regions. Our contact replacement algorithm is implemented in platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

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

    International Nuclear Information System (INIS)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E.; Eghbalnia, Hamid R.

    2012-01-01

    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 ( 1 H– 15 N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy ( 1 H– 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 resonances for a

  4. 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

  5. Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH

    International Nuclear Information System (INIS)

    Volk, Jochen; Herrmann, Torsten; Wuethrich, Kurt

    2008-01-01

    MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustness

  6. 4D experiments measured with APSY for automated backbone resonance assignments of large proteins

    International Nuclear Information System (INIS)

    Krähenbühl, Barbara; Boudet, Julien; Wider, Gerhard

    2013-01-01

    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.

  7. 1H and 15N resonance assignments of oxidized flavodoxin from Anacystis nidulans with 3D NMR

    International Nuclear Information System (INIS)

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

    1991-01-01

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

  8. Methods for sequential resonance assignment in solid, uniformly 13C, 15N labelled peptides: Quantification and application to antamanide

    International Nuclear Information System (INIS)

    Detken, Andreas; Hardy, Edme H.; Ernst, Matthias; Kainosho, Masatsune; Kawakami, Toru; Aimoto, Saburo; Meier, Beat H.

    2001-01-01

    The application of adiabatic polarization-transfer experiments to resonance assignment in solid, uniformly 13 C- 15 N-labelled polypeptides is demonstrated for the cyclic decapeptide antamanide. A homonuclear correlation experiment employing the DREAM sequence for adiabatic dipolar transfer yields a complete assignment of the C α and aliphatic side-chain 13 C resonances to amino acid types. The same information can be obtained from a TOBSY experiment using the recently introduced P9 1 12 TOBSY sequence, which employs the J couplings as a transfer mechanism. A comparison of the two methods is presented. Except for some aromatic phenylalanine resonances, a complete sequence-specific assignment of the 13 C and 15 N resonances in antamanide is achieved by a series of selective or broadband adiabatic triple-resonance experiments. Heteronuclear transfer by adiabatic-passage Hartmann-Hahn cross polarization is combined with adiabatic homonuclear transfer by the DREAM and rotational-resonance tickling sequences into two- and three-dimensional experiments. The performance of these experiments is evaluated quantitatively

  9. Sequence-specific {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments for intestinal fatty-acid-binding protein complexed with palmitate (15.4 kDA)

    Energy Technology Data Exchange (ETDEWEB)

    Hodsdon, M.E.; Toner, J.J.; Cistola, D.P. [Washington Univ. School of Medicine, St. Louis, MO (United States)

    1994-12-01

    Intestinal fatty-acid-binding protein (I-FABP) belongs to a family of soluble, cytoplasmic proteins that are thought to function in the intracellular transport and trafficking of polar lipids. Individual members of this protein family have distinct specificities and affinities for fatty acids, cholesterol, bile salts, and retinoids. We are comparing several retinol- and fatty-acid-binding proteins from intestine in order to define the factors that control molecular recognition in this family of proteins. We have established sequential resonance assignments for uniformly {sup 13}C/{sup 15}N-enriched I-FABP complexed with perdeuterated palmitate at pH7.2 and 37{degrees}C. The assignment strategy was similar to that introduced for calmodulin. We employed seven three-dimensional NMR experiments to establish scalar couplings between backbone and sidechain atoms. Backbone atoms were correlated using triple-resonance HNCO, HNCA, TOCSY-HMQC, HCACO, and HCA(CO)N experiments. Sidechain atoms were correlated using CC-TOCSY, HCCH-TOCSY, and TOCSY-HMQC. The correlations of peaks between three-dimensional spectra were established in a computer-assisted manner using NMR COMPASS (Molecular Simulations, Inc.) Using this approach, {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments have been established for 120 of the 131 residues of I-FABP. For 18 residues, amide {sup 1}H and {sup 15}N resonances were unobservable, apparently because of the rapid exchange of amide protons with bulk water at pH 7.2. The missing amide protons correspond to distinct amino acid patterns in the protein sequence, which will be discussed. During the assignment process, several sources of ambiguity in spin correlations were observed. To overcome this ambiguity, the additional inter-residue correlations often observed in the HNCA experiment were used as cross-checks for the sequential backbone assignments.

  10. A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments

    International Nuclear Information System (INIS)

    Schubert, Mario; Labudde, Dirk; Leitner, Dietmar; Oschkinat, Hartmut; Schmieder, Peter

    2005-01-01

    The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step. This is nowadays almost exclusively performed using triple-resonance experiments. The conventional strategy utilizes one or more pairs of three dimensional spectra to obtain redundant information and thus reliable assignments. Here, a modified strategy for obtaining sequence specific assignments based on two dimensional amino acid type selective triple-resonance experiments is proposed. These experiments can be recorded with good resolution in a relatively short time. They provide very specific and redundant information, in particular on sequential connectivities, that drastically increases the ease and reliability of the assignment procedure, done either manually or in an automated fashion. The new strategy is demonstrated with the protein domain PB1 from yeast CDC24p

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

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  12. P-wave assignment of 232Th neutron resonances

    International Nuclear Information System (INIS)

    Corvi, F.; Pasquariello, G.; Veen, T. van der

    1978-01-01

    A method of p-wave assignment which exploits the parity dependence of the primary capture γ-ray spectrum was applied to the 232 Th resonance. The yield of capture γ-rays above 4.4 MeV from a 6 mm thick metallic thorium disk was measured in the neutron energy range 20-2200 eV and compared to a similar run with γ-rays in the range 3.7 - 4.4 MeV. A total of 58 resonances showing an enhancement of the high energy γ-ray yield were assigned as p-waves. Assuming that their reduced neutron widths follow a Porter-Thomas distribution, their average value and then the p-wave strength function S 1 were estimated with a maximum likelihood method. The results are: average neutron width=3.4(+0.8 or -0.6)meV; S 1 = 2.0 (+0.5 or -0.4).10 -4

  13. An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming

    KAUST Repository

    Abbas, Ahmed; Guo, Xianrong; Jing, Bingyi; Gao, Xin

    2014-01-01

    positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas

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

    Energy Technology Data Exchange (ETDEWEB)

    Zuiderweg, Erik R. P., E-mail: zuiderwe@umich.edu; Bagai, Ireena [The University of Michigan Medical School, Department of Biological Chemistry (United States); Rossi, Paolo [Rutgers University, Center for Integrative Proteomics Research (United States); Bertelsen, Eric B. [Arbor Communications, Inc. (United States)

    2013-10-15

    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 Multiplication-Sign 10{sup 260} 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.

  15. Sequence-specific 1H-NMR assignments for the aromatic region of several biologically active, monomeric insulins including native human insulin.

    Science.gov (United States)

    Roy, M; Lee, R W; Kaarsholm, N C; Thøgersen, H; Brange, J; Dunn, M F

    1990-06-12

    The aromatic region of the 1H-FT-NMR spectrum of the biologically fully-potent, monomeric human insulin mutant, B9 Ser----Asp, B27 Thr----Glu has been investigated in D2O. At 1 to 5 mM concentrations, this mutant insulin is monomeric above pH 7.5. Coupling and amino acid classification of all aromatic signals is established via a combination of homonuclear one- and two-dimensional methods, including COSY, multiple quantum filters, selective spin decoupling and pH titrations. By comparisons with other insulin mutants and with chemically modified native insulins, all resonances in the aromatic region are given sequence-specific assignments without any reliance on the various crystal structures reported for insulin. These comparisons also give the sequence-specific assignments of most of the aromatic resonances of the mutant insulins B16 Tyr----Glu, B27 Thr----Glu and B25 Phe----Asp and the chemically modified species des-(B23-B30) insulin and monoiodo-Tyr A14 insulin. Chemical dispersion of the assigned resonances, ring current perturbations and comparisons at high pH have made possible the assignment of the aromatic resonances of human insulin, and these studies indicate that the major structural features of the human insulin monomer (including those critical to biological function) are also present in the monomeric mutant.

  16. 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)

    Zuiderweg, Erik R. P.; Bagai, Ireena; Rossi, Paolo; Bertelsen, Eric B.

    2013-01-01

    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 × 10 260 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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  18. An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming

    KAUST Repository

    Abbas, Ahmed

    2014-04-19

    Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on \\'slices\\', which are one-dimensional vectors in three-dimensional spectra that correspond to certain (N, H) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx. © 2014 Springer Science+Business Media.

  19. Automated solid-state NMR resonance assignment of protein microcrystals and amyloids

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Elena [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany); Gath, Julia [ETH Zurich, Physical Chemistry (Switzerland); Habenstein, Birgit [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France); Ravotti, Francesco; Szekely, Kathrin; Huber, Matthias [ETH Zurich, Physical Chemistry (Switzerland); Buchner, Lena [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany); Boeckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Guentert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

    2013-07-15

    Solid-state NMR is an emerging structure determination technique for crystalline and non-crystalline protein assemblies, e.g., amyloids. Resonance assignment constitutes the first and often very time-consuming step to a structure. We present ssFLYA, a generally applicable algorithm for automatic assignment of protein solid-state NMR spectra. Application to microcrystals of ubiquitin and the Ure2 prion C-terminal domain, as well as amyloids of HET-s(218-289) and {alpha}-synuclein yielded 88-97 % correctness for the backbone and side-chain assignments that are classified as self-consistent by the algorithm, and 77-90 % correctness if also assignments classified as tentative by the algorithm are included.

  20. Automated solid-state NMR resonance assignment of protein microcrystals and amyloids

    International Nuclear Information System (INIS)

    Schmidt, Elena; Gath, Julia; Habenstein, Birgit; Ravotti, Francesco; Székely, Kathrin; Huber, Matthias; Buchner, Lena; Böckmann, Anja; Meier, Beat H.; Güntert, Peter

    2013-01-01

    Solid-state NMR is an emerging structure determination technique for crystalline and non-crystalline protein assemblies, e.g., amyloids. Resonance assignment constitutes the first and often very time-consuming step to a structure. We present ssFLYA, a generally applicable algorithm for automatic assignment of protein solid-state NMR spectra. Application to microcrystals of ubiquitin and the Ure2 prion C-terminal domain, as well as amyloids of HET-s(218–289) and α-synuclein yielded 88–97 % correctness for the backbone and side-chain assignments that are classified as self-consistent by the algorithm, and 77–90 % correctness if also assignments classified as tentative by the algorithm are included

  1. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Falk, Alexander S.; Siemer, Ansgar B., E-mail: asiemer@usc.edu [Keck School of Medicine of USC, Department of Biochemistry and Molecular Medicine, Zilkha Neurogenetic Institute (United States)

    2016-11-15

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

  2. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy

    International Nuclear Information System (INIS)

    Falk, Alexander S.; Siemer, Ansgar B.

    2016-01-01

    Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution. Here, we show that it is nevertheless possible to record 3D HNCO, HNCA, and HNcoCA spectra on these intrinsically disordered domains and to obtain site-specific assignments.

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

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  4. 13C, 15N Resonance Assignment of Parts of the HET-s Prion Protein in its Amyloid Form

    International Nuclear Information System (INIS)

    Siemer, Ansgar B.; Ritter, Christiane; Steinmetz, Michel O.; Ernst, Matthias; Riek, Roland; Meier, Beat H.

    2006-01-01

    The partial 15 N and 13 C solid-state NMR resonance assignment of the HET-s prion protein fragment 218-289 in its amyloid form is presented. It is based on experiments measured at MAS frequencies in the range of 20-40 kHz using exclusively adiabatic polarization-transfer schemes. The resonance assignment within each residue is based on two-dimensional 13 C-- 13 C correlation spectra utilizing the DREAM mixing scheme. The sequential linking of the assigned residues used a set of two- and three-dimensional 15 N-- 13 C correlation experiments. Almost all cross peaks visible in the spectra are assigned, but only resonances from 43 of the 78 amino-acid residues could be detected. The missing residues are thought to be highly disordered and/or highly dynamic giving rise to broad resonance lines that escaped detection in the experiments applied. The line widths of the observed resonances are narrow and comparable to line widths observed in micro-crystalline samples. The 43 assigned residues are located in two fragments of about 20 residues

  5. An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

    Science.gov (United States)

    Kamisetty, Hetunandan; Bailey-Kellogg, Chris; Pandurangan, Gopal

    2006-01-15

    Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to

  6. {sup 13}C, {sup 15}N Resonance Assignment of Parts of the HET-s Prion Protein in its Amyloid Form

    Energy Technology Data Exchange (ETDEWEB)

    Siemer, Ansgar B. [Physical Chemistry (Switzerland); Ritter, Christiane [Salk Institute, Structural Biology Laboratory (United States); Steinmetz, Michel O. [Paul Scherrer Institut, Biomolecular Research, Structural Biology (Switzerland); Ernst, Matthias [Physical Chemistry (Switzerland); Riek, Roland [Salk Institute, Structural Biology Laboratory (United States); Meier, Beat H. [Physical Chemistry (Switzerland)

    2006-02-15

    The partial {sup 15}N and {sup 13}C solid-state NMR resonance assignment of the HET-s prion protein fragment 218-289 in its amyloid form is presented. It is based on experiments measured at MAS frequencies in the range of 20-40 kHz using exclusively adiabatic polarization-transfer schemes. The resonance assignment within each residue is based on two-dimensional {sup 13}C--{sup 13}C correlation spectra utilizing the DREAM mixing scheme. The sequential linking of the assigned residues used a set of two- and three-dimensional {sup 15}N--{sup 13}C correlation experiments. Almost all cross peaks visible in the spectra are assigned, but only resonances from 43 of the 78 amino-acid residues could be detected. The missing residues are thought to be highly disordered and/or highly dynamic giving rise to broad resonance lines that escaped detection in the experiments applied. The line widths of the observed resonances are narrow and comparable to line widths observed in micro-crystalline samples. The 43 assigned residues are located in two fragments of about 20 residues.

  7. Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

    KAUST Repository

    Jang, Richard; Gao, Xin; Li, Ming

    2011-01-01

    In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg's contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, 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 human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

  8. Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

    KAUST Repository

    Jang, Richard

    2011-03-01

    In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg\\'s contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, 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 human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

  9. Protein resonance assignment at MAS frequencies approaching 100 kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods

    Energy Technology Data Exchange (ETDEWEB)

    Penzel, Susanne; Smith, Albert A.; Agarwal, Vipin; Hunkeler, Andreas [ETH Zürich, Physical Chemistry (Switzerland); Org, Mai-Liis; Samoson, Ago, E-mail: ago.samoson@ttu.ee [Tallinn University of Technology, NMR Instituut, Tartu Teadus, Tehnomeedikum (Estonia); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Université de Lyon 1, Institut de Biologie et Chimie des Protéines (France); Ernst, Matthias, E-mail: maer@ethz.ch; Meier, Beat H., E-mail: beme@ethz.ch [ETH Zürich, Physical Chemistry (Switzerland)

    2015-10-15

    We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T{sub 2}′ times and a site-specific comparison of T{sub 2}′ at 93 kHz versus 60 kHz MAS frequency. A quantitative analysis of transfer efficiencies of building blocks, as they are used for typical 3D experiments, was performed. To do this, we compared dipolar-coupling and J-coupling based transfer steps. The building blocks were then combined into 3D experiments for sequential resonance assignment, where we evaluated signal-to-noise ratio and information content of the different 3D spectra in order to identify the best assignment strategy. Based on this comparison, six experiments were selected to optimally assign the model protein ubiquitin, solely using spectra acquired at 93 kHz MAS. Within 3 days of instrument time, the required spectra were recorded from which the backbone resonances have been assigned to over 96 %.

  10. Inferential backbone assignment for sparse data

    International Nuclear Information System (INIS)

    Vitek, Olga; Bailey-Kellogg, Chris; Craig, Bruce; Vitek, Jan

    2006-01-01

    This paper develops an approach to protein backbone NMR assignment that effectively assigns large proteins while using limited sets of triple-resonance experiments. Our approach handles proteins with large fractions of missing data and many ambiguous pairs of pseudoresidues, and provides a statistical assessment of confidence in global and position-specific assignments. The approach is tested on an extensive set of experimental and synthetic data of up to 723 residues, with match tolerances of up to 0.5 ppm for C α and C β resonance types. The tests show that the approach is particularly helpful when data contain experimental noise and require large match tolerances. The keys to the approach are an empirical Bayesian probability model that rigorously accounts for uncertainty in the data at all stages in the analysis, and a hybrid stochastic tree-based search algorithm that effectively explores the large space of possible assignments

  11. Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

    Science.gov (United States)

    Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik

    2015-01-01

    The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

  12. Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

    Directory of Open Access Journals (Sweden)

    Markus Niklasson

    2015-01-01

    Full Text Available The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

  13. A new strategy for backbone resonance assignment in large proteins using a MQ-HACACO experiment

    International Nuclear Information System (INIS)

    Pervushin, Konstantin; Eletsky, Alexander

    2003-01-01

    A new strategy of backbone resonance assignment is proposed based on a combination of the most sensitive TROSY-type triple resonance experiments such as TROSY-HNCA and TROSY-HNCO with a new 3D multiple-quantum HACACO experiment. The favourable relaxation properties of the multiple-quantum coherences and signal detection using the 13 C' antiphase coherences optimize the performance of the proposed experiment for application to larger proteins. In addition to the 1 H N , 15 N, 13 C α and 13 C' chemical shifts the 3D multiple-quantum HACACO experiment provides assignment for the 1 H α resonances in contrast to previously proposed experiments for large proteins. The strategy is demonstrated with the 44 kDa uniformly 15 N, 13 C-labeled and fractionally 35% deuterated trimeric B. subtilis Chorismate Mutase measured at 20 deg. C and 9 deg. C. Measurements at the lower temperature indicate that the new strategy can be applied to even larger proteins with molecular weights up to 80 kDa

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

    International Nuclear Information System (INIS)

    Takeuchi, Koh; Heffron, Gregory; Sun, Zhen-Yu J.; Frueh, Dominique P.; Wagner, Gerhard

    2010-01-01

    Heteronuclear direct-detection experiments, which utilize the slower relaxation properties of low γ nuclei, such as 13 C have recently been proposed for sequence-specific assignment and structural analyses of large, unstructured, and/or paramagnetic proteins. Here we present two novel 15 N direct-detection experiments. The CAN experiment sequentially connects amide 15 N resonances using 13 C α chemical shift matching, and the CON experiment connects the preceding 13 C' 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 13 C-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 15 N 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 15 N observe CAN experiment is 16% higher than in the 13 C 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 C α 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 D 2 O. Thus, these features and the superior resolution of 15 N-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.

  15. Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

    Science.gov (United States)

    Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

    2017-07-19

    Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

  16. 1H NMR studies of plastocyanin from Scenedesmus obliquus: Complete sequence-specific assignment, secondary structure analysis, and global fold

    International Nuclear Information System (INIS)

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

    1988-01-01

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

  17. Complete assignment of the methionyl carbonyl carbon resonance in switch variant anti-dansyl antibodies labeled with [1-13C]methionine

    International Nuclear Information System (INIS)

    Kato, Koichi; Matsunaga, C.; Igarashi, Takako; Kim, Hahyung; Odaka, Asano; Shimada, Ichio; Arata, Yoji

    1991-01-01

    A 13 C NMR study is reported of switch variant anti-dansyl antibodies developed by Dangl et al. who had used the fluorescence-activated cell sorter to select and clone these variants. These switch variant antibodies possess the identical V H , V L , and C L domains in conjunction with different heavy chain constant regions. In the present study, switch variant antibodies of IgG1, IgG2a, and IgG2b subclasses were used along with a short-chain IgG2a antibody, in which the entire C H 1 domain is deleted. The switch variant antibodies were specifically labeled with [1- 13 C]methionine by growing hybridoma cells in serum-free medium. Assignments of all the methionyl carbonyl carbon resonances have been completed by using the intact antibodies along with their fragments and recombined proteins in which either heavy or light chain is labeled. A double labeling method has played a crucial role in the process of the spectral assignments. The strategy used for the assignments has been described in detail. In incorporating 15 N-labeled amino acids into the antibodies for the double labeling, isotope dilution caused a serious problem except in the cases of [α- 15 N]lysine and [ 15 N]threonine, both of which cannot become the substrate of transaminases. It was found that β-chloro-L-alanine is most effective in suppressing the isotope scrambling. So far, spectral assignments by the double labeling method have been possible with 15 N-labeled Ala, His, Ile, Lys, Met, Ser, Thr, Tyr, and Val. On the basis of the results of the present 13 C study, possible use of the assigned carbonyl carbon resonances for the elucidation of the structure-function relationship in the antibody system has been briefly discussed

  18. TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra

    Energy Technology Data Exchange (ETDEWEB)

    Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor [University of Warsaw, Faculty of Chemistry (Poland); Billeter, Martin, E-mail: martin.billeter@chem.gu.se [University of Gothenburg, Biophysics Group, Department of Chemistry and Molecular Biology (Sweden)

    2012-09-15

    While NMR studies of proteins typically aim at structure, dynamics or interactions, resonance assignments represent in almost all cases the initial step of the analysis. With increasing complexity of the NMR spectra, for example due to decreasing extent of ordered structure, this task often becomes both difficult and time-consuming, and the recording of high-dimensional data with high-resolution may be essential. Random sampling of the evolution time space, combined with sparse multidimensional Fourier transform (SMFT), allows for efficient recording of very high dimensional spectra ({>=}4 dimensions) while maintaining high resolution. However, the nature of this data demands for automation of the assignment process. Here we present the program TSAR (Tool for SMFT-based Assignment of Resonances), which exploits all advantages of SMFT input. Moreover, its flexibility allows to process data from any type of experiments that provide sequential connectivities. The algorithm was tested on several protein samples, including a disordered 81-residue fragment of the {delta} subunit of RNA polymerase from Bacillus subtilis containing various repetitive sequences. For our test examples, TSAR achieves a high percentage of assigned residues without any erroneous assignments.

  19. Specific labeling and assignment strategies of valine methyl groups for NMR studies of high molecular weight proteins

    Energy Technology Data Exchange (ETDEWEB)

    Mas, Guillaume; Crublet, Elodie [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France); Hamelin, Olivier [CNRS (France); Gans, Pierre; Boisbouvier, Jérôme, E-mail: jerome.boisbouvier@ibs.fr [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France)

    2013-09-28

    The specific protonation of valine and leucine methyl groups in proteins is typically achieved by overexpressing proteins in M9/D{sub 2}O medium supplemented with either labeled α-ketoisovalerate for the labeling of the four prochiral methyl groups or with 2-acetolactate for the stereospecific labeling of the valine and leucine side chains. However, when these labeling schemes are applied to large protein assemblies, significant overlap between the correlations of the valine and leucine methyl groups occurs, hampering the analysis of 2D methyl-TROSY spectra. Analysis of the leucine and valine biosynthesis pathways revealed that the incorporation of labeled precursors in the leucine pathway can be inhibited by the addition of exogenous l-leucine-d{sub 10}. We exploited this property to label stereospecifically the pro-R and pro-S methyl groups of valine with minimal scrambling to the leucine residues. This new labeling protocol was applied to the 468 kDa homododecameric peptidase TET2 to decrease the complexity of its NMR spectra. All of the pro-S valine methyl resonances of TET2 were assigned by combining mutagenesis with this innovative labeling approach. The assignments were transferred to the pro-R groups using an optimally labeled sample and a set of triple resonance experiments. This improved labeling scheme enables us to overcome the main limitation of overcrowding in the NMR spectra of prochiral methyl groups, which is a prerequisite for the site-specific measurement of the structural and dynamic parameters or for the study of interactions in very large protein assemblies.

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  2. Complete assignment of the methionyl carbonyl carbon resonance in switch variant anti-dansyl antibodies labeled with (1- sup 13 C)methionine

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Koichi; Matsunaga, C.; Igarashi, Takako; Kim, Hahyung; Odaka, Asano; Shimada, Ichio; Arata, Yoji (Univ. of Tokyo, Hongo (Japan))

    1991-01-01

    A {sup 13}C NMR study is reported of switch variant anti-dansyl antibodies developed by Dangl et al. who had used the fluorescence-activated cell sorter to select and clone these variants. These switch variant antibodies possess the identical V{sub H}, V{sub L}, and C{sub L} domains in conjunction with different heavy chain constant regions. In the present study, switch variant antibodies of IgG1, IgG2a, and IgG2b subclasses were used along with a short-chain IgG2a antibody, in which the entire C{sub H}1 domain is deleted. The switch variant antibodies were specifically labeled with (1-{sup 13}C)methionine by growing hybridoma cells in serum-free medium. Assignments of all the methionyl carbonyl carbon resonances have been completed by using the intact antibodies along with their fragments and recombined proteins in which either heavy or light chain is labeled. A double labeling method has played a crucial role in the process of the spectral assignments. The strategy used for the assignments has been described in detail. In incorporating {sup 15}N-labeled amino acids into the antibodies for the double labeling, isotope dilution caused a serious problem except in the cases of ({alpha}-{sup 15}N)lysine and ({sup 15}N)threonine, both of which cannot become the substrate of transaminases. It was found that {beta}-chloro-L-alanine is most effective in suppressing the isotope scrambling. So far, spectral assignments by the double labeling method have been possible with {sup 15}N-labeled Ala, His, Ile, Lys, Met, Ser, Thr, Tyr, and Val. On the basis of the results of the present {sup 13}C study, possible use of the assigned carbonyl carbon resonances for the elucidation of the structure-function relationship in the antibody system has been briefly discussed.

  3. Sequence-specific assignment of methyl groups from the neuronal SNARE complex using lanthanide-induced pseudocontact shifts

    International Nuclear Information System (INIS)

    Pan, Yun-Zu; Quade, Bradley; Brewer, Kyle D.; Szabo, Monika; Swarbrick, James D.; Graham, Bim; Rizo, Josep

    2016-01-01

    Neurotransmitter release depends critically on the neuronal SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin, as well as on other proteins such as Munc18-1, Munc13-1 and synaptotagmin-1. Although three-dimensional structures are available for these components, it is still unclear how they are assembled between the synaptic vesicle and plasma membranes to trigger fast, Ca 2+ -dependent membrane fusion. Methyl TROSY NMR experiments provide a powerful tool to study complexes between these proteins, but assignment of the methyl groups of the SNARE complex is hindered by its limited solubility. Here we report the assignment of the isoleucine, leucine, methionine and valine methyl groups of the four SNARE motifs of syntaxin-1, SNAP-25 and synaptobrevin within the SNARE complex based solely on measurements of lanthanide-induced pseudocontact shifts. Our results illustrate the power of this approach to assign protein resonances without the need of triple resonance experiments and provide an invaluable tool for future structural studies of how the SNARE complex binds to other components of the release machinery.

  4. Sequence-specific assignment of methyl groups from the neuronal SNARE complex using lanthanide-induced pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Yun-Zu; Quade, Bradley; Brewer, Kyle D. [University of Texas Southwestern Medical Center, Department of Biophysics (United States); Szabo, Monika; Swarbrick, James D.; Graham, Bim [Monash Institute of Pharmaceutical Sciences, Monash University (Australia); Rizo, Josep, E-mail: Jose.Rizo-Rey@UTSouthwestern.edu [University of Texas Southwestern Medical Center, Department of Biophysics (United States)

    2016-12-15

    Neurotransmitter release depends critically on the neuronal SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin, as well as on other proteins such as Munc18-1, Munc13-1 and synaptotagmin-1. Although three-dimensional structures are available for these components, it is still unclear how they are assembled between the synaptic vesicle and plasma membranes to trigger fast, Ca{sup 2+}-dependent membrane fusion. Methyl TROSY NMR experiments provide a powerful tool to study complexes between these proteins, but assignment of the methyl groups of the SNARE complex is hindered by its limited solubility. Here we report the assignment of the isoleucine, leucine, methionine and valine methyl groups of the four SNARE motifs of syntaxin-1, SNAP-25 and synaptobrevin within the SNARE complex based solely on measurements of lanthanide-induced pseudocontact shifts. Our results illustrate the power of this approach to assign protein resonances without the need of triple resonance experiments and provide an invaluable tool for future structural studies of how the SNARE complex binds to other components of the release machinery.

  5. Resonance assignment of disordered protein with repetitive and overlapping sequence using combinatorial approach reveals initial structural propensities and local restrictions in the denatured state

    Energy Technology Data Exchange (ETDEWEB)

    Malik, Nikita; Kumar, Ashutosh, E-mail: askutoshk@iitb.ac.in [Indian Institute of Technology Bombay, Department of Bioscience and Bioengineering (India)

    2016-09-15

    NMR resonance assignment of intrinsically disordered proteins poses a challenge because of the limited dispersion of amide proton chemical shifts. This becomes even more complex with the increase in the size of the system. Residue specific selective labeling/unlabeling experiments have been used to resolve the overlap, but require multiple sample preparations. Here, we demonstrate an assignment strategy requiring only a single sample of uniformly labeled {sup 13}C,{sup 15}N-protein. We have used a combinatorial approach, involving 3D-HNN, CC(CO)NH and 2D-MUSIC, which allowed us to assign a denatured centromeric protein Cse4 of 229 residues. Further, we show that even the less sensitive experiments, when used in an efficient manner can lead to the complete assignment of a complex system without the use of specialized probes in a relatively short time frame. The assignment of the amino acids discloses the presence of local structural propensities even in the denatured state accompanied by restricted motion in certain regions that provides insights into the early folding events of the protein.

  6. Resonance assignment of disordered protein with repetitive and overlapping sequence using combinatorial approach reveals initial structural propensities and local restrictions in the denatured state

    International Nuclear Information System (INIS)

    Malik, Nikita; Kumar, Ashutosh

    2016-01-01

    NMR resonance assignment of intrinsically disordered proteins poses a challenge because of the limited dispersion of amide proton chemical shifts. This becomes even more complex with the increase in the size of the system. Residue specific selective labeling/unlabeling experiments have been used to resolve the overlap, but require multiple sample preparations. Here, we demonstrate an assignment strategy requiring only a single sample of uniformly labeled "1"3C,"1"5N-protein. We have used a combinatorial approach, involving 3D-HNN, CC(CO)NH and 2D-MUSIC, which allowed us to assign a denatured centromeric protein Cse4 of 229 residues. Further, we show that even the less sensitive experiments, when used in an efficient manner can lead to the complete assignment of a complex system without the use of specialized probes in a relatively short time frame. The assignment of the amino acids discloses the presence of local structural propensities even in the denatured state accompanied by restricted motion in certain regions that provides insights into the early folding events of the protein.

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  8. Solid state NMR sequential resonance assignments and conformational analysis of the 2x10.4 kDa dimeric form of the Bacillus subtilis protein Crh

    Energy Technology Data Exchange (ETDEWEB)

    Boeckmann, Anja [Institut de Biologie et Chimie des Proteines, C.N.R.S UMR 5086 (France)], E-mail: a.bockmann@ibcp.fr; Lange, Adam [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany); Galinier, Anne [Institut de Biologie Structurale et Microbiologie, C.N.R.S UPR 9043 (France); Luca, Sorin [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany); Giraud, Nicolas; Juy, Michel [Institut de Biologie et Chimie des Proteines, C.N.R.S UMR 5086 (France); Heise, Henrike [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany); Montserret, Roland; Penin, Francois [Institut de Biologie et Chimie des Proteines, C.N.R.S UMR 5086 (France); Baldus, Marc [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany)], E-mail: maba@mpibpc.mpg.de

    2003-12-15

    Solid state NMR sample preparation and resonance assignments of the U-[{sup 13}C,{sup 15}N] 2x10.4 kDa dimeric form of the regulatory protein Crh in microcrystalline, PEG precipitated form are presented. Intra- and interresidue correlations using dipolar polarization transfer methods led to nearly complete sequential assignments of the protein, and to 88% of all {sup 15}N, {sup 13}C chemical shifts. For several residues, the resonance assignments differ significantly from those reported for the monomeric form analyzed by solution state NMR. Dihedral angles obtained from a TALOS-based statistical analysis suggest that the microcrystalline arrangement of Crh must be similar to the domain-swapped dimeric structure of a single crystal form recently solved using X-ray crystallography. For a limited number of protein residues, a remarkable doubling of the observed NMR resonances is observed indicative of local static or dynamic conformational disorder. Our study reports resonance assignments for the largest protein investigated by solid state NMR so far and describes the conformational dimeric variant of Crh with previously unknown chemical shifts.

  9. 13C-detected NMR experiments for automatic resonance assignment of IDPs and multiple-fixing SMFT processing

    International Nuclear Information System (INIS)

    Dziekański, Paweł; Grudziąż, Katarzyna; Jarvoll, Patrik; Koźmiński, Wiktor; Zawadzka-Kazimierczuk, Anna

    2015-01-01

    Intrinsically disordered proteins (IDPs) have recently attracted much interest, due to their role in many biological processes, including signaling and regulation mechanisms. High-dimensional 13 C direct-detected NMR experiments have proven exceptionally useful in case of IDPs, providing spectra with superior peak dispersion. Here, two such novel experiments recorded with non-uniform sampling are introduced, these are 5D HabCabCO(CA)NCO and 5D HNCO(CA)NCO. Together with the 4D (HACA)CON(CA)NCO, an extension of the previously published 3D experiments (Pantoja-Uceda and Santoro in J Biomol NMR 59:43–50, 2014. doi: 10.1007/s10858-014-9827-1 10.1007/s10858-014-9827-1 ), they form a set allowing for complete and reliable resonance assignment of difficult IDPs. The processing is performed with sparse multidimensional Fourier transform based on the concept of restricting (fixing) some of spectral dimensions to a priori known resonance frequencies. In our study, a multiple-fixing method was developed, that allows easy access to spectral data. The experiments were tested on a resolution-demanding alpha-synuclein sample. Due to superior peak dispersion in high-dimensional spectrum and availability of the sequential connectivities between four consecutive residues, the overwhelming majority of resonances could be assigned automatically using the TSAR program

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

    Energy Technology Data Exchange (ETDEWEB)

    Yamamoto, Yasuhiko

    1987-09-28

    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 /sup 1/H-/sup 13/C 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 22/sup 0/C, 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.

  11. Reflective practice: assessment of assignments in English for Specific Purposes

    Directory of Open Access Journals (Sweden)

    Galina Kavaliauskiené

    2007-10-01

    Full Text Available The construct alternative assessment has been widely used in higher education. It is often defined as any type of assessment of learners who provide a response to an assignment. The key features of alternative assessment are active participation of learners in self-evaluation of their performance, and the development of reflective thinking through reflective thinking (Schön, 1983. The success of alternative assessment in language teaching is predetermined by student’s performance and demonstrates learner’s language proficiency in contemporary communicative classrooms. This paper aims at researching the influence of students’ evaluations of various assignments for their linguistic development in English for Specific Purposes (ESP. The study uses learners’ assessment of different assignments and learners’ in-course and post-course written reflections on benefits to language mastery. Learners’ assignments included were contributions to portfolios (dossiers, such as essays and summaries, oral presentations, short impromptu talks, creative tasks, tests, and self-assessment notes (reflections on activities in learning ESP. Findings were obtained for two streams of the project participants. Results showed that self-assessment was beneficial for learners’ linguistic development. The context of learners’ reflections reveals that the attitudes to various assignments are affected by success or failure in students’ performance. Reflective practice might help teachers develop ways of dealing with previously identified difficulties and improve the quality of teaching.

  12. Sequence determination and resonance assignments of an Azomonas siderophore using 13C natural abundance 13C-1H HNCA experiment

    Czech Academy of Sciences Publication Activity Database

    Wasielewski, E.; Abdallah, M. A.; Kyslík, Pavel; Kieffer, B.

    2001-01-01

    Roč. 4, - (2001), s. 765-770 ISSN 1387-1609 Institutional research plan: CEZ:AV0Z5020903 Keywords : determination * resonance * assignments Subject RIV: EE - Microbiology, Virology Impact factor: 0.555, year: 2001

  13. Resonance assignments of the myristoylated Y28F/Y67F mutant of the Mason-Pfizer monkey virus matrix protein

    Czech Academy of Sciences Publication Activity Database

    Doležal, Michal; Hrabal, R.; Ruml, T.; Rumlová, Michaela

    2015-01-01

    Roč. 9, č. 2 (2015), s. 229-233 ISSN 1874-2718 Institutional support: RVO:61388963 Keywords : isotopic labeling * matrix protein * M-PMV * myristoylation * resonance assignment * reverse labeling Subject RIV: CE - Biochemistry Impact factor: 0.687, year: 2015

  14. High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry (Poland); Sanderova, Hana; Krasny, Libor [Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria, Department of Bacteriology (Czech Republic)

    2012-04-15

    Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using {delta} subunit (20 kDa) of Bacillus subtilis RNA polymerase that has an 81-amino acid disordered part containing various repetitive sequences.

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  16. Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III

    Energy Technology Data Exchange (ETDEWEB)

    Krisnamoorthi, R.; Yuxi Gong; Chanlan Sun Lin (Kansas State Univ., Manhattan (United States)); VanderVelde, D. (Univ. of Kansas, Lawrence (United States))

    1992-01-28

    The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific {sup 1}H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns, a 3{sub 10}-helix, and a triple-stranded {beta}-sheet. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. These chemical shift changes were relatively small compared to changes that occurred upon hydrolysis of the reactive-site peptide bond between Arg 5 and Ile6 in CMTI-III.

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

    International Nuclear Information System (INIS)

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

    1986-01-01

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

  18. Empirical Equation Based Chirality (n, m Assignment of Semiconducting Single Wall Carbon Nanotubes from Resonant Raman Scattering Data

    Directory of Open Access Journals (Sweden)

    Md Shamsul Arefin

    2012-12-01

    Full Text Available This work presents a technique for the chirality (n, m assignment of semiconducting single wall carbon nanotubes by solving a set of empirical equations of the tight binding model parameters. The empirical equations of the nearest neighbor hopping parameters, relating the term (2n, m with the first and second optical transition energies of the semiconducting single wall carbon nanotubes, are also proposed. They provide almost the same level of accuracy for lower and higher diameter nanotubes. An algorithm is presented to determine the chiral index (n, m of any unknown semiconducting tube by solving these empirical equations using values of radial breathing mode frequency and the first or second optical transition energy from resonant Raman spectroscopy. In this paper, the chirality of 55 semiconducting nanotubes is assigned using the first and second optical transition energies. Unlike the existing methods of chirality assignment, this technique does not require graphical comparison or pattern recognition between existing experimental and theoretical Kataura plot.

  19. Empirical Equation Based Chirality (n, m) Assignment of Semiconducting Single Wall Carbon Nanotubes from Resonant Raman Scattering Data

    Science.gov (United States)

    Arefin, Md Shamsul

    2012-01-01

    This work presents a technique for the chirality (n, m) assignment of semiconducting single wall carbon nanotubes by solving a set of empirical equations of the tight binding model parameters. The empirical equations of the nearest neighbor hopping parameters, relating the term (2n− m) with the first and second optical transition energies of the semiconducting single wall carbon nanotubes, are also proposed. They provide almost the same level of accuracy for lower and higher diameter nanotubes. An algorithm is presented to determine the chiral index (n, m) of any unknown semiconducting tube by solving these empirical equations using values of radial breathing mode frequency and the first or second optical transition energy from resonant Raman spectroscopy. In this paper, the chirality of 55 semiconducting nanotubes is assigned using the first and second optical transition energies. Unlike the existing methods of chirality assignment, this technique does not require graphical comparison or pattern recognition between existing experimental and theoretical Kataura plot. PMID:28348319

  20. Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: Assignment of aromatic resonances with application to protein folding, structure, and dynamics

    International Nuclear Information System (INIS)

    Weiss, M.A.; Shoelson, S.E.; Nguyen, D.T.; O'Shea, E.; Karplus, M.; Khait, I.; Neuringer, L.J.; Inouye, K.; Frank, B.H.; Beckage, M.

    1989-01-01

    The aromatic 1 H NMR resonances of the insulin monomer are assigned at 500 MHz by comparative studies of chemically modified and genetically altered variants, including a mutant insulin (PheB25 → Leu) associated with diabetes mellitus. The two histidines, three phenylalanines, and four tyrosines are observed to be in distinct local environments; their assignment provides sensitive markers for studies of tertiary structure, protein dynamics, and protein folding. The environments of the tyrosine residues have also been investigated by photochemically induced dynamic nuclear polarization (photo-CIDNP) and analyzed in relation to packing constrains in the crystal structures of insulin. Dimerization involving specific B-chain interactions is observed with increasing protein concentration and is shown to depend on temperature, pH, and solvent composition. The differences between proinsulin and mini-proinsulin suggest a structural mechanism for the observation that the fully reduced B29-A1 analogue folds more efficiently than proinsulin to form the correct pattern of disulfide bonds. These results are discussed in relation to molecular mechanics calculations of insulin based on the available crystal structures

  1. Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl–methyl nuclear overhauser enhancement spectroscopy

    International Nuclear Information System (INIS)

    Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius

    2011-01-01

    Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ∼1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl–methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.

  2. Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear overhauser enhancement spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius, E-mail: mariusc@mail.nih.gov [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)

    2011-11-15

    Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to {approx}1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl-methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.

  3. On the interpretation and rotational assignment of degenerate four-wave mixing spectra: Four-photon line strengths for crossover resonances in NO A 2Σ+--X 2Π

    International Nuclear Information System (INIS)

    Friedman-Hill, E.J.; Rahn, L.A.; Farrow, R.L.

    1994-01-01

    We present here a set of equations specifically adapted to simulation of fully resonant, high-resolution, phase-conjugate degenerate four-wave mixing (DFWM) in molecular gases. Signal-intensity dependence on molecular wave functions, lifetimes, and laser beam polarizations is explicitly included in these equations. The emphasis of the presentation is on both physically intuitive interpretation and a practical, ''cookbook'' approach to spectral simulation. We present experimental verification of our calculations drawn from the spectrum of dilute NO in N 2 at low pressures. Both degenerate two-level and three-level (crossover) resonances were observed. The experimental spectral intensities are accurately reproduced by the expressions presented here. We point out some of the subtleties of DFWM spectra that could be used as aids to interpretation, especially the use of laser polarization as a probe for spectral line assignments

  4. A high quality nuclear magnetic resonance solution structure of peptide deformylase from Escherichia coli: application of an automated assignment strategy using GARANT.

    Science.gov (United States)

    O'Connell, J F; Pryor, K D; Grant, S K; Leiting, B

    1999-04-01

    The NMR structure of the peptide deformylase (PDF) (1-150) from Escherichia coli, which is an essential enzyme that removes the formyl group from nascent polypeptides and represents a potential target for drug discovery, was determined using 15N/13C doubly labeled protein. Nearly completely automated assignment routines were employed to assign three-dimensional triple resonance, 15N-resolved and 13C-resolved NOESY spectra using the program GARANT. This assignment strategy, demonstrated on a 17 kDa protein, is a significant advance in the automation of NMR data assignment and structure determination that will accelerate future work. A total of 2302 conformational constraints were collected as input for the distance geometry program DYANA. After restrained energy minimization with the program X-PLOR the 20 best conformers characterize a high quality structure with an average of 0.43 A for the root-mean-square deviation calculated from the backbone atoms N, C alpha and C', and 0.81 A for all heavy atoms of the individual conformers relative to the mean coordinates for residues 1 to 150. The globular fold of PDF contains two alpha-helices comprising residues 25-40, 125-138, six beta-strands 57-60, 70-77, 85-88, 98-101, 105-111, 117-123 and one 3(10) helix comprising residues 49-51. The C-terminal helix contains the HEXXH motif positioning a zinc ligand in a similar fashion to other metalloproteases, with the third ligand being cysteine and the fourth presumably a water. The three-dimensional structure of PDF affords insight into the substrate recognition and specificity for N-formylated over N-acetylated substrates and is compared to other PDF structures.

  5. A high quality nuclear magnetic resonance solution structure of peptide deformylase from Escherichia coli: Application of an automated assignment strategy using GARANT

    International Nuclear Information System (INIS)

    O'Connell, John F.; Pryor, KellyAnn D.; Grant, Stephan K.; Leiting, Barbara

    1999-01-01

    The NMR structure of the peptide deformylase (PDF) (1-150) from Escherichia coli, which is an essential enzyme that removes the formyl group from nascent polypeptides and represents a potential target for drug discovery, was determined using 15N/13C doubly labeled protein. Nearly completely automated assignment routines were employed to assign three-dimensional triple resonance, 15N-resolved and 13C-resolved NOESY spectra using the program GARANT. This assignment strategy, demonstrated on a 17 kDa protein, is a significant advance in the automation of NMR data assignment and structure determination that will accelerate future work. A total of 2302 conformational constraints were collected as input for the distance geometry program DYANA. After restrained energy minimization with the program X-PLOR the 20 best conformers characterize a high quality structure with an average of 0.43 A for the root-mean-square deviation calculated from the backbone atoms N, Cα and C', and 0.81 A for all heavy atoms of the individual conformers relative to the mean coordinates for residues 1 to 150. The globular fold of PDF contains two α-helices comprising residues 25-40, 125-138, six β-strands 57-60, 70-77, 85-88, 98-101, 105-111, 117-123 and one 310 helix comprising residues 49-51. The C-terminal helix contains the HEXXH motif positioning a zinc ligand in a similar fashion to other metalloproteases, with the third ligand being cysteine and the fourth presumably a water. The three-dimensional structure of PDF affords insight into the substrate recognition and specificity for N-formylated over N-acetylated substrates and is compared to other PDF structures

  6. Partially-deuterated samples of HET-s(218–289) fibrils: assignment and deuterium isotope effect

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Albert A.; Ravotti, Francesco; Testori, Emilie; Cadalbert, Riccardo; Ernst, Matthias, E-mail: maer@ethz.ch [ETH Zürich, Physical Chemistry (Switzerland); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zürich, Physical Chemistry (Switzerland)

    2017-02-15

    Fast magic-angle spinning and partial sample deuteration allows direct detection of {sup 1}H in solid-state NMR, yielding significant gains in mass sensitivity. In order to further analyze the spectra, {sup 1}H detection requires assignment of the {sup 1}H resonances. In this work, resonance assignments of backbone H{sup N} and Hα are presented for HET-s(218–289) fibrils, based on the existing assignment of Cα, Cβ, C’, and N resonances. The samples used are partially deuterated for higher spectral resolution, and the shifts in resonance frequencies of Cα and Cβ due to the deuterium isotope effect are investigated. It is shown that the deuterium isotope effect can be estimated and used for assigning resonances of deuterated samples in solid-state NMR, based on known resonances of the protonated protein.

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

    International Nuclear Information System (INIS)

    Yang, Yu; Fritzsching, Keith J.; Hong, Mei

    2013-01-01

    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

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

    Science.gov (United States)

    Yang, Yu; Fritzsching, Keith J; Hong, Mei

    2013-11-01

    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 assignment for a

  9. Can magnetic resonance imaging differentiate undifferentiated arthritis?

    DEFF Research Database (Denmark)

    Østergaard, Mikkel; Duer, Anne; Hørslev-Petersen, K

    2005-01-01

    A high sensitivity for the detection of inflammatory and destructive changes in inflammatory joint diseases makes magnetic resonance imaging potentially useful for assigning specific diagnoses, such as rheumatoid arthritis and psoriatic arthritis in arthritides, that remain undifferentiated after...... conventional clinical, biochemical and radiographic examinations. With recent data as the starting point, the present paper describes the current knowledge on magnetic resonance imaging in the differential diagnosis of undifferentiated arthritis....

  10. Quality of pharmacy-specific Medical Subject Headings (MeSH) assignment in pharmacy journals indexed in MEDLINE.

    Science.gov (United States)

    Minguet, Fernando; Salgado, Teresa M; van den Boogerd, Lucienne; Fernandez-Llimos, Fernando

    2015-01-01

    The Medical Subject Headings (MeSH) is the National Library of Medicine (NLM) controlled vocabulary for indexing articles. Inaccuracies in the MeSH thesaurus have been reported for several areas including pharmacy. To assess the quality of pharmacy-specific MeSH assignment to articles indexed in pharmacy journals. The 10 journals containing the highest number of articles published in 2012 indexed under the MeSH 'Pharmacists' were identified. All articles published over a 5-year period (2008-2012) in the 10 previously selected journals were retrieved from PubMed. MeSH terms used to index these articles were extracted and pharmacy-specific MeSH terms were identified. The frequency of use of pharmacy-specific MeSH terms was calculated across journals. A total of 6989 articles were retrieved from the 10 pharmacy journals, of which 328 (4.7%) were articles not fully indexed and therefore did not contain any MeSH terms assigned. Among the 6661 articles fully indexed, the mean number of MeSH terms was 10.1 (SD = 4.0), being 1.0 (SD = 1.3) considered as Major MeSH. Both values significantly varied across journals. The mean number of pharmacy-specific MeSH terms per article was 0.9 (SD = 1.2). A total of 3490 (52.4%) of the 6661 articles were indexed in pharmacy journals without a single pharmacy-specific MeSH. Of the total 67193 MeSH terms assigned to articles, on average 10.5% (SD = 13.9) were pharmacy-specific MeSH. A statistically significant different pattern of pharmacy-specific MeSH assignment was identified across journals (Kruskal-Wallis P journals can be improved to further enhance evidence gathering in pharmacy. Over half of the articles published in the top-10 journals publishing pharmacy literature were indexed without a single pharmacy-specific MeSH. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    International Nuclear Information System (INIS)

    Swain, Monalisa; Atreya, Hanudatta S.

    2009-01-01

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

  12. Assigning spectra of chaotic molecules with diabatic correlation diagrams

    International Nuclear Information System (INIS)

    Rose, J.P.; Kellman, M.E.

    1996-01-01

    An approach for classifying and organizing spectra of highly excited vibrational states of molecules is investigated. As a specific example, we analyze the spectrum of an effective spectroscopic fitting Hamiltonian for H 2 O. In highly excited spectra, multiple resonance couplings and anharmonicity interact to give branching of the N original normal modes into new anharmonic modes, accompanied by the onset of widespread chaos. The anharmonic modes are identified by means of a bifurcation analysis of the spectroscopic Hamiltonian. A diabatic correlation diagram technique is developed to assign the levels with approximate open-quote open-quote dynamical close-quote close-quote quantum numbers corresponding to the dynamics determined from the bifurcation analysis. The resulting assignment shows significant disturbance from the conventional spectral pattern organization into sequences and progressions. The open-quote open-quote dynamical close-quote close-quote assignment is then converted into an assignment in terms of open-quote open-quote nominal close-quote close-quote quantum numbers that function like the N normal mode quantum numbers at low energy. The nominal assignments are used to reconstruct, as much as possible, an organization of the spectrum resembling the usual separation into sequences and progressions. copyright 1996 American Institute of Physics

  13. Stimulation of Protein Expression Through the Harmonic Resonance of Frequency-Specific Music.

    Science.gov (United States)

    Orhan, Ibrahim Y; Gulbahar, Burak A

    2016-12-01

    The use of specific frequencies for specific individual amino acids may increase the potential energy of protein molecules in the medium [1]. The resonance would also increase the movement of particles in the cytosol, increasing the collisions necessary for the conduction of protein expression. The clash of two waves that share frequencies will exhibit an increase in energy through an increase in amplitude [2]. The increase in energy would in turn increase the number of collisions forming the tRNA-amino acid, increasing the amino acid acquiry for ribosomes to improve intracellular efficiency in gene expression. To test the hypothesis, Red Fluorescent Protein (RFP) in transformated BL-21 strains of E. coli and p53 protein of MCF-7 were examined after exposure to sounds of specific frequencies. Through the exposure of the experimental systems to a sequence of sounds that match the frequencies of specific amino acids, the levels of RFP exhibition respective to the control groups in the bacterial medium increased two-fold in terms of RFU. The experiments that targeted the p53 protein with the 'music' showed a decrease in the cell prevalence in the MCF-7 type breast cancer cells by 28%, by decreasing the speed of tumour formation. Exposure to 'music' that was designed through assigning a musical note for every single one of the twenty unique amino acids, produced both an analytical and a visible shift in protein synthesis, making it as potential tool for reducing procedural time uptake.

  14. Encoding efficiency of suprathreshold stochastic resonance on stimulus-specific information

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Fabing, E-mail: fabing.duan@gmail.com [Institute of Complexity Science, Qingdao University, Qingdao 266071 (China); Chapeau-Blondeau, François, E-mail: chapeau@univ-angers.fr [Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), Université d' Angers, 62 avenue Notre Dame du Lac, 49000 Angers (France); Abbott, Derek, E-mail: derek.abbott@adelaide.edu.au [Centre for Biomedical Engineering (CBME) and School of Electrical & Electronic Engineering, The University of Adelaide, Adelaide, SA 5005 (Australia)

    2016-01-08

    In this paper, we evaluate the encoding efficiency of suprathreshold stochastic resonance (SSR) based on a local information-theoretic measure of stimulus-specific information (SSI), which is the average specific information of responses associated with a particular stimulus. The theoretical and numerical analyses of SSIs reveal that noise can improve neuronal coding efficiency for a large population of neurons, which leads to produce increased information-rich responses. The SSI measure, in contrast to the global measure of average mutual information, can characterize the noise benefits in finer detail for describing the enhancement of neuronal encoding efficiency of a particular stimulus, which may be of general utility in the design and implementation of a SSR coding scheme. - Highlights: • Evaluating the noise-enhanced encoding efficiency via stimulus-specific information. • New form of stochastic resonance based on the measure of encoding efficiency. • Analyzing neural encoding schemes from suprathreshold stochastic resonance detailedly.

  15. Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments

    International Nuclear Information System (INIS)

    Slupsky, Carolyn M.; Boyko, Robert F.; Booth, Valerie K.; Sykes, Brian D.

    2003-01-01

    Complete and accurate NMR spectral assignment is a prerequisite for high-throughput automated structure determination of biological macromolecules. However, completely automated assignment procedures generally encounter difficulties for all but the most ideal data sets. Sources of these problems include difficulty in resolving correlations in crowded spectral regions, as well as complications arising from dynamics, such as weak or missing peaks, or atoms exhibiting more than one peak due to exchange phenomena. Smartnotebook is a semi-automated assignment software package designed to combine the best features of the automated and manual approaches. The software finds and displays potential connections between residues, while the spectroscopist makes decisions on which connection is correct, allowing rapid and robust assignment. In addition, smartnotebook helps the user fit chains of connected residues to the primary sequence of the protein by comparing the experimentally determined chemical shifts with expected shifts derived from a chemical shift database, while providing bookkeeping throughout the assignment procedure

  16. Sequence-specific assignments in the 1H NMR spectrum of the human inflammatory protein C5a

    International Nuclear Information System (INIS)

    Zuiderweg, E.R.P.; Mollison, K.W.; Henkin, J.; Carter, G.W.

    1988-01-01

    Full sequence-specific assignments for the 1 H NMR lines of the backbone protons of the human complement factor C5a are described and documented. The results were obtained by largely following the methodology developed by Wuethrich et al. Assignments for the majority of the amino acid side chain protons were obtained by using a comparison of double- and triple-quantum-filtered two-dimensional correlated experiments together with the analysis of relayed coherence transfer spectra. The assignments provide the basis for the determination of the thus far unknown three-dimensional structure of C5a from nuclear Overhauser enhancement distance constraints

  17. Covariance NMR Processing and Analysis for Protein Assignment.

    Science.gov (United States)

    Harden, Bradley J; Frueh, Dominique P

    2018-01-01

    During NMR resonance assignment it is often necessary to relate nuclei to one another indirectly, through their common correlations to other nuclei. Covariance NMR has emerged as a powerful technique to correlate such nuclei without relying on error-prone peak peaking. However, false-positive artifacts in covariance spectra have impeded a general application to proteins. We recently introduced pre- and postprocessing steps to reduce the prevalence of artifacts in covariance spectra, allowing for the calculation of a variety of 4D covariance maps obtained from diverse combinations of pairs of 3D spectra, and we have employed them to assign backbone and sidechain resonances in two large and challenging proteins. In this chapter, we present a detailed protocol describing how to (1) properly prepare existing 3D spectra for covariance, (2) understand and apply our processing script, and (3) navigate and interpret the resulting 4D spectra. We also provide solutions to a number of errors that may occur when using our script, and we offer practical advice when assigning difficult signals. We believe such 4D spectra, and covariance NMR in general, can play an integral role in the assignment of NMR signals.

  18. Resonance Raman Optical Activity and Surface Enhanced Resonance Raman Optical Activity analysis of Cytochrome C

    DEFF Research Database (Denmark)

    Johannessen, Christian; Abdali, Salim; White, Peter C.

    2007-01-01

    High quality Resonance Raman (RR) and resonance Raman Optical Activity (ROA) spectra of cytochrome c were obtained in order to perform full assignment of spectral features of the resonance ROA spectrum. The resonance ROA spectrum of cytochrome c revealed a distinct spectral signature pattern due...... to resonance enhanced skeletal porphyrin vibrations, more pronounced than any contribution from the protein back-bone. Combining the intrinsic resonance enhancement of cytochrome c with surface plasmon enhancement by colloidal silver particles, the Surface Enhanced Resonance Raman Scattering (SERRS) and Chiral...... Enhanced Raman Spectroscopy (ChERS) spectra of the protein were successfully obtained at very low concentration (as low as 1 µM). The assignment of spectral features was based on the information obtained from the RR and resonance ROA spectra. Excellent agreement between RR and SERRS spectra is reported...

  19. Automated backbone assignment of labeled proteins using the threshold accepting algorithm

    International Nuclear Information System (INIS)

    Leutner, Michael; Gschwind, Ruth M.; Liermann, Jens; Schwarz, Christian; Gemmecker, Gerd; Kessler, Horst

    1998-01-01

    The sequential assignment of backbone resonances is the first step in the structure determination of proteins by heteronuclear NMR. For larger proteins, an assignment strategy based on proton side-chain information is no longer suitable for the use in an automated procedure. Our program PASTA (Protein ASsignment by Threshold Accepting) is therefore designed to partially or fully automate the sequential assignment of proteins, based on the analysis of NMR backbone resonances plus C β information. In order to overcome the problems caused by peak overlap and missing signals in an automated assignment process, PASTA uses threshold accepting, a combinatorial optimization strategy, which is superior to simulated annealing due to generally faster convergence and better solutions. The reliability of this algorithm is shown by reproducing the complete sequential backbone assignment of several proteins from published NMR data. The robustness of the algorithm against misassigned signals, noise, spectral overlap and missing peaks is shown by repeating the assignment with reduced sequential information and increased chemical shift tolerances. The performance of the program on real data is finally demonstrated with automatically picked peak lists of human nonpancreatic synovial phospholipase A 2 , a protein with 124 residues

  20. Assignment of 1H, 13C, and 15N resonances of WT matrix protein and its R55F mutant from Mason-Pfizer monkey virus

    Czech Academy of Sciences Publication Activity Database

    Vlach, J.; Lipov, J.; Veverka, V.; Rumlová, Michaela; Ruml, T.; Hrabal, R.

    2005-01-01

    Roč. 31, - (2005), s. 381-382 ISSN 0925-2738 R&D Projects: GA ČR GA203/03/0490 Institutional research plan: CEZ:AV0Z4055905 Keywords : Mason-Pfizer monkey virus * NMR resonance assignment * matrix protein Subject RIV: CE - Biochemistry Impact factor: 2.180, year: 2005

  1. Resonance Assignments and Secondary Structure Analysis of Dynein Light Chain 8 by Magic-angle Spinning NMR Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Shangjin; Butterworth, Andrew H.; Paramasivam, Sivakumar; Yan, Si; Lightcap, Christine M.; Williams, John C.; Polenova, Tatyana E.

    2011-08-04

    Dynein light chain LC8 is the smallest subunit of the dynein motor complex and has been shown to play important roles in both dynein-dependent and dynein-independent physiological functions via its interaction with a number of its binding partners. It has also been linked to pathogenesis including roles in viral infections and tumorigenesis. Structural information for LC8-target proteins is critical to understanding the underlying function of LC8 in these complexes. However, some LC8-target interactions are not amenable to structural characterization by conventional structural biology techniques owing to their large size, low solubility, and crystallization difficulties. Here, we report magic-angle spinning (MAS) NMR studies of the homodimeric apo-LC8 protein as a first effort in addressing more complex, multi-partner, LC8-based protein assemblies. We have established site-specific backbone and side-chain resonance assignments for the majority of the residues of LC8, and show TALOS+-predicted torsion angles ø and ψ in close agreement with most residues in the published LC8 crystal structure. Data obtained through these studies will provide the first step toward using MAS NMR to examine the LC8 structure, which will eventually be used to investigate protein–protein interactions in larger systems that cannot be determined by conventional structural studies.

  2. Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

    Science.gov (United States)

    Krishnamoorthi, R; Gong, Y X; Lin, C L; VanderVelde, D

    1992-01-28

    The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific 1H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns (residues 8-12 and 24-27), a 3(10)-helix (residues 13-16), and a triple-stranded beta-sheet (residues 8-10, 29-27, and 21-25). This secondary structure is similar to that of CMTI-I [Holak, T. A., Gondol, D., Otlewski, J., & Wilusz, T. (1989) J. Mol. Biol. 210, 635-648], which has a Glu instead of a Lys at position 9. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30 degrees C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. Many of these residues are functionally important in that they make contact with atoms of the enzyme in the trypsin-inhibitor complex, as revealed by X-ray crystallography [Bode, W., Greyling, H. J., Huber, R., Otlewski, J., & Wilusz, T. (1989) FEBS Lett. 242, 285-292].(ABSTRACT TRUNCATED AT 250 WORDS)

  3. Synthesis of 24-methyl sterols sterospecifically labelled with 2H in the isopropyl methyl groups. 13C NMR spectral assignment of C-26 and C-27 resonances

    International Nuclear Information System (INIS)

    Colombo, D.; Ronchetti, F.; Toma, L.

    1990-01-01

    Through analysis of the 13 C NMR spectra of (25S)-[27- 2 H]campesterol (1) and (25R)-[26- 2 H]dihydrobrassicasterol (2), the C-26 and C-27 resonances have been unambiguously assigned; the biosynthetic applications are discussed. (author)

  4. The Context-Specific Conceptions of Learning in Case-Based Accounting Assignments, Students' Characteristics and Performance

    Science.gov (United States)

    Moilanen, Sinikka

    2017-01-01

    The present study contributes to accounting education literature by describing context-specific conceptions of learning related to case assignments, and by exploring the associations between the conceptions of learning, students' characteristics and performance. The data analysed consist of 1320 learning diaries of 336 students, connected with…

  5. Practical aspects of NMR signal assignment in larger and challenging proteins

    Science.gov (United States)

    Frueh, Dominique P.

    2014-01-01

    NMR has matured into a technique routinely employed for studying proteins in near physiological conditions. However, applications to larger proteins are impeded by the complexity of the various correlation maps necessary to assign NMR signals. This article reviews the data analysis techniques traditionally employed for resonance assignment and describes alternative protocols necessary for overcoming challenges in large protein spectra. In particular, simultaneous analysis of multiple spectra may help overcome ambiguities or may reveal correlations in an indirect manner. Similarly, visualization of orthogonal planes in a multidimensional spectrum can provide alternative assignment procedures. We describe examples of such strategies for assignment of backbone, methyl, and nOe resonances. We describe experimental aspects of data acquisition for the related experiments and provide guidelines for preliminary studies. Focus is placed on large folded monomeric proteins and examples are provided for 37, 48, 53, and 81 kDa proteins. PMID:24534088

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-02-15

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

  7. Specific detection of proteins using Nanomechanical resonators

    DEFF Research Database (Denmark)

    Fischer, Lee MacKenzie; Wright, V.A.; Guthy, C.

    2008-01-01

    of probes onto their surfaces in order to enable the specificity of the detection. Such nanoresonator-based specific detection of proteins is here reported using streptavidin as target system, and immobilized biotin as probe. Nanomechanical resonators resistant to stiction were first realized from silicon...... carbonitride using a novel fabrication method. Vapor-phase deposition of mercaptopropyl trimethoxysilane was performed, and an added mass of 2.22 +/- 0.07 fg/mu m(2) was measured. This linker molecule was used to attach biotin onto the devices, enabling the specific detection of streptavidin. A mass of 3.6 fg....../mu m(2) was attributed to the added streptavidin, corresponding to one molecule per 27 nm(2). The specificity of this recognition was confirmed by exposing the devices to a solution of streptavidin that was already saturated with biotin. An additional negative control was also performed by also...

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

    Science.gov (United States)

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

    2011-04-01

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

  9. (1)H, (13)C, and (15)N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog.

    Science.gov (United States)

    Moro, Sean L; Cocco, Melanie J

    2015-10-01

    The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the (15)N, (1)H, and (13)C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains.

  10. Systematic assignment of Feshbach resonances via an asymptotic bound state model

    NARCIS (Netherlands)

    Goosen, M.; Kokkelmans, SJ.J.M.F.

    2008-01-01

    We present an Asymptotic Bound state Model (ABM), which is useful to predict Feshbach resonances. The model utilizes asymptotic properties of the interaction potentials to represent coupled molecular wavefunctions. The bound states of this system give rise to Feshbach resonances, localized at the

  11. Backbone resonance assignments for G protein α(i3) subunit in the GDP-bound state.

    Science.gov (United States)

    Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

    2014-10-01

    Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein α subunit with GDP (Gα·GDP) and the G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα·GTP) and Gβγ. Then, Gα·GTP and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. The G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human Gαi3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of Gα(i3) in complex with a GTP-analogue, GTPγS, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTPγS-bound states, as indicated in the crystal structures. The assignments of Gα(i3)·GDP would be useful for the analyses of the dynamics of Gα(i3) and its interactions with various target molecules.

  12. High resolution bone material property assignment yields robust subject specific finite element models of complex thin bone structures.

    Science.gov (United States)

    Pakdel, Amirreza; Fialkov, Jeffrey; Whyne, Cari M

    2016-06-14

    Accurate finite element (FE) modeling of complex skeletal anatomy requires high resolution in both meshing and the heterogeneous mapping of material properties onto the generated mesh. This study introduces Node-based elastic Modulus Assignment with Partial-volume correction (NMAP) as a new approach for FE material property assignment to thin bone structures. The NMAP approach incorporates point spread function based deblurring of CT images, partial-volume correction of CT image voxel intensities and anisotropic interpolation and mapping of CT intensity assignment to FE mesh nodes. The NMAP procedure combined with a derived craniomaxillo-facial skeleton (CMFS) specific density-isotropic elastic modulus relationship was applied to produce specimen-specific FE models of 6 cadaveric heads. The NMAP procedure successfully generated models of the complex thin bone structures with surface elastic moduli reflective of cortical bone material properties. The specimen-specific CMFS FE models were able to accurately predict experimental strains measured under in vitro temporalis and masseter muscle loading (r=0.93, slope=1.01, n=5). The strength of this correlation represents a robust validation for CMFS FE modeling that can be used to better understand load transfer in this complex musculoskeletal system. The developed methodology offers a systematic process-flow able to address the complexity of the CMFS that can be further applied to create high-fidelity models of any musculoskeletal anatomy. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  14. Measurement of specific heat and specific absorption rate by nuclear magnetic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Gultekin, David H., E-mail: david.gultekin@aya.yale.edu [Department of Electrical Engineering, Yale University, New Haven, CT 06520 (United States); Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 (United States); Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 (United States); Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232 (United States); Gore, John C. [Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232 (United States); Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN 37232 (United States); Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232 (United States); Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37232 (United States); Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232 (United States)

    2010-05-20

    We evaluate a nuclear magnetic resonance (NMR) method of calorimetry for the measurement of specific heat (c{sub p}) and specific absorption rate (SAR) in liquids. The feasibility of NMR calorimetry is demonstrated by experimental measurements of water, ethylene glycol and glycerol using any of three different NMR parameters (chemical shift, spin-spin relaxation rate and equilibrium nuclear magnetization). The method involves heating the sample using a continuous wave laser beam and measuring the temporal variation of the spatially averaged NMR parameter by non-invasive means. The temporal variation of the spatially averaged NMR parameter as a function of thermal power yields the ratio of the heat capacity to the respective nuclear thermal coefficient, from which the specific heat can be determined for the substance. The specific absorption rate is obtained by subjecting the liquid to heating by two types of radiation, radiofrequency (RF) and near-infrared (NIR), and by measuring the change in the nuclear spin phase shift by a gradient echo imaging sequence. These studies suggest NMR may be a useful tool for measurements of the thermal properties of liquids.

  15. Resonance Raman study of benzyl radical

    DEFF Research Database (Denmark)

    Langkilde, F.W.; Bajdor, K.; Wilbrandt, R.

    1992-01-01

    Time-resolved resonance Raman spectra are obtained of benzyl radicals created by laser flash photolysis of benzylchloride and diphenylacetone in solution. The spectra are obtained in resonance with the intense 2 2A2-1 B-2(2) transition of benzyl. The strong Raman bands are assigned to totally...... symmetric a1 modes. The remaining observed bands are tentatively assigned to fundamental modes of b1, a2, and b2 symmetry, and to overtones and combinations. The resonance Raman spectra are found to be quite different from previous fluorescence spectra of benzyl, and the origins of these differences...

  16. Combination of liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry with 13C-labeling for chemical assignment of sulfur-containing metabolites in onion bulbs.

    Science.gov (United States)

    Nakabayashi, Ryo; Sawada, Yuji; Yamada, Yutaka; Suzuki, Makoto; Hirai, Masami Yokota; Sakurai, Tetsuya; Saito, Kazuki

    2013-02-05

    Phytochemicals containing heteroatoms (N, O, S, and halogens) often have biological activities that are beneficial to humans. Although targeted profiling methods for such phytochemicals are expected to contribute to rapid chemical assignments, thus making phytochemical genomics and crop breeding much more efficient, there are few profiling methods for the metabolites. Here, as an ultrahigh performance approach, we propose a practical profiling method for S-containing metabolites (S-omics) using onions (Allium cepa) as a representative species and (12)C- and (13)C-based mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses by liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry (LC-FTICR-MS). Use of the ultrahigh quality data from FTICR-MS enabled simplifying the previous methods to determine specific elemental compositions. MS analysis with a resolution of >250,000 full width at half-maximum and a mass accuracy of ions from other ions on the basis of the natural abundance of (32)S and (34)S and the mass differences among the S isotopes. Comprehensive peak picking using the theoretical mass difference (1.99579 Da) between (32)S-containing monoisotopic ions and their (34)S-substituted counterparts led to the assignment of 67 S-containing monoisotopic ions from the (12)C-based MS spectra, which contained 4693 chromatographic ions. The unambiguous elemental composition of 22 ions was identified through comparative analysis of the (12)C- and (13)C-based MS spectra. Finally, of these, six ions were found to be derived from S-alk(en)ylcysteine sulfoxides and glutathione derivatives. This S-atom-driven approach afforded an efficient chemical assignment of S-containing metabolites, suggesting its potential application for screening not only S but also other heteroatom-containing metabolites in MS-based metabolomics.

  17. 1H and 31P resonance assignments and secondary structure of hairpin conformer of IA mismatched oligonucleotide d-GGTACIAGTACC

    International Nuclear Information System (INIS)

    Chary, K.V.R.; Rastogi, V.K.; Govil, Girjesh

    1994-01-01

    Almost complete 1 H and 31 P resonance assignments of two coexisting conformers, duplex and an hairpin, of d-GGTACIAGTACC at 1.25mM concentration and 305 K have been achieved. The results demonstrate that the hairpin conformer has a structure with two purines I6 and A7 forming a two-base loop on a B-DNA stem. Stacking is continued on the 5'-side of the loop, with the I6 stacked upon C5. The base A7, on the 3'-side of the loop stacks partially with I6. The glycosidic angle for G8 is in the anti domain and it maintains normal Watson-Crick base-pairing with the opposite C5. (author). 28 refs., 7 figs., 2 tabs

  18. Ner protein of phage Mu: Assignments using {sup 13}C/{sup 15}N-labeled protein

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-01

    The Ner protein is a small (74-amino acid) DNA-binding protein that regulates a switch between the lysogenic and lytic stages of phage Mu. It inhibits expression of the C repressor gene and down-regulates its own expression. Two-dimensional NMR experiments on uniformly {sup 15}N-labeled protein provided most of the backbone and some of the sidechain proton assignments. The secondary structure determination using two-dimensional NOESY experiments showed that Ner consists of five {alpha}-helices. However, because most of the sidechain protons could not be assigned, the full structure was not determined. Using uniformly {sup 13}C/{sup 15}N-labeled Ner and a set of three-dimensional experiments, we were able to assign all of the backbone and 98% of the sidechain protons. In particular, the CBCANH and CBCA(CO)NH experiments were used to sequentially assign the C{alpha} and C{beta} resonances; the HCCH-CTOCSY and HCCH-COSY were used to assign sidechain carbon and proton resonances.

  19. Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein

    International Nuclear Information System (INIS)

    Żerko, Szymon; Byrski, Piotr; Włodarczyk-Pruszyński, Paweł; Górka, Michał; Ledolter, Karin; Masliah, Eliezer; Konrat, Robert; Koźmiński, Wiktor

    2016-01-01

    New experiments dedicated for large IDPs backbone resonance assignment are presented. The most distinctive feature of all described techniques is the employment of MOCCA-XY16 mixing sequences to obtain effective magnetization transfers between carbonyl carbon backbone nuclei. The proposed 4 and 5 dimensional experiments provide a high dispersion of obtained signals making them suitable for use in the case of large IDPs (application to 354 a. a. residues of Tau protein 3x isoform is presented) as well as provide both forward and backward connectivities. What is more, connecting short chains interrupted with proline residues is also possible. All the experiments employ non-uniform sampling.

  20. Five and four dimensional experiments for robust backbone resonance assignment of large intrinsically disordered proteins: application to Tau3x protein

    Energy Technology Data Exchange (ETDEWEB)

    Żerko, Szymon; Byrski, Piotr; Włodarczyk-Pruszyński, Paweł; Górka, Michał [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland); Ledolter, Karin [University of Vienna, Department of Computational and Structural Biology, Max F. Perutz Laboratories (Austria); Masliah, Eliezer [University of California, San Diego, Departments of Neuroscience and Pathology (United States); Konrat, Robert [University of Vienna, Department of Computational and Structural Biology, Max F. Perutz Laboratories (Austria); Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

    2016-08-15

    New experiments dedicated for large IDPs backbone resonance assignment are presented. The most distinctive feature of all described techniques is the employment of MOCCA-XY16 mixing sequences to obtain effective magnetization transfers between carbonyl carbon backbone nuclei. The proposed 4 and 5 dimensional experiments provide a high dispersion of obtained signals making them suitable for use in the case of large IDPs (application to 354 a. a. residues of Tau protein 3x isoform is presented) as well as provide both forward and backward connectivities. What is more, connecting short chains interrupted with proline residues is also possible. All the experiments employ non-uniform sampling.

  1. Double resonance capacitance spectroscopy (DORCAS): A new experimental technique for assignment of X-ray absorption peaks to surface sites of semiconductor

    CERN Document Server

    Ishii, M

    2003-01-01

    As a new microspectroscopy for semiconductor surface analysis using an X-ray beam, double resonance capacitance spectroscopy (DORCAS) is proposed. For a microscopic X-ray absorption measurement, a local capacitance change owing to X-ray induced emission of localized electrons is detected by a microprobe. The applied bias voltage V sub b dependence of the capacitance also provides information on the surface density of state. The resonance of the Fermi energy with a surface level by V sub b control makes possible the selection of the observable surface site in the X-ray absorption measurements, i.e. site-specific spectroscopy. The double resonance of the surface site selection (V sub b resonance) and the resonant X-ray absorption of the selected site (photon energy h nu resonance) enhances the capacitance signal. The DORCAS measurement of the GaAs surface shows correlation peaks at h nu=10.402 keV and V sub b =-0.4 V and h nu=10.429 keV and V sub b =+0.1 V, indicating that these resonant X-ray absorption peaks ...

  2. Role of magnetic resonance imaging in assigning sex in an ...

    African Journals Online (AJOL)

    A three years old child with ambiguous genitalia since birth had been referred to Muhimbili National Hospital (MNH),a tertiary referral hospital, in order to be evaluated and assigned sex correctly. Due to periphery location of the referring center, social and economic constraints, the child was not presented earlier. Physical ...

  3. CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

    International Nuclear Information System (INIS)

    Wang Jianyong; Wang Tianzhi; Zuiderweg, Erik R. P.; Crippen, Gordon M.

    2005-01-01

    Rapid analysis of protein structure, interaction, and dynamics requires fast and automated assignments of 3D protein backbone triple-resonance NMR spectra. We introduce a new depth-first ordered tree search method of automated assignment, CASA, which uses hand-edited peak-pick lists of a flexible number of triple resonance experiments. The computer program was tested on 13 artificially simulated peak lists for proteins up to 723 residues, as well as on the experimental data for four proteins. Under reasonable tolerances, it generated assignments that correspond to the ones reported in the literature within a few minutes of CPU time. The program was also tested on the proteins analyzed by other methods, with both simulated and experimental peaklists, and it could generate good assignments in all relevant cases. The robustness was further tested under various situations

  4. Resonance capture and Saturn's rings

    International Nuclear Information System (INIS)

    Patterson, C.W.

    1986-05-01

    We have assigned the resonances apparently responsible for the stabilization of the Saturn's shepherd satellites and for the substructure seen in the F-ring and the ringlets in the C-ring. We show that Saturn's narrow ringlets have a substructure determined by three-body resonances with Saturn's ringmoons and the sun. We believe such resonances have important implications to satellite formation. 17 refs., 1 fig., 1 tab

  5. 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.

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

    International Nuclear Information System (INIS)

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

    1998-01-01

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

  7. Resonance Raman assignment and evidence for noncoupling of individual 2- and 4-vinyl vibrational modes in a monomeric cyanomethemoglobin

    International Nuclear Information System (INIS)

    Gersonde, K.; Yu, N.T.; Lin, S.H.; Smith, K.M.; Parish, D.W.

    1989-01-01

    We have investigated the resonance Raman spectra of monomeric insect cyanomethemoglobins (CTT III and CTT IV) reconstituted with (1) protohemes IX selectively deuterated at the 4-vinyl as well as the 2,4-divinyls, (2) monovinyl-truncated hemes such as pemptoheme (2-hydrogen, 4-vinyl) and isopemptoheme (2-vinyl, 4-hydrogen), (3) symmetric hemes such as protoheme III (with 2- and 3-vinyls) and protoheme XIII (with 1- and 4-vinyls), and (4) hemes without 2- and 4-vinyls such as mesoheme IX, deuteroheme IX, 2,4-dimethyldeuteroheme IX, and 2,4-dibromodeuteroheme IX. Evidence is presented that the highly localized vinyl C = C stretching vibrations at the 2- and 4-positions of the heme in these cyanomet CTT hemoglobins are noncoupled and inequivalent; i.e., the 1631- and 1624-cm-1 lines have been assigned to 2-vinyl and 4-vinyl, respectively. The elimination of the 2-vinyl (in pemptoheme) or the 4-vinyl (in isopemptoheme) does not affect the C = C stretching frequency of the remaining vinyl. Furthermore, two low-frequency vinyl bending modes at 412 and 591 cm-1 exhibit greatly different resonance Raman intensities between 2-vinyl and 4-vinyl. The observed intensity at 412 cm-1 is primarily derived from 4-vinyl, whereas the 591-cm-1 line results exclusively from the 2-vinyl. Again, there is no significant coupling between 2-vinyl and 4-vinyl for these two bending modes

  8. Electronically excited negative ion resonant states in chloroethylenes

    Energy Technology Data Exchange (ETDEWEB)

    Khvostenko, O.G., E-mail: khv@mail.ru; Lukin, V.G.; Tuimedov, G.M.; Khatymova, L.Z.; Kinzyabulatov, R.R.; Tseplin, E.E.

    2015-02-15

    Highlights: • Several novel dissociative negative ion channels were revealed in chloroethylenes. • The electronically excited resonant states were recorded in all chloroethylenes under study. • The states were assigned to the inter-shell types, but not to the core-excited Feshbach one. - Abstract: The negative ion mass spectra of the resonant electron capture by molecules of 1,1-dichloroethylene, 1,2-dichloroethylene-cis, 1,2-dichloroethylene-trans, trichloroethylene and tetrachloroethylene have been recorded in the 0–12 eV range of the captured electron energy using static magnetic sector mass spectrometer modified for operation in the resonant electron capture regime. As a result, several novel low-intensive dissociation channels were revealed in the compounds under study. Additionally, the negative ion resonant states were recorded at approximately 3–12 eV, mostly for the first time. These resonant states were assigned to the electronically excited resonances of the inter-shell type by comparing their energies with those of the parent neutral molecules triplet and singlet electronically excited states known from the energy-loss spectra obtained by previous studies.

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

    Directory of Open Access Journals (Sweden)

    Alexandra Born

    2018-06-01

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

  10. Using expert knowledge to incorporate uncertainty in cause-of-death assignments for modeling of cause-specific mortality

    Science.gov (United States)

    Walsh, Daniel P.; Norton, Andrew S.; Storm, Daniel J.; Van Deelen, Timothy R.; Heisy, Dennis M.

    2018-01-01

    Implicit and explicit use of expert knowledge to inform ecological analyses is becoming increasingly common because it often represents the sole source of information in many circumstances. Thus, there is a need to develop statistical methods that explicitly incorporate expert knowledge, and can successfully leverage this information while properly accounting for associated uncertainty during analysis. Studies of cause-specific mortality provide an example of implicit use of expert knowledge when causes-of-death are uncertain and assigned based on the observer's knowledge of the most likely cause. To explicitly incorporate this use of expert knowledge and the associated uncertainty, we developed a statistical model for estimating cause-specific mortality using a data augmentation approach within a Bayesian hierarchical framework. Specifically, for each mortality event, we elicited the observer's belief of cause-of-death by having them specify the probability that the death was due to each potential cause. These probabilities were then used as prior predictive values within our framework. This hierarchical framework permitted a simple and rigorous estimation method that was easily modified to include covariate effects and regularizing terms. Although applied to survival analysis, this method can be extended to any event-time analysis with multiple event types, for which there is uncertainty regarding the true outcome. We conducted simulations to determine how our framework compared to traditional approaches that use expert knowledge implicitly and assume that cause-of-death is specified accurately. Simulation results supported the inclusion of observer uncertainty in cause-of-death assignment in modeling of cause-specific mortality to improve model performance and inference. Finally, we applied the statistical model we developed and a traditional method to cause-specific survival data for white-tailed deer, and compared results. We demonstrate that model selection

  11. The assignment of dissociative electron attachment bands in compounds containing hydroxyl and amino groups

    International Nuclear Information System (INIS)

    Skalicky, Tomas; Allan, Michael

    2004-01-01

    Dissociative electron attachment (DEA) spectra were recorded for methanol, phenol, diethylamine, tetramethylhydrazine, piperazine, pyrrole and N,N-dimethylaniline. Comparison with He I photoelectron spectra permitted the assignment of virtually all DEA bands in the saturated compounds to core excited Feshbach resonances with double occupation of Rydberg-like orbitals and various Koopmans' states of the positive ion as a core. These resonances shift to lower energies with alkyl substitution, in contrast to the shape resonances, and are found at surprisingly low energies in the amines. The DEA spectra in the unsaturated compounds show no or only weak evidence for the Rydberg-type Feshbach resonances. It is proposed that DEA in saturated polyatomic molecules containing hydroxyl and amino groups is in general dominated by this type of resonance

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

    International Nuclear Information System (INIS)

    Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A.

    2015-01-01

    Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone 1 H N , 15 N H , and 13 C′ resonance assignments to be completed from a single pair of 3D experiments

  13. PARAssign-paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Skinner, Simon P., E-mail: skinnersp@chem.leidenuniv.nl [Leiden University, Gorlaeus Laboratories, Leiden Institute of Chemistry (Netherlands); Moshev, Mois, E-mail: mois@monomon.me [Leiden University, Leiden Institute of Advanced Computer Science (Netherlands); Hass, Mathias A. S., E-mail: hassmas@chem.leidenuniv.nl; Ubbink, Marcellus, E-mail: m.ubbink@chem.leidenuniv.nl [Leiden University, Gorlaeus Laboratories, Leiden Institute of Chemistry (Netherlands)

    2013-04-15

    The use of paramagnetic NMR data for the refinement of structures of proteins and protein complexes is widespread. However, the power of paramagnetism for protein assignment has not yet been fully exploited. PARAssign is software that uses pseudocontact shift data derived from several paramagnetic centers attached to the protein to obtain amide and methyl assignments. The ability of PARAssign to perform assignment when the positions of the paramagnetic centers are known and unknown is demonstrated. PARAssign has been tested using synthetic data for methyl assignment of a 47 kDa protein, and using both synthetic and experimental data for amide assignment of a 14 kDa protein. The complex fitting space involved in such an assignment procedure necessitates that good starting conditions are found, both regarding placement and strength of paramagnetic centers. These starting conditions are obtained through automated tensor placement and user-defined tensor parameters. The results presented herein demonstrate that PARAssign is able to successfully perform resonance assignment in large systems with a high degree of reliability. This software provides a method for obtaining the assignments of large systems, which may previously have been unassignable, by using 2D NMR spectral data and a known protein structure.

  14. 1H, 15N and 13C backbone and side-chain resonance assignments of a family 32 carbohydrate-binding module from the Clostridium perfringens NagH.

    Science.gov (United States)

    Grondin, Julie M; Chitayat, Seth; Ficko-Blean, Elizabeth; Boraston, Alisdair B; Smith, Steven P

    2012-10-01

    The Gram-positive anaerobe Clostridium perfringens is an opportunistic bacterial pathogen that secretes a battery of enzymes involved in glycan degradation. These glycoside hydrolases are thought to be involved in turnover of mucosal layer glycans, and in the spread of major toxins commonly associated with the development of gastrointestinal diseases and gas gangrene in humans. These enzymes employ multi-modularity and carbohydrate-binding function to degrade extracellular eukaryotic host sugars. Here, we report the full (1)H, (15)N and (13)C chemical shift resonance assignments of the first family 32 carbohydrate-binding module from NagH, a secreted family 84 glycoside hydrolase.

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

    Energy Technology Data Exchange (ETDEWEB)

    Motackova, Veronika; Novacek, Jiri [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic); Zawadzka-Kazimierczuk, Anna; Kazimierczuk, Krzysztof [University of Warsaw, Faculty of Chemistry (Poland); Zidek, Lukas, E-mail: lzidek@chemi.muni.c [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic); Sanderova, Hana; Krasny, Libor [Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology (Czech Republic); Kozminski, Wiktor [University of Warsaw, Faculty of Chemistry (Poland); Sklenar, Vladimir [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic)

    2010-11-15

    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, {delta} 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.

  16. Mars - robust automatic backbone assignment of proteins

    International Nuclear Information System (INIS)

    Jung, Young-Sang; Zweckstetter, Markus

    2004-01-01

    MARS a program for robust automatic backbone assignment of 13 C/ 15 N labeled proteins is presented. MARS does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds and it can work with a wide variety of NMR experiments. Using only 13 C α / 13 C β connectivity information, MARS allows automatic, error-free assignment of 96% of the 370-residue maltose-binding protein. MARS can successfully be used when data are missing for a substantial portion of residues or for proteins with very high chemical shift degeneracy such as partially or fully unfolded proteins. Other sources of information, such as residue specific information or known assignments from a homologues protein, can be included into the assignment process. MARS exports its result in SPARKY format. This allows visual validation and integration of automated and manual assignment

  17. 1H, 15N, and 13C resonance assignments of the third domain from the S. aureus innate immune evasion protein Eap.

    Science.gov (United States)

    Herrera, Alvaro I; Ploscariu, Nicoleta T; Geisbrecht, Brian V; Prakash, Om

    2018-04-01

    Staphylococcus aureus is a widespread and persistent pathogen of humans and livestock. The bacterium expresses a wide variety of virulence proteins, many of which serve to disrupt the host's innate immune system from recognizing and clearing bacteria with optimal efficiency. The extracellular adherence protein (Eap) is a multidomain protein that participates in various protein-protein interactions that inhibit the innate immune response, including both the complement system (Woehl et al in J Immunol 193:6161-6171, 2014) and Neutrophil Serine Proteases (NSPs) (Stapels et al in Proc Natl Acad Sci USA 111:13187-13192, 2014). The third domain of Eap, Eap3, is an ~ 11 kDa protein that was recently shown to bind complement component C4b (Woehl et al in Protein Sci 26:1595-1608, 2017) and therefore play an essential role in inhibiting the classical and lectin pathways of complement (Woehl et al in J Immunol 193:6161-6171, 2014). Since structural characterization of Eap3 is still incomplete, we acquired a series of 2D and 3D NMR spectra of Eap3 in solution. Here we report the backbone and side-chain 1 H, 15 N, and 13 C resonance assignments of Eap3 and its predicted secondary structure via the TALOS-N server. The assignment data have been deposited in the BMRB data bank under accession number 27087.

  18. Photoemission study of Kr 3d→np autoionization resonances

    International Nuclear Information System (INIS)

    Lindle, D.W.; Heimann, P.A.; Ferrett, T.A.; Piancastelli, M.N.; Shirley, D.A.

    1987-01-01

    Resonant photoelectron spectra of Kr have been taken in the photon-energy ranges of the 3d/sub 5/2/→5p,6p and 3d/sub 3/2/→5p excitations. The spectra, which closely resemble normal Kr + 3d/sup -1/ Auger spectra, illustrate the importance of ''spectator'' Auger-like decay for inner-shell resonances, in which the initially excited electron does not participate in the core-hole deexcitation process, except to respond to the change in the atomic potential. Possible assignments for some of the spectator decay channels are discussed based on photoemission intensity measurements at the different 3d resonances. These assignments suggest that shake-up (e.g., 5p→6p) of the ''spectator'' electron during the decay process is not quite as important as previously suspected. The resonance profiles of some of the more intense satellites have been determined over the 3d→np resonances. Very small resonance effects also were observed in the partial cross section for 4p subshell ionization, which produced asymmetric Fano-type profiles. The 4p angular distribution, in contrast, exhibits a pronounced effect in the resonance energy range. The 4p results demonstrate that nonspectator autoionization also is present

  19. The contribution of emotional empathy to approachability judgements assigned to emotional faces is context specific

    Directory of Open Access Journals (Sweden)

    Megan L Willis

    2015-08-01

    Full Text Available Previous research on approachability judgements has indicated that facial expressions modulate how these judgements are made, but the relationship between emotional empathy and context in this decision-making process has not yet been examined. This study examined the contribution of emotional empathy to approachability judgements assigned to emotional faces in different contexts. One hundred and twenty female participants completed the Questionnaire Measure of Emotional Empathy. Participants provided approachability judgements to faces displaying angry, disgusted, fearful, happy, neutral and sad expressions, in three different contexts – when evaluating whether they would approach another individual to: 1 receive help; 2 give help; or 3 when no contextual information was provided. In addition, participants were also required to provide ratings of perceived threat, emotional intensity and label facial expressions. Emotional empathy significantly predicted approachability ratings for specific emotions in each context, over and above the contribution of perceived threat and intensity, which were associated with emotional empathy. Higher emotional empathy predicted less willingness to approach people with angry and disgusted faces to receive help, and a greater willingness to approach people with happy faces to receive help. Higher emotional empathy also predicted a greater willingness to approach people with sad faces to offer help, and more willingness to approach people with happy faces when no contextual information was provided. These results highlight the important contribution of individual differences in emotional empathy in predicting how approachability judgements are assigned to facial expressions in context.

  20. A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins

    International Nuclear Information System (INIS)

    Plevin, Michael J.; Hamelin, Olivier; Boisbouvier, Jérôme; Gans, Pierre

    2011-01-01

    A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-[ 13 C]glucose and subsaturating amounts of 2-[ 13 C]methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional 1 H- 13 C correlation spectra. Protein samples are conveniently prepared using the same media composition as the main uniformly-labeled sample and contain higher levels of isotope-enrichment than fractional labeling approaches. This new strategy thus represents an economically-attractive, robust alternative for obtaining isotopically-encoded stereospecific NMR assignments of prochiral methyl groups.

  1. Nuclear magnetic resonance study of interaction of ligands with Streptococcus faecium dihydrofolate reductase labeled with [#betta#-13C]tryptophan

    International Nuclear Information System (INIS)

    London, R.E.; Groff, J.P.; Cocco, L.; Blakley, R.L.

    1982-01-01

    Dihydrofolate reductase from Streptococcus faecium has been labeled with [#betta#- 13 C]tryptophan. We have determined changes occurring in the chemical shifts and line widths of the four resonances of the 13 C NMR spectrum of the labeled enzyme, due to its interaction with various ligands. These include the coenzyme, NPDPH and related nucleotides, folate and its polyglutamate derivatives, and many inhibitors including methotrexate and trimethoprim. In addition, paramagnetic relaxation effects produced by a bound spin-labeled analogue of 2'-phosphoadenosine-5'-diphosphoribose on the tryptophan C/sup #betta#/ carbons have been measured. Distances calculated from the relaxation data have been compared with corresponding distances in the crystallographic model of the NADPH-methotrexate ternary complex of Lactobacillus casei reductase. The paramagnetic relaxation data indicate that the two downfield resonances (1 and 2) correspond to tryptophans (W/sub A/ and W/sub B/) that are more remote from the catalytic site, and from the crystallographic model these are seen to be Trp-115 and Trp-160. The upfield resonances (3 and 4) that show broadening due to chemical exchange correspond to closer residues (W/sub C/ and W/sub D/), and these are identified with Trp-6 and Trp-22. However, the relaxation data do not permit specific assignments within the nearer and farther pairs. Although resonance 3, which is split due to chemical exchange, was formerly assigned to Trp-6, data obtained for the enzyme in the presence of various ligands are better interpreted if resonance 3 is assigned to Trp-22, which is located on a loop that joins elements of secondary structure and forms one side of the ligand-binding cavity

  2. Assigning breed origin to alleles in crossbred animals.

    Science.gov (United States)

    Vandenplas, Jérémie; Calus, Mario P L; Sevillano, Claudia A; Windig, Jack J; Bastiaansen, John W M

    2016-08-22

    For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorphisms (SNPs) may differ between purebred and crossbred animals for several reasons: (1) differences in linkage disequilibrium between SNP alleles and a quantitative trait locus; (2) differences in genetic backgrounds (e.g., dominance and epistatic interactions); and (3) differences in environmental conditions, which result in genotype-by-environment interactions. Thus, SNP effects may be breed-specific, which has led to the development of genomic evaluations for crossbred performance that take such effects into account. However, to estimate breed-specific effects, it is necessary to know breed origin of alleles in crossbred animals. Therefore, our aim was to develop an approach for assigning breed origin to alleles of crossbred animals (termed BOA) without information on pedigree and to study its accuracy by considering various factors, including distance between breeds. The BOA approach consists of: (1) phasing genotypes of purebred and crossbred animals; (2) assigning breed origin to phased haplotypes; and (3) assigning breed origin to alleles of crossbred animals based on a library of assigned haplotypes, the breed composition of crossbred animals, and their SNP genotypes. The accuracy of allele assignments was determined for simulated datasets that include crosses between closely-related, distantly-related and unrelated breeds. Across these scenarios, the percentage of alleles of a crossbred animal that were correctly assigned to their breed origin was greater than 90 %, and increased with increasing distance between breeds, while the percentage of incorrectly assigned alleles was always less than 2 %. For the remaining alleles, i.e. 0 to 10 % of all alleles of a crossbred animal, breed origin could not be assigned. The BOA approach accurately assigns

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

    International Nuclear Information System (INIS)

    Habenstein, Birgit; Wasmer, Christian; Bousset, Luc; Sourigues, Yannick; Schütz, Anne; Loquet, Antoine; Meier, Beat H.; Melki, Ronald; Böckmann, Anja

    2011-01-01

    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 13 C, 15 N 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.

  4. 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.

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

    International Nuclear Information System (INIS)

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

    1998-01-01

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

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

    Science.gov (United States)

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

    2018-05-02

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

  7. Resonant vibrations of self-interstitials in fcc metals with application to specific heat and neutron scattering

    International Nuclear Information System (INIS)

    Ram, P.N.; Dederichs, P.H.

    1981-07-01

    Some aspects of resonant vibrations of self-interstitials in the 100-dumbbell configuration in fcc-metals are discussed by extending previous calculations of Zeller et al. and Schober et al. Employing a simple defect model with nearest-neighbour interaction the local frequency spectrum of the defect is calculated showing several localized modes and low-frequency resonant modes. The change in the total density of states due to the defects is expressed as the derivative of a generalized phase shift which is used to calculate the change in the lattic specific heat due to single interstitials. Inelastic neutron scattering away from the one-phonon lines is proposed as a method to observe the resonant modes induced by self-interstitials. The model calculation in Cu shows that the well defined resonant modes due to dumbbell vibrations have appreciable intensity and could presumably be detected in neutron scattering measurements. The effect of di-interstitials on the phonon dispersion in Al is also discussed. (orig./GSCH)

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

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  9. Backbone resonance assignments of the outer membrane lipoprotein FrpD from Neisseria meningitidis

    Czech Academy of Sciences Publication Activity Database

    Bumba, Ladislav; Sviridova, E.; Kutá-Smatanová, Ivana; Řezáčová, Pavlína; Veverka, Václav

    2014-01-01

    Roč. 8, č. 1 (2014), s. 53-55 ISSN 1874-2718 R&D Projects: GA ČR(CZ) GAP207/11/0717; GA MŠk(CZ) LK11205 Institutional support: RVO:61388963 ; RVO:61388971 ; RVO:67179843 Keywords : Neisseria meningitidis * FrpC * FrpD * backbone assignments * NMR * iron-regulated protein Subject RIV: CE - Biochemistry Impact factor: 0.760, year: 2014

  10. MetaboID: a graphical user interface package for assignment of 1H NMR spectra of bodyfluids and tissues.

    Science.gov (United States)

    MacKinnon, Neil; Somashekar, Bagganahalli S; Tripathi, Pratima; Ge, Wencheng; Rajendiran, Thekkelnaycke M; Chinnaiyan, Arul M; Ramamoorthy, Ayyalusamy

    2013-01-01

    Nuclear magnetic resonance based measurements of small molecule mixtures continues to be confronted with the challenge of spectral assignment. While multi-dimensional experiments are capable of addressing this challenge, the imposed time constraint becomes prohibitive, particularly with the large sample sets commonly encountered in metabolomic studies. Thus, one-dimensional spectral assignment is routinely performed, guided by two-dimensional experiments on a selected sample subset; however, a publicly available graphical interface for aiding in this process is currently unavailable. We have collected spectral information for 360 unique compounds from publicly available databases including chemical shift lists and authentic full resolution spectra, supplemented with spectral information for 25 compounds collected in-house at a proton NMR frequency of 900 MHz. This library serves as the basis for MetaboID, a Matlab-based user interface designed to aid in the one-dimensional spectral assignment process. The tools of MetaboID were built to guide resonance assignment in order of increasing confidence, starting from cursory compound searches based on chemical shift positions to analysis of authentic spike experiments. Together, these tools streamline the often repetitive task of spectral assignment. The overarching goal of the integrated toolbox of MetaboID is to centralize the one dimensional spectral assignment process, from providing access to large chemical shift libraries to providing a straightforward, intuitive means of spectral comparison. Such a toolbox is expected to be attractive to both experienced and new metabolomic researchers as well as general complex mixture analysts. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm

    International Nuclear Information System (INIS)

    Hefke, Frederik; Bagaria, Anurag; Reckel, Sina; Ullrich, Sandra Johanna; Dötsch, Volker; Glaubitz, Clemens; Güntert, Peter

    2011-01-01

    We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273–6279 (1982)), types of amino acids are labeled with 13 C or/and 15 N such that cross peaks between 13 CO(i – 1) and 15 NH(i) result only for pairs of sequentially adjacent amino acids of which the first is labeled with 13 C and the second with 15 N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. Our computer algorithm UPLABEL for optimal unique pair labeling, implemented in the program CYANA and in a standalone program, and also available through a web portal, uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns. The method is illustrated for the assignment of the human G-protein coupled receptor bradykinin B2 (B 2 R) and applied as a starting point for the backbone assignment of the membrane protein proteorhodopsin.

  12. (1)H, (13)C, (15)N backbone and side-chain resonance assignment of Nostoc sp. C139A variant of the heme-nitric oxide/oxygen binding (H-NOX) domain.

    Science.gov (United States)

    Alexandropoulos, Ioannis I; Argyriou, Aikaterini I; Marousis, Kostas D; Topouzis, Stavros; Papapetropoulos, Andreas; Spyroulias, Georgios A

    2016-10-01

    The H-NOX (Heme-nitric oxide/oxygen binding) domain is conserved across eukaryotes and bacteria. In human soluble guanylyl cyclase (sGC) the H-NOX domain functions as a sensor for the gaseous signaling agent nitric oxide (NO). sGC contains the heme-binding H-NOX domain at its N-terminus, which regulates the catalytic site contained within the C-terminal end of the enzyme catalyzing the conversion of GTP (guanosine 5'-triphosphate) to GMP (guanylyl monophosphate). Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 183-residue H-NOX domain from Nostoc sp. through solution NMR.

  13. Sequence-specific 1H NMR assignments, secondary structure, and location of the calcium binding site in the first epidermal growth factor like domain of blood coagulation factor IX

    International Nuclear Information System (INIS)

    Huang, L.H.; Cheng, H.; Sweeney, W.V.; Pardi, A.; Tam, J.P.

    1991-01-01

    Factor IX is a blood clotting protein that contains three regions, including a γ-carboxyglutamic acid (Gla) domain, two tandemly connected epidermal growth factor like (EGF-like) domains, and a serine protease region. The protein exhibits a high-affinity calcium binding site in the first EGF0like domain, in addition to calcium binding in the Gla domain. The first EGF-like domain, factor IX (45-87), has been synthesized. Sequence-specific resonance assignment of the peptide has been made by using 2D NMR techniques, and its secondary structure has been determined. The protein is found to have two antiparallel β-sheets, and preliminary distance geometry calculations indicate that the protein has two domains, separated by Trp 28 , with the overall structure being similar to that of EGF. An NMR investigation of the calcium-bound first EGF-like domain indicates the presence and location of a calcium binding site involving residues on both strands of one of the β-sheets as well as the N-terminal region of the peptide. These results suggest that calcium binding in the first EGF-like domain could induce long-range (possibly interdomain) conformational changes in factor IX, rather than causing structural alterations in the EGF-like domain itself

  14. 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.

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  16. 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.

  17. Sequential assignment of proline-rich regions in proteins: Application to modular binding domain complexes

    International Nuclear Information System (INIS)

    Kanelis, Voula; Donaldson, Logan; Muhandiram, D.R.; Rotin, Daniela; Forman-Kay, Julie D.; Kay, Lewis E.

    2000-01-01

    Many protein-protein interactions involve amino acid sequences containing proline-rich motifs and even poly-proline stretches. The lack of amide protons in such regions complicates assignment, since 1 HN-based triple-resonance assignment strategies cannot be employed. Two such systems that we are currently studying include an SH2 domain from the protein Crk with a region containing 9 prolines in a 14 amino acid sequence, as well as a WW domain that interacts with a proline-rich target. A modified version of the HACAN pulse scheme, originally described by Bax and co-workers [Wang et al. (1995) J. Biomol. NMR, 5, 376-382], and an experiment which correlates the intra-residue 1 H α , 13 C α / 13 C β chemical shifts with the 15 N shift of the subsequent residue are presented and applied to the two systems listed above, allowing sequential assignment of the molecules

  18. Study of the giant multipole resonances, especially the isoscalar giant E2 resonance in 208Pb by inelastic electron scattering with medium and high energy resolution

    International Nuclear Information System (INIS)

    Kuehner, E.G.F.

    1982-01-01

    In the nucleus 208 Pb giant multipole resonances were looked for by inelastic electron scattering up to excitation energies of Esub(x) = 35 MeV. Twelve spectra were taken up at incident energies of Esub(o) = 45-65 MeV under scattering angles from upsilon = 93 0 to 165 0 . The cross sections extracted from this were analyzed by means of DWBA calculations using RPA amplitudes from a model with separable residual interaction. Basing on this analysis for the first time it could be shown that the maximum in the electron scattering cross section at Esub(x) approx.= 14 MeV can be consistently described as a superposition of the Jsup(π) = 1 - , ΔT = 1 with a Jsup(π) = 0 + , ΔT = 0 giant resonance. Furthermore the spectra under backward scattering angles indicate the existence of a magnetic excitation at Esub(x) approx.= 15 MeV which is interpreted as Jsup(π) = 3 + giant resonance. Besides under forwards angles a further weak excitation appears at Esub(x) approx.= 14.6 MeV which is very well compatible with Jsup(π) = 2 + . At Esub(x) = 17.5 MeV a Jsup(π) = 3 - resonance was found which recently is also observed in (α,α') scattering experiments and therefore gets a ΔT = 0 assignment. A further resonance at Esub(x) approx.= 21 MeV has also Jsup(π) = 3 - character but has partly to be assigned to a Jsup(π) = 1 - , ΔT = 0 excitation. At Esub(x) = 23.8 MeV a Jsup(π) = 2 + excitation was found which gels because of model predictions a ΔT = 1 assignment. (orig./HSI) [de

  19. Study of the giant multipole resonances especially of the isoscalar giant E2 resonance in 208Pb by medium and high energy resolution inelastic electron scattering

    International Nuclear Information System (INIS)

    Kuehner, G.

    1982-01-01

    In the nucleus 208 Pb giant multipole resonances up to excitation energies of Esub(x) = 35 MeV were looked for by medium resolution inelastic electron scattering. Twelve spectra were taken up at incident energies of E 0 = 45-65 MeV under scattering angles from upsilon = 93 0 to 165 0 . The cross sections extracted from this were analyzed by means of DWBA calculations using RPA amplitudes from a model with separable residual interaction. On the base of this analysis for the first time it could be shown that the maximum in the electron scattering cross section at Esub(x) approx.= 14 MeV can be consistently described as superposition of the Jsup(π) = 1 - , ΔT = 1 with a Jsup(π) = 0 + , ΔT = 0 giant resonance. Furthermore the spectra under backward scattering angles indicate the existence of a magnetic excitation at Esub(x) approx.= 15 MeV which is interpreted as Jsup(π) = 3 + giant resonance. Besides under forward angles a further weak excitation at Esub(x) approx.= 14.6 MeV appears which is very well compatible with Jsup(π) = 2 + . At Esub(x) = 17.5 MeV a Jsup(π) = 3 - resonance was found which recently is observed also in (α, α') experiments and therefore gets a ΔT = 0 assignment. A further resonance at Esub(x) approx.= 21 MeV has also a Jsup(π) = 3 - character but has to be partly assigned to a Jsup(π) = 1 - , ΔT = 0 excitation. At Esub(x) = 23.8 MeV a Jsup(π) = 2 + excitation was found which gets because of model predictions a ΔT = 1 assignment. (orig./HSI) [de

  20. Effortless assignment with 4D covariance sequential correlation maps.

    Science.gov (United States)

    Harden, Bradley J; Mishra, Subrata H; Frueh, Dominique P

    2015-11-01

    Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. The discovery of resonances in multibaryon systems. Pt. 3. Λ p-resonances

    International Nuclear Information System (INIS)

    Shahbazian, B.A.; Temnikov, P.P.; Timonina, A.A.; Rozhdestvenskij, A.M.

    1978-01-01

    Dibaryon Λ p resonance of 2256 MeV/c 2 mass, GITA 2 (depending on the spin Jsub(Λp)) width, and Jsup(p) > O + spin-parity assignments is discovered. The statistical significance of the corresponding peak in Λ p effective mass spectra is defined by more than five standard deviations. Its production effective cross section in n 12 C collisions at =7.0 GeV/c is estimated to be sigmasub(pr) (2256)=(85.3+-20.0)μb, whereas the formation effective cross section in Λ p → Λ p interactions is sigmasub(f) (2256) = 5.3(2Jsub(Λp)+1) mb. The Λp effective mass spectra which have been investigated in this experiment reveal, apart the well known approximately(Msub(Λ+Msub(p)) MeV/c 2 and 2128 MeV/c 2 peaks, enhancements including 2256 MeV/c 2 peak near the most of the resonance mass values predicted by MIT Bag Model. Possible mechanisms of multibaryon resonance formation are discussed. According to the hypercharge selection rule Y <= 1 multibaryon resonances are shown to be ultra-high density superstrange objects

  2. Backbone assignment and secondary structure of the PsbQ protein from Photosystem II

    Czech Academy of Sciences Publication Activity Database

    Horničáková, M.; Kohoutová, Jaroslava; Schlagnitweit, J.; Wohlschlager, Ch.; Ettrich, Rüdiger; Fiala, R.; Schoefberger, W.; Müller, N.

    2011-01-01

    Roč. 5, č. 2 (2011), s. 169-175 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LC06010 Institutional research plan: CEZ:AV0Z60870520 Keywords : Photosystem II * PsbQ * Missing link * NMR resonance assignment * Protein-protein interaction Subject RIV: BO - Biophysics Impact factor: 0.720, year: 2011 http://www.springerlink.com/content/3n38075w5h1l1082/fulltext.pdf

  3. Calibration of a joint time assignment and mode choice model system

    OpenAIRE

    Greeven, Paulina; Jara-Diaz, Sergio R.; Munizaga, Marcela A.; Axhausen, Kay W.

    2005-01-01

    In this paper we report the results of applying a new microeconomic framework to model time assignment to activities, goods consumption and mode choice jointly (Jara-Díaz and Guevara, 2003; Jara-Díaz and Guerra, 2003) that identifies the links between these decisions and permits the calculation of all the components of the subjective value of time defined in the literature: the value of time as a resource, value of assigning time to a specific activity and the value of saving time in a specif...

  4. Auxiliary programs for resonance parameter storage and retrieval system REPSTOR. XTOREP, ETOREP, REPTOINP, REPRENUM, REPIMRG, TREP, PASSIGN, JCONV

    International Nuclear Information System (INIS)

    Nakagawa, Tsuneo; Kikuchi, Yasuyuki; Fukahori, Tokio

    1999-06-01

    This report describes functions and usage of eight auxiliary computer programs for REPSTOR that is a computer program for collecting the resonance parameters and evaluating them. The programs are XTOREP to convert the experimental data in EXFOR to the REPSTOR input data, ETOREP to convert the data in ENDF format to the REPSTOR input data, REPTOINP to change the data in a REPSTOR file into the REPSTOR input format, REPRENUM to renumber the level number of resonance levels, REPIMRG to merge the XTOREP output data sets, TREP to calculate mean values of resonance parameters, widths of individual resonances, etc., PASSIGN to assign orbital angular momentum by using Bayse theorem, and JCONV to assign total spin. (author)

  5. Cholangiocarcinoma in Cirrhosis: Value of Hepatocyte Specific Magnetic Resonance Imaging.

    Science.gov (United States)

    Piscaglia, Fabio; Iavarone, Massimo; Galassi, Marzia; Vavassori, Sara; Renzulli, Matteo; Forzenigo, Laura Virginia; Granito, Alessandro; Salvatore, Veronica; Sangiovanni, Angelo; Golfieri, Rita; Colombo, Massimo; Bolondi, Luigi

    2015-10-01

    The diagnosis of intrahepatic cholangiocellular carcinoma (ICC) remains elusive at imaging, which is a critical issue in cirrhotic patients in whom a diagnosis of hepatocellular carcinoma (HCC) can be established only by imaging. The aim of the study was to evaluate the potential of MRI in the diagnosis of ICC in cirrhosis using 'hepatocyte-specific' Gadolinium (Gd)-based contrast agents. Sixteen histologically proven and retrospectively identified ICCs on cirrhosis were investigated with hepatocyte-specific magnetic resonance contrast agents (6 in Bologna with Gd-EOB-DTPA and 10 in Milan with Gd-BOPTA). The control group consisted of 41 consecutively and prospectively collected nodules (31 HCCs) imaged with Gd-EOB-DTPA. Fifteen ICC nodules (94%) displayed hypointensity in the hepatobiliary phase, suggesting malignancy. Thirteen cholangiocarcinomas (81%) showed hyperenhancement in the venous phase. Only 2 cholangiocarcinoma nodules showed hypoenhancement in the venous phase, corresponding to washout, in both cases preceded by rim enhancement in arterial phase. All the hepatocarcinomas showed hypointensity in hepatobiliary phase, but was always preceded by hypointensity in the venous phase; arterial rim enhancement was never observed in any hepatocarcinoma or regenerative nodule. MRI with hepatocyte-specific Gd-based contrast agents showed a pattern of malignancy in almost all the ICCs, concurrently avoiding misdiagnosis with hepatocarcinoma. These findings suggest a greater diagnostic capacity for this technique compared with the results of MRI with conventional contrast agents reported in the literature in this setting. © 2015 S. Karger AG, Basel.

  6. Ability of preoperative 3.0-Tesla magnetic resonance imaging to predict the absence of side-specific extracapsular extension of prostate cancer.

    Science.gov (United States)

    Hara, Tomohiko; Nakanishi, Hiroyuki; Nakagawa, Tohru; Komiyama, Motokiyo; Kawahara, Takashi; Manabe, Tomoko; Miyake, Mototaka; Arai, Eri; Kanai, Yae; Fujimoto, Hiroyuki

    2013-10-01

    Recent studies have shown an improvement in prostate cancer diagnosis with the use of 3.0-Tesla magnetic resonance imaging. We retrospectively assessed the ability of this imaging technique to predict side-specific extracapsular extension of prostate cancer. From October 2007 to August 2011, prostatectomy was carried out in 396 patients after preoperative 3.0-Tesla magnetic resonance imaging. Among these, 132 (primary sample) and 134 patients (validation sample) underwent 12-core prostate biopsy at the National Cancer Center Hospital of Tokyo, Japan, and at other institutions, respectively. In the primary dataset, univariate and multivariate analyses were carried out to predict side-specific extracapsular extension using variables determined preoperatively, including 3.0-Tesla magnetic resonance imaging findings (T2-weighted and diffusion-weighted imaging). A prediction model was then constructed and applied to the validation study sample. Multivariate analysis identified four significant independent predictors (P Tesla diffusion-weighted magnetic resonance imaging findings, ≥2 positive biopsy cores on each side and a maximum percentage of positive cores ≥31% on each side. The negative predictive value was 93.9% in the combination model with these four predictors, meanwhile the positive predictive value was 33.8%. Good reproducibility of these four significant predictors and the combination model was observed in the validation study sample. The side-specific extracapsular extension prediction by the biopsy Gleason score and factors associated with tumor location, including a positive 3.0-Tesla diffusion-weighted magnetic resonance imaging finding, have a high negative predictive value, but a low positive predictive value. © 2013 The Japanese Urological Association.

  7. "Miss! I'm Done!" Finishing Craft Assignments as a Situated Activity System in Preschool

    Science.gov (United States)

    Deunk, Marjolein; Berenst, Jan; de Glopper, Kees

    2010-01-01

    We describe the Situated Activity System of finishing craft assignments in preschool: the specific, routinized way that child and teacher jointly close the child's craft assignment, employing a specific discourse pattern. We analyzed the interactions of 14 Dutch children between 2.1 and 3.10 years old while they were finishing their craft…

  8. Grouping puts figure-ground assignment in context by constraining propagation of edge assignment.

    Science.gov (United States)

    Brooks, Joseph L; Brook, Joseph L; Driver, Jon

    2010-05-01

    Figure-ground organization involves the assignment of edges to a figural shape on one or the other side of each dividing edge. Established visual cues for edge assignment primarily concern relatively local rather than contextual factors. In the present article, we show that an assignment for a locally unbiased edge can be affected by an assignment of a remote contextual edge that has its own locally biased assignment. We find that such propagation of edge assignment from the biased remote context occurs only when the biased and unbiased edges are grouped. This new principle, whereby grouping constrains the propagation of figural edge assignment, emerges from both subjective reports and an objective short-term edge-matching task. It generalizes from moving displays involving grouping by common fate and collinearity, to static displays with grouping by similarity of edge-contrast polarity, or apparent occlusion. Our results identify a new contextual influence on edge assignment. They also identify a new mechanistic relation between grouping and figure-ground processes, whereby grouping between remote elements can constrain the propagation of edge assignment between those elements. Supplemental materials for this article may be downloaded from http://app.psychonomic-journals.org/content/supplemental.

  9. 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…

  10. FLEET ASSIGNMENT MODELLING

    Directory of Open Access Journals (Sweden)

    2016-01-01

    Full Text Available The article is devoted to the airline scheduling process and methods of its modeling. This article describes the main stages of airline scheduling process (scheduling, fleet assignment, revenue management, operations, their features and interactions. The main part of scheduling process is fleet assignment. The optimal solution of the fleet assignment problem enables airlines to increase their incomes up to 3 % due to quality improving of connections and execution of the planned number of flights operated by less number of aircraft than usual or planned earlier. Fleet assignment of scheduling process is examined and Conventional Leg-Based Fleet Assignment Model is analyzed. Finally strong and weak aspects of the model (SWOT are released and applied. The article gives a critical analysis of FAM model, with the purpose of identi- fying possible options and constraints of its use (for example, in cases of short-term and long-term planning, changing the schedule or replacing the aircraft, as well as possible ways to improve the model.

  11. Facilitated assignment of large protein NMR signals with covariance sequential spectra using spectral derivatives.

    Science.gov (United States)

    Harden, Bradley J; Nichols, Scott R; Frueh, Dominique P

    2014-09-24

    Nuclear magnetic resonance (NMR) studies of larger proteins are hampered by difficulties in assigning NMR resonances. Human intervention is typically required to identify NMR signals in 3D spectra, and subsequent procedures depend on the accuracy of this so-called peak picking. We present a method that provides sequential connectivities through correlation maps constructed with covariance NMR, bypassing the need for preliminary peak picking. We introduce two novel techniques to minimize false correlations and merge the information from all original 3D spectra. First, we take spectral derivatives prior to performing covariance to emphasize coincident peak maxima. Second, we multiply covariance maps calculated with different 3D spectra to destroy erroneous sequential correlations. The maps are easy to use and can readily be generated from conventional triple-resonance experiments. Advantages of the method are demonstrated on a 37 kDa nonribosomal peptide synthetase domain subject to spectral overlap.

  12. Two-dimensional nuclear magnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    Bax, A.; Lerner, L.

    1986-01-01

    Great spectral simplification can be obtained by spreading the conventional one-dimensional nuclear magnetic resonance (NMR) spectrum in two independent frequency dimensions. This so-called two-dimensional NMR spectroscopy removes spectral overlap, facilitates spectral assignment, and provides a wealth of additional information. For example, conformational information related to interproton distances is available from resonance intensities in certain types of two-dimensional experiments. Another method generates 1 H NMR spectra of a preselected fragment of the molecule, suppressing resonances from other regions and greatly simplifying spectral appearance. Two-dimensional NMR spectroscopy can also be applied to the study of 13 C and 15 N, not only providing valuable connectivity information but also improving sensitivity of 13 C and 15 N detection by up to two orders of magnitude. 45 references, 10 figures

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-06-15

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

  14. 1H, 15N and 13C resonance assignments of the J-domain of co-chaperone Sis1 from Saccharomyces cerevisiae.

    Science.gov (United States)

    Pinheiro, Glaucia M S; Amorim, Gisele C; Iqbal, Anwar; Ramos, C H I; Almeida, Fabio C L

    2018-04-30

    Protein folding in the cell is usually aided by molecular chaperones, from which the Hsp70 (Hsp = heat shock protein) family has many important roles, such as aiding nascent folding and participating in translocation. Hsp70 has ATPase activity which is stimulated by binding to the J-domain present in co-chaperones from the Hsp40 family. Hsp40s have many functions, as for instance the binding to partially folded proteins to be delivered to Hsp70. However, the presence of the J-domain characterizes Hsp40s or, by this reason, as J-proteins. The J-domain alone can stimulate Hsp70 ATPase activity. Apparently, it also maintains the same conformation as in the whole protein although structural information on full J-proteins is still missing. This work reports the 1 H, 15 N and 13 C resonance assignments of the J-domain of a Hsp40 from Saccharomyces cerevisiae, named Sis1. Secondary structure and order parameter prediction from chemical shifts are also reported. Altogether, the data show that Sis1 J-domain is highly structured and predominantly formed by α-helices, results that are in very good agreement with those previously reported for the crystallographic structure.

  15. Phase modulated 2D HSQC-TOCSY for unambiguous assignment of overlapping spin systems

    Science.gov (United States)

    Singh, Amrinder; Dubey, Abhinav; Adiga, Satish K.; Atreya, Hanudatta S.

    2018-01-01

    We present a new method that allows one to unambiguously resolve overlapping spin systems often encountered in biomolecular systems such as peptides and proteins or in samples containing a mixture of different molecules such as in metabolomics. We address this problem using the recently proposed phase modulation approach. By evolving the 1H chemical shifts in a conventional two dimensional (2D) HSQC-TOCSY experiment for a fixed delay period, the phase/intensity of set of cross peaks belonging to one spin system are modulated differentially relative to those of its overlapping counterpart, resulting in their discrimination and recognition. The method thus accelerates the process of identification and resonance assignment of individual compounds in complex mixtures. This approach facilitated the assignment of molecules in the embryo culture medium used in human assisted reproductive technology.

  16. Towards unsupervised polyaromatic hydrocarbons structural assignment from SA-TIMS-FTMS data.

    Science.gov (United States)

    Benigni, Paolo; Marin, Rebecca; Fernandez-Lima, Francisco

    2015-10-01

    With the advent of high resolution ion mobility analyzers and their coupling to ultrahigh resolution mass spectrometers, there is a need to further develop a theoretical workflow capable of correlating experimental accurate mass and mobility measurements with tridimensional candidate structures. In the present work, a general workflow is described for unsupervised tridimensional structural assignment based on accurate mass measurements, mobility measurements, in silico 2D-3D structure generation, and theoretical mobility calculations. In particular, the potential of this workflow will be shown for the analysis of polyaromatic hydrocarbons from Coal Tar SRM 1597a using selected accumulation - trapped ion mobility spectrometry (SA-TIMS) coupled to Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The proposed workflow can be adapted to different IMS scenarios, can utilize different collisional cross-section calculators and has the potential to include MS n and IMS n measurements for faster and more accurate tridimensional structural assignment.

  17. Identification of threshold prostate specific antigen levels to optimize the detection of clinically significant prostate cancer by magnetic resonance imaging/ultrasound fusion guided biopsy.

    Science.gov (United States)

    Shakir, Nabeel A; George, Arvin K; Siddiqui, M Minhaj; Rothwax, Jason T; Rais-Bahrami, Soroush; Stamatakis, Lambros; Su, Daniel; Okoro, Chinonyerem; Raskolnikov, Dima; Walton-Diaz, Annerleim; Simon, Richard; Turkbey, Baris; Choyke, Peter L; Merino, Maria J; Wood, Bradford J; Pinto, Peter A

    2014-12-01

    Prostate specific antigen sensitivity increases with lower threshold values but with a corresponding decrease in specificity. Magnetic resonance imaging/ultrasound targeted biopsy detects prostate cancer more efficiently and of higher grade than standard 12-core transrectal ultrasound biopsy but the optimal population for its use is not well defined. We evaluated the performance of magnetic resonance imaging/ultrasound targeted biopsy vs 12-core biopsy across a prostate specific antigen continuum. We reviewed the records of all patients enrolled in a prospective trial who underwent 12-core transrectal ultrasound and magnetic resonance imaging/ultrasound targeted biopsies from August 2007 through February 2014. Patients were stratified by each of 4 prostate specific antigen cutoffs. The greatest Gleason score using either biopsy method was compared in and across groups as well as across the population prostate specific antigen range. Clinically significant prostate cancer was defined as Gleason 7 (4 + 3) or greater. Univariate and multivariate analyses were performed. A total of 1,003 targeted and 12-core transrectal ultrasound biopsies were performed, of which 564 diagnosed prostate cancer for a 56.2% detection rate. Targeted biopsy led to significantly more upgrading to clinically significant disease compared to 12-core biopsy. This trend increased more with increasing prostate specific antigen, specifically in patients with prostate specific antigen 4 to 10 and greater than 10 ng/ml. Prostate specific antigen 5.2 ng/ml or greater captured 90% of upgrading by targeted biopsy, corresponding to 64% of patients who underwent multiparametric magnetic resonance imaging and subsequent fusion biopsy. Conversely a greater proportion of clinically insignificant disease was detected by 12-core vs targeted biopsy overall. These differences persisted when controlling for potential confounders on multivariate analysis. Prostate cancer upgrading with targeted biopsy increases

  18. 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.

  19. Assignment of histidine resonances in the 1H NMR (500 MHz) spectrum of subtilisin BPN' using site-directed mutagenesis

    International Nuclear Information System (INIS)

    Bycroft, M.; Fersht, A.R.

    1988-01-01

    A spin-echo pulse sequence has been used to resolve the six histidine C-2H protons in the 500-MHz NMR spectrum of subtilisin BPN'. Five of these residues have been substituted by site-directed mutagenesis, and this has enabled a complete assignment of these protons to be obtained. Analysis of the pH titration curves of these signals has provided microscopic pK a 's for the six histidines in this enzyme. The pK a 's of the histidine residues in subtilisin BPN' have been compared with the values obtained for the histidines in the homologous enzyme from Bacillus licheniformis (subtilisin Carlsberg). Four of the five conserved histidines titrate with essentially identical pK a 's in the two enzymes. It therefore appears that the assignments made for these residues in subtilisin BPN' can be transferred to subtilisin Carlsberg. On the basis of these assignments, the one histidine that titrates with a substantially different pK a in the two enzymes can be assigned to histidine-238. This difference in pK a has been attributed to a Trp to Lys substitution at position 241 in subtilisin Carlsberg

  20. Missing and Spurious Level Corrections for Nuclear Resonances

    International Nuclear Information System (INIS)

    Mitchell, G E; Agvaanluvsan, U; Pato, M P; Shriner, J F

    2005-01-01

    Neutron and proton resonances provide detailed level density information. However, due to experimental limitations, some levels are missed and some are assigned incorrect quantum numbers. The standard method to correct for missing levels uses the experimental widths and the Porter-Thomas distribution. Analysis of the spacing distribution provides an independent determination of the fraction of missing levels. We have derived a general expression for such an imperfect spacing distribution using the maximum entropy principle and applied it to a variety of nuclear resonance data. The problem of spurious levels has not been extensively addressed

  1. Myocardial late gadolinium enhancement in specific cardiomyopathies by cardiovascular magnetic resonance: a preliminary experience.

    Science.gov (United States)

    Silva, Caterina; Moon, James C; Elkington, Andrew G; John, Anna S; Mohiaddin, Raad H; Pennell, Dudley J

    2007-12-01

    Late gadolinium enhancement cardiovascular magnetic resonance (CMR) can visualize myocardial interstitial abnormalities. The aim of this study was to assess whether regions of abnormal myocardium can also be visualized by late enhancement gadolinium CMR in the specific cardiomyopathies. A retrospective review of all referrals for gadolinium CMR with specific cardiomyopathy over 20 months. Nine patients with different specific cardiomyopathies were identified. Late enhancement was demonstrated in all patients, with a mean signal intensity of 390 +/- 220% compared with normal regions. The distribution pattern of late enhancement was unlike the subendocardial late enhancement related to coronary territories found in myocardial infarction. The affected areas included papillary muscles (sarcoid), the mid-myocardium (Anderson-Fabry disease, glycogen storage disease, myocarditis, Becker muscular dystrophy) and the global sub-endocardium (systemic sclerosis, Loeffler's endocarditis, amyloid, Churg-Strauss). Focal myocardial late gadolinium enhancement is found in the specific cardiomyopathies, and the pattern is distinct from that seen in infarction. Further systematic studies are warranted to assess whether the pattern and extent of late enhancement may aid diagnosis and prognostic assessment.

  2. Nuclear resonance vibrational spectroscopy applied to [Fe(OEP)(NO)]: the vibrational assignments of five-coordinate ferrous heme-nitrosyls and implications for electronic structure.

    Science.gov (United States)

    Lehnert, Nicolai; Galinato, Mary Grace I; Paulat, Florian; Richter-Addo, George B; Sturhahn, Wolfgang; Xu, Nan; Zhao, Jiyong

    2010-05-03

    This study presents Nuclear Resonance Vibrational Spectroscopy (NRVS) data on the five-coordinate (5C) ferrous heme-nitrosyl complex [Fe(OEP)(NO)] (1, OEP(2-) = octaethylporphyrinato dianion) and the corresponding (15)N(18)O labeled complex. The obtained spectra identify two isotope sensitive features at 522 and 388 cm(-1), which shift to 508 and 381 cm(-1), respectively, upon isotope labeling. These features are assigned to the Fe-NO stretch nu(Fe-NO) and the in-plane Fe-N-O bending mode delta(ip)(Fe-N-O), the latter has been unambiguously assigned for the first time for 1. The obtained NRVS data were simulated using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Since complex 1 can potentially exist in 12 different conformations involving the FeNO and peripheral ethyl orientations, extended density functional theory (DFT) calculations and QCC-NCA simulations were performed to determine how these conformations affect the NRVS properties of [Fe(OEP)NO]. These results show that the properties and force constants of the FeNO unit are hardly affected by the conformational changes involving the ethyl substituents. On the other hand, the NRVS-active porphyrin-based vibrations around 340-360, 300-320, and 250-270 cm(-1) are sensitive to the conformational changes. The spectroscopic changes observed in these regions are due to selective mechanical couplings of one component of E(u)-type (in ideal D(4h) symmetry) porphyrin-based vibrations with the in-plane Fe-N-O bending mode. This leads to the observed variations in Fe(OEP) core mode energies and NRVS intensities without affecting the properties of the FeNO unit. The QCC-NCA simulated NRVS spectra of 1 show excellent agreement with experiment, and indicate that conformer F is likely present in the samples of this complex investigated here. The observed porphyrin-based vibrations in the NRVS spectra of 1 are also assigned based on the QCC-NCA results. The obtained force constants of the Fe-NO and N

  3. Position statement. The right to accept or reject an assignment. American Nurses Association.

    Science.gov (United States)

    1996-01-01

    The American Nurses Association (ANA) believes that nurses should reject assignment that puts patients or themselves in serious, immediate jeopardy. ANA supports the nurses obligation to reject an assignment in these situations even where there is not a specific legal protection for rejecting such an assignment. The professional obligations to the nurse to safeguard clients are grounded in the ethical norms of the profession, the Standards of Clinical Nursing Practice and state nurse practice acts.

  4. UOP LDR 300 All Assignments New

    OpenAIRE

    ADMIN

    2018-01-01

    UOP LDR 300 All Assignments New Check this A+ tutorial guideline at http://www.ldr300assignment.com/ldr-300-uop/ldr-300-all-assignments-latest For more classes visit http://www.ldr300assignment.com LDR 300 Week 1 Assignment Leadership Assessment (2 Papers) LDR 300 Week 2 Assignment Leadership Theories Matrix (2 Set) LDR 300 Week 2 Assignment Formulating Leadership Part I (2 Papers) LDR 300 Week 3 Assignment Interaction and Influence Amo...

  5. Web-Based Problem-Solving Assignment and Grading System

    Science.gov (United States)

    Brereton, Giles; Rosenberg, Ronald

    2014-11-01

    In engineering courses with very specific learning objectives, such as fluid mechanics and thermodynamics, it is conventional to reinforce concepts and principles with problem-solving assignments and to measure success in problem solving as an indicator of student achievement. While the modern-day ease of copying and searching for online solutions can undermine the value of traditional assignments, web-based technologies also provide opportunities to generate individualized well-posed problems with an infinite number of different combinations of initial/final/boundary conditions, so that the probability of any two students being assigned identical problems in a course is vanishingly small. Such problems can be designed and programmed to be: single or multiple-step, self-grading, allow students single or multiple attempts; provide feedback when incorrect; selectable according to difficulty; incorporated within gaming packages; etc. In this talk, we discuss the use of a homework/exam generating program of this kind in a single-semester course, within a web-based client-server system that ensures secure operation.

  6. Fair Package Assignment

    Science.gov (United States)

    Lahaie, Sébastien; Parkes, David C.

    We consider the problem of fair allocation in the package assignment model, where a set of indivisible items, held by single seller, must be efficiently allocated to agents with quasi-linear utilities. A fair assignment is one that is efficient and envy-free. We consider a model where bidders have superadditive valuations, meaning that items are pure complements. Our central result is that core outcomes are fair and even coalition-fair over this domain, while fair distributions may not even exist for general valuations. Of relevance to auction design, we also establish that the core is equivalent to the set of anonymous-price competitive equilibria, and that superadditive valuations are a maximal domain that guarantees the existence of anonymous-price competitive equilibrium. Our results are analogs of core equivalence results for linear prices in the standard assignment model, and for nonlinear, non-anonymous prices in the package assignment model with general valuations.

  7. On the extreme points of the core of neighbour games and assignment games

    NARCIS (Netherlands)

    Hamers, H.J.M.; Klijn, F.; Solymosi, T.; Tijs, S.H.; Pere Villar, J.

    1999-01-01

    Neighbour games arise from certain matching or sequencing situations in which only some specific pairs of players can obtain a positive gain. As a consequence, neighbour games are as well assignment games as line graph restricted games. We will show that the intersection of the class of assignment

  8. Magnetic resonance imaging of the ear for patient-specific reconstructive surgery.

    Directory of Open Access Journals (Sweden)

    Luc Nimeskern

    Full Text Available INTRODUCTION: Like a fingerprint, ear shape is a unique personal feature that should be reconstructed with a high fidelity during reconstructive surgery. Ear cartilage tissue engineering (TE advantageously offers the possibility to use novel 3D manufacturing techniques to reconstruct the ear, thus allowing for a detailed auricular shape. However it also requires detailed patient-specific images of the 3D cartilage structures of the patient's intact contralateral ear (if available. Therefore the aim of this study was to develop and evaluate an imaging strategy for acquiring patient-specific ear cartilage shape, with sufficient precision and accuracy for use in a clinical setting. METHODS AND MATERIALS: Magnetic resonance imaging (MRI was performed on 14 volunteer and six cadaveric auricles and manually segmented. Reproducibility of cartilage volume (Cg.V, surface (Cg.S and thickness (Cg.Th was assessed, to determine whether raters could repeatedly define the same volume of interest. Additionally, six cadaveric auricles were harvested, scanned and segmented using the same procedure, then dissected and scanned using high resolution micro-CT. Correlation between MR and micro-CT measurements was assessed to determine accuracy. RESULTS: Good inter- and intra-rater reproducibility was observed (precision errors 0.82, but low for Cg.Th (0.95 demonstrated high accuracy. DISCUSSION AND CONCLUSION: This study demonstrated that precision and accuracy of the proposed method was high enough to detect patient-specific variation in ear cartilage geometry. The present study provides a clinical strategy to access the necessary information required for the production of 3D ear scaffolds for TE purposes, including detailed patient-specific shape. Furthermore, the protocol is applicable in daily clinical practice with existing infrastructure.

  9. Spin measurements for 147Sm+n resonances: Further evidence for nonstatistical effects

    International Nuclear Information System (INIS)

    Koehler, P. E.; Ullmann, J. L.; Bredeweg, T. A.; O'Donnell, J. M.; Reifarth, R.; Rundberg, R. S.; Vieira, D. J.; Wouters, J. M.

    2007-01-01

    We have determined the spins J of resonances in the 147 Sm(n,γ) reaction by measuring multiplicities of γ-ray cascades following neutron capture. Using this technique, we were able to determine J values for all but 14 of the 141 known resonances below E n =1 keV, including 41 firm J assignments for resonances whose spins previously were either unknown or tentative. These new spin assignments, together with previously determined resonance parameters, allowed us to extract level spacings (D 0,3 =11.76±0.93 and D 0,4 =11.21±0.85 eV) and neutron strength functions (10 4 S 0,3 =4.70±0.91 and 10 4 S 0,4 =4.93±0.92) for J=3 and 4 resonances, respectively. Furthermore, cumulative numbers of resonances and cumulative reduced neutron widths as functions of resonance energy indicate that very few resonances of either spin have been missed below E n =700 eV. This conclusion is strengthened by the facts that, over this energy range, Wigner distributions calculated using these D 0 values agree with the measured nearest-neighbor level spacings to within the experimental uncertainties, and that the Δ 3 values calculated from the data also agree with the expected values. Because a nonstatistical effect recently was reported near E n =350 eV from an analysis of 147 Sm(n,α) data, we divided the data into two regions; 0 n n n 0 distribution for resonances below 350 eV is consistent with the expected Porter-Thomas distribution. However, we found that Γ n 0 data in the 350 n 2 distribution having ν≥2 We discuss possible explanations for these observed nonstatistical effects and their possible relation to similar effects previously observed in other nuclides

  10. Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra.

    Science.gov (United States)

    Tolić, Nikola; Liu, Yina; Liyu, Andrey; Shen, Yufeng; Tfaily, Malak M; Kujawinski, Elizabeth B; Longnecker, Krista; Kuo, Li-Jung; Robinson, Errol W; Paša-Tolić, Ljiljana; Hess, Nancy J

    2017-12-05

    Ultrahigh resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work, we describe software Formularity with a user-friendly interface for CIA function and newly developed search function Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. Tap water and HOC spike in Suwannee River NOM were used to assess HOC identification in complex environmental samples. Strategies for reconciliation of CIA and IPA assignments were discussed. Software and sample databases with documentation are freely available.

  11. NMR experiments for resonance assignments of 13C, 15N doubly-labeled flexible polypeptides: Application to the human prion protein hPrP(23-230)

    International Nuclear Information System (INIS)

    Liu Aizhuo; Riek, Roland; Wider, Gerhard; Schroetter, Christine von; Zahn, Ralph; Wuethrich, Kurt

    2000-01-01

    A combination of three heteronuclear three-dimensional NMR experiments tailored for sequential resonance assignments in uniformly 15 N, 13 C-labeled flexible polypeptide chains is described. The 3D (H)N(CO-TOCSY)NH, 3D (H)CA(CO-TOCSY)NH and 3D (H)CBCA(CO-TOCSY)NH schemes make use of the favorable 15 N chemical shift dispersion in unfolded polypeptides, exploit the slow transverse 15 N relaxation rates of unfolded polypeptides in high resolution constant-time [ 1 H, 15 N]-correlation experiments, and use carbonyl carbon homonuclear isotropic mixing to transfer magnetization sequentially along the amino acid sequence. Practical applications are demonstrated with the 100-residue flexible tail of the recombinant human prion protein, making use of spectral resolution up to 0.6 Hz in the 15 N dimension, simultaneous correlation with the two adjacent amino acid residues to overcome problems associated with spectral overlap, and the potential of the presently described experiments to establish nearest-neighbor correlations across proline residues in the amino acid sequence

  12. Plagiarism-Proofing Assignments

    Science.gov (United States)

    Johnson, Doug

    2004-01-01

    Mr. Johnson has discovered that the higher the level of student engagement and creativity, the lower the probability of plagiarism. For teachers who would like to see such desirable results, he describes the characteristics of assignments that are most likely to produce them. Two scenarios of types of assignments that avoid plagiarism are…

  13. Magnetic Resonance Sensors

    Directory of Open Access Journals (Sweden)

    Robert H. Morris

    2014-11-01

    Full Text Available Magnetic Resonance finds countless applications, from spectroscopy to imaging, routinely in almost all research and medical institutions across the globe. It is also becoming more frequently used for specific applications in which the whole instrument and system is designed for a dedicated application. With beginnings in borehole logging for the petro-chemical industry Magnetic Resonance sensors have been applied to fields as varied as online process monitoring for food manufacture and medical point of care diagnostics. This great diversity is seeing exciting developments in magnetic resonance sensing technology published in application specific journals where they are often not seen by the wider sensor community. It is clear that there is enormous interest in magnetic resonance sensors which represents a significant growth area. The aim of this special edition of Sensors was to address the wide distribution of relevant articles by providing a forum to disseminate cutting edge research in this field in a single open source publication.[...

  14. Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO)

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-07-15

    We present a novel automated strategy (PISTACHIO) for the probabilistic assignment of backbone and sidechain chemical shifts in proteins. The algorithm uses peak lists derived from various NMR experiments as input and provides as output ranked lists of assignments for all signals recognized in the input data as constituting spin systems. PISTACHIO was evaluated by comparing its performance with raw peak-picked data from 15 proteins ranging from 54 to 300 residues; the results were compared with those achieved by experts analyzing the same datasets by hand. As scored against the best available independent assignments for these proteins, the first-ranked PISTACHIO assignments were 80-100% correct for backbone signals and 75-95% correct for sidechain signals. The independent assignments benefited, in a number of cases, from structural data (e.g. from NOESY spectra) that were unavailable to PISTACHIO. Any number of datasets in any combination can serve as input. Thus PISTACHIO can be used as datasets are collected to ascertain the current extent of secure assignments, to identify residues with low assignment probability, and to suggest the types of additional data needed to remove ambiguities. The current implementation of PISTACHIO, which is available from a server on the Internet, supports input data from 15 standard double- and triple-resonance experiments. The software can readily accommodate additional types of experiments, including data from selectively labeled samples. The assignment probabilities can be carried forward and refined in subsequent steps leading to a structure. The performance of PISTACHIO showed no direct dependence on protein size, but correlated instead with data quality (completeness and signal-to-noise). PISTACHIO represents one component of a comprehensive probabilistic approach we are developing for the collection and analysis of protein NMR data.

  15. Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO)

    International Nuclear Information System (INIS)

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

    2005-01-01

    We present a novel automated strategy (PISTACHIO) for the probabilistic assignment of backbone and sidechain chemical shifts in proteins. The algorithm uses peak lists derived from various NMR experiments as input and provides as output ranked lists of assignments for all signals recognized in the input data as constituting spin systems. PISTACHIO was evaluated by comparing its performance with raw peak-picked data from 15 proteins ranging from 54 to 300 residues; the results were compared with those achieved by experts analyzing the same datasets by hand. As scored against the best available independent assignments for these proteins, the first-ranked PISTACHIO assignments were 80-100% correct for backbone signals and 75-95% correct for sidechain signals. The independent assignments benefited, in a number of cases, from structural data (e.g. from NOESY spectra) that were unavailable to PISTACHIO. Any number of datasets in any combination can serve as input. Thus PISTACHIO can be used as datasets are collected to ascertain the current extent of secure assignments, to identify residues with low assignment probability, and to suggest the types of additional data needed to remove ambiguities. The current implementation of PISTACHIO, which is available from a server on the Internet, supports input data from 15 standard double- and triple-resonance experiments. The software can readily accommodate additional types of experiments, including data from selectively labeled samples. The assignment probabilities can be carried forward and refined in subsequent steps leading to a structure. The performance of PISTACHIO showed no direct dependence on protein size, but correlated instead with data quality (completeness and signal-to-noise). PISTACHIO represents one component of a comprehensive probabilistic approach we are developing for the collection and analysis of protein NMR data

  16. Acupuncture at Waiguan (SJ5) and sham points influences activation of functional brain areas of ischemic stroke patients: a functional magnetic resonance imaging study

    OpenAIRE

    Qi, Ji; Chen, Junqi; Huang, Yong; Lai, Xinsheng; Tang, Chunzhi; Yang, Junjun; Chen, Hua; Qu, Shanshan

    2014-01-01

    Most studies addressing the specificity of meridians and acupuncture points have focused mainly on the different neural effects of acupuncture at different points in healthy individuals. This study examined the effects of acupuncture on brain function in a pathological context. Sixteen patients with ischemic stroke were randomly assigned to true point group (true acupuncture at right Waiguan (SJ5)) and sham point group (sham acupuncture). Results of functional magnetic resonance imaging revea...

  17. Electroexcitation of giant resonances in 181Ta

    International Nuclear Information System (INIS)

    Hicks, R.S.; Auer, I.P.; Bergstrom, J.C.; Caplan, H.S.

    1977-01-01

    The giant resonance region of 181 Ta has been investigated by means of inelastic electron scattering with primary electron energies of 79.1 to 118.3 MeV. A peak-fitting procedure was employed to separate the measured spectrum into nine different resonance components. Multipolarity and strength assignments were deduced using DWBA analysis with the Goldhaber-Teller and Steinwedel-Jensen models. In addition to the well-known giant dipole structure, other resonances were identified at 23.2+-0.3 MeV (E2), 9.5+-0.2 and 11.5+-0.2 MeV (E2 or E0), 19.5+-0.8 MeV (E3), 3.70+-0.14 MeV (E3 or E4), and 5.40+-0.15 MeV (E4 or E5). The model dependence of the analysis is discussed. (Auth.)

  18. Developing Team Skills through a Collaborative Writing Assignment

    Science.gov (United States)

    Thomas, Theda Ann

    2014-01-01

    Employers want students who are able to work effectively as members of a team, and expect universities to develop this ability in their graduates. This paper proposes a framework for a collaborative writing assignment that specifically develops students' ability to work in teams. The framework has been tested using two iterations of an action…

  19. Time-resolved resonance raman spectrum of all-trans-diphenylbutadiene in the lowest excited singlet state

    DEFF Research Database (Denmark)

    Wilbrandt, Robert Walter; Jensen, Niels-Henrik; Langkilde, F.W.

    1984-01-01

    The resonance Raman spectrwn of all-trans-diphenylbutadiene in its lowest excited S1 state excited in resonance with the S1 → Sn absorption band at 650 nm in non-polar solvents is reported. Three vibrational bands at 1572, 1481 and 1165 cm−1 are observed. A possible assignment of the the 1481 cm−...

  20. Nonlinear resonances

    CERN Document Server

    Rajasekar, Shanmuganathan

    2016-01-01

    This introductory text presents the basic aspects and most important features of various types of resonances and anti-resonances in dynamical systems. In particular, for each resonance, it covers the theoretical concepts, illustrates them with case studies, and reviews the available information on mechanisms, characterization, numerical simulations, experimental realizations, possible quantum analogues, applications and significant advances made over the years. Resonances are one of the most fundamental phenomena exhibited by nonlinear systems and refer to specific realizations of maximum response of a system due to the ability of that system to store and transfer energy received from an external forcing source. Resonances are of particular importance in physical, engineering and biological systems - they can prove to be advantageous in many applications, while leading to instability and even disasters in others. The book is self-contained, providing the details of mathematical derivations and techniques invo...

  1. A method to assign failure rates for piping reliability assessments

    International Nuclear Information System (INIS)

    Gamble, R.M.; Tagart, S.W. Jr.

    1991-01-01

    This paper reports on a simplified method that has been developed to assign failure rates that can be used in reliability and risk studies of piping. The method can be applied on a line-by-line basis by identifying line and location specific attributes that can lead to piping unreliability from in-service degradation mechanisms and random events. A survey of service experience for nuclear piping reliability also was performed. The data from this survey provides a basis for identifying in-service failure attributes and assigning failure rates for risk and reliability studies

  2. Introduction lecture to magnetic resonance

    International Nuclear Information System (INIS)

    Conard, J.

    1980-01-01

    This lecture deals with all that is common either to electron paramagnetic resonance (E.P.R.) or to nuclear magnetic resonance (N.M.R.). It will present, in an as elementary form as possible, the main concepts used in magnetic resonance emphasizing some aspects, specific for interface science. (orig./BHO)

  3. Magnetic resonance fingerprinting.

    Science.gov (United States)

    Ma, Dan; Gulani, Vikas; Seiberlich, Nicole; Liu, Kecheng; Sunshine, Jeffrey L; Duerk, Jeffrey L; Griswold, Mark A

    2013-03-14

    Magnetic resonance is an exceptionally powerful and versatile measurement technique. The basic structure of a magnetic resonance experiment has remained largely unchanged for almost 50 years, being mainly restricted to the qualitative probing of only a limited set of the properties that can in principle be accessed by this technique. Here we introduce an approach to data acquisition, post-processing and visualization--which we term 'magnetic resonance fingerprinting' (MRF)--that permits the simultaneous non-invasive quantification of multiple important properties of a material or tissue. MRF thus provides an alternative way to quantitatively detect and analyse complex changes that can represent physical alterations of a substance or early indicators of disease. MRF can also be used to identify the presence of a specific target material or tissue, which will increase the sensitivity, specificity and speed of a magnetic resonance study, and potentially lead to new diagnostic testing methodologies. When paired with an appropriate pattern-recognition algorithm, MRF inherently suppresses measurement errors and can thus improve measurement accuracy.

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

    International Nuclear Information System (INIS)

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

    1989-01-01

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

  5. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  6. Exploring an ultracold Fermi-Fermi mixture: Interspecies Feshbach resonances and scattering properties of 6Li and 40K

    NARCIS (Netherlands)

    Wille, E.; Spiegelhalder, F.M.; Kerner, G.; Naik, D.; Trenkwalder, A.; Hendl, G.; Schreck, F.; Grimm, R.; Tiecke, T.G.; Walraven, J.T.M.; Kokkelmans, S.J.J.M.F.; Tiesinga, E.; Julienne, P.S.

    2008-01-01

    We report on the observation of Feshbach resonances in an ultracold mixture of two fermionic species, 6Li and 40K. The experimental data are interpreted using a simple asymptotic bound state model and full coupled channels calculations. This unambiguously assigns the observed resonances in terms of

  7. Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra

    Energy Technology Data Exchange (ETDEWEB)

    Tolic, Nikola; Liu, Yina; Liyu, Andrey V.; Shen, Yufeng; Tfaily, Malak M.; Kujawinski, Elizabeth B.; Longnecker, Krista; Kuo, Li-Jung; Robinson, Errol W.; Pasa Tolic, Ljiljana; Hess, Nancy J.

    2017-11-13

    Ultrahigh-resolution mass spectrometry, such as Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work we describe a user friendly interface for CIA, titled Formularity, which includes an additional functionality to perform search of formulas based on an Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. The HOC spike in NOM and tap water were used to assess HOC identification in natural and anthropogenic matrices. Strategies for reconciliation of CIA and IPA assignments are discussed. Software and sample databases with documentation are freely available from the PNNL OMICS software repository https://omics.pnl.gov/software/formularity.

  8. Electrothermal Frequency Modulated Resonator for Mechanical Memory

    KAUST Repository

    Hafiz, Md Abdullah Al

    2016-08-18

    In this paper, we experimentally demonstrate a mechanical memory device based on the nonlinear dynamics of an electrostatically actuated microelectromechanical resonator utilizing an electrothermal frequency modulation scheme. The microstructure is deliberately fabricated as an in-plane shallow arch to achieve geometric quadratic nonlinearity. We exploit this inherent nonlinearity of the arch and drive it at resonance with minimal actuation voltage into the nonlinear regime, thereby creating softening behavior, hysteresis, and coexistence of states. The hysteretic frequency band is controlled by the electrothermal actuation voltage. Binary values are assigned to the two allowed dynamical states on the hysteretic response curve of the arch resonator with respect to the electrothermal actuation voltage. Set-and-reset operations of the memory states are performed by applying controlled dc pulses provided through the electrothermal actuation scheme, while the read-out operation is performed simultaneously by measuring the motional current through a capacitive detection technique. This novel memory device has the advantages of operating at low voltages and under room temperature. [2016-0043

  9. Parent state swapping of resonances in electron-hydrogen molecule scattering

    International Nuclear Information System (INIS)

    Stibbe, D.T.

    1997-01-01

    Ab initio R-matrix scattering calculations are presented for electron-H 2 as a function of H 2 bond length. It is found that 2 Σ u + and 2Π u resonances in the 10 eV region appear to be associated with multiple 'parent' target states and that the resonances can swap parents as a function of internuclear separation. It is shown how these phenomena provide an explanation for the inconsistencies in previous assignments of resonances in this region and other anomalies such as pronounced isotopic effects. It is suggested that this parent swapping behaviour is likely to be a common feature of electron-impact excitation of other molecules and is particularly important for any models that include nuclear motion. (author)

  10. The phase-resolved photoacoustic method to indicate chemical assignments of paracetamol

    Science.gov (United States)

    Camilotti, J. G.; Somer, A.; Costa, G. F.; Ribeiro, M. A.; Bonardi, C.; Cruz, G. K.; Gómez, S. L.; Beltrame, F. L.; Medina, A. N.; Sato, F.; Astrath, N. G. C.; Novatski, A.

    2014-03-01

    In this work, the phase-resolved photoacoustic method was applied to provide specific information on the chemical assignments of paracetamol in the near-infrared region. Two broad bands, centered at 1370 and 1130 nm, were well-resolved using this method, making it possible to assign the peaks centered at 1398, 1355 and 1295 nm to a C-H combination from a CH3 structure and the peak at 1305 nm to a C-H combination from the aromatic ring. This information represents a new finding in chemical studies regarding this medicament.

  11. Wildlife forensic science: A review of genetic geographic origin assignment.

    Science.gov (United States)

    Ogden, Rob; Linacre, Adrian

    2015-09-01

    Wildlife forensic science has become a key means of enforcing legislation surrounding the illegal trade in protected and endangered species. A relatively new dimension to this area of forensic science is to determine the geographic origin of a seized sample. This review focuses on DNA testing, which relies on assignment of an unknown sample to its genetic population of origin. Key examples of this are the trade in timber, fish and ivory and these are used only to illustrate the large number of species for which this type of testing is potentially available. The role of mitochondrial and nuclear DNA markers is discussed, alongside a comparison of neutral markers with those exhibiting signatures of selection, which potentially offer much higher levels of assignment power to address specific questions. A review of assignment tests is presented along with detailed methods for evaluating error rates and considerations for marker selection. The availability and quality of reference data are of paramount importance to support assignment applications and ensure reliability of any conclusions drawn. The genetic methods discussed have been developed initially as investigative tools but comment is made regarding their use in courts. The potential to compliment DNA markers with elemental assays for greater assignment power is considered and finally recommendations are made for the future of this type of testing. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Machine-Specific Magnetic Resonance Imaging Quality Control Procedures for Stereotactic Radiosurgery Treatment Planning.

    Science.gov (United States)

    Fatemi, Ali; Taghizadeh, Somayeh; Yang, Claus Chunli; R Kanakamedala, Madhava; Morris, Bart; Vijayakumar, Srinivasan

    2017-12-18

    Purpose Magnetic resonance (MR) images are necessary for accurate contouring of intracranial targets, determination of gross target volume and evaluation of organs at risk during stereotactic radiosurgery (SRS) treatment planning procedures. Many centers use magnetic resonance imaging (MRI) simulators or regular diagnostic MRI machines for SRS treatment planning; while both types of machine require two stages of quality control (QC), both machine- and patient-specific, before use for SRS, no accepted guidelines for such QC currently exist. This article describes appropriate machine-specific QC procedures for SRS applications. Methods and materials We describe the adaptation of American College of Radiology (ACR)-recommended QC tests using an ACR MRI phantom for SRS treatment planning. In addition, commercial Quasar MRID 3D and Quasar GRID 3D phantoms were used to evaluate the effects of static magnetic field (B 0 ) inhomogeneity, gradient nonlinearity, and a Leksell G frame (SRS frame) and its accessories on geometrical distortion in MR images. Results QC procedures found in-plane distortions (Maximum = 3.5 mm, Mean = 0.91 mm, Standard deviation = 0.67 mm, >2.5 mm (%) = 2) in X-direction (Maximum = 2.51 mm, Mean = 0.52 mm, Standard deviation = 0.39 mm, > 2.5 mm (%) = 0) and in Y-direction (Maximum = 13. 1 mm , Mean = 2.38 mm, Standard deviation = 2.45 mm, > 2.5 mm (%) = 34) in Z-direction and < 1 mm distortion at a head-sized region of interest. MR images acquired using a Leksell G frame and localization devices showed a mean absolute deviation of 2.3 mm from isocenter. The results of modified ACR tests were all within recommended limits, and baseline measurements have been defined for regular weekly QC tests. Conclusions With appropriate QC procedures in place, it is possible to routinely obtain clinically useful MR images suitable for SRS treatment planning purposes. MRI examination for SRS planning can benefit from the improved localization and planning

  13. 1H HR-MAS NMR and S180 cells: metabolite assignment and evaluation of pulse sequence

    International Nuclear Information System (INIS)

    Oliveira, Aline L. de; Martinelli, Bruno César B.; Lião, Luciano M.; Pereira, Flávia C.; Silveira-Lacerda, Elisangela P.; Alcantara, Glaucia B.

    2014-01-01

    High resolution magic angle spinning 1 H nuclear magnetic resonance spectroscopy (HR-MAS NMR) is a useful technique for evaluation of intact cells and tissues. However, optimal NMR parameters are crucial in obtaining reliable results. To identify the key steps for the optimization of HR-MAS NMR parameters, we assessed different pulse sequences and NMR parameters using sarcoma 180 (S180) cells. A complete assignment of the metabolites of S180 is given to assist future studies. (author)

  14. Concentration of acrylamide in a polyacrylamide gel affects VP4 gene coding assignment of group A equine rotavirus strains with P[12] specificity

    Science.gov (United States)

    2010-01-01

    Background It is universally acknowledged that genome segment 4 of group A rotavirus, the major etiologic agent of severe diarrhea in infants and neonatal farm animals, encodes outer capsid neutralization and protective antigen VP4. Results To determine which genome segment of three group A equine rotavirus strains (H-2, FI-14 and FI-23) with P[12] specificity encodes the VP4, we analyzed dsRNAs of strains H-2, FI-14 and FI-23 as well as their reassortants by polyacrylamide gel electrophoresis (PAGE) at varying concentrations of acrylamide. The relative position of the VP4 gene of the three equine P[12] strains varied (either genome segment 3 or 4) depending upon the concentration of acrylamide. The VP4 gene bearing P[3], P[4], P[6], P[7], P[8] or P[18] specificity did not exhibit this phenomenon when the PAGE running conditions were varied. Conclusions The concentration of acrylamide in a PAGE gel affected VP4 gene coding assignment of equine rotavirus strains bearing P[12] specificity. PMID:20573245

  15. Using HL7 in hospital staff assignments.

    Science.gov (United States)

    Unluturk, Mehmet S

    2014-02-01

    Hospital staff assignments are the instructions that allocate the hospital staff members to the hospital beds. Currently, hospital administrators make the assignments without accessing the information regarding the occupancy of the hospital beds and the acuity of the patient. As a result, administrators cannot distinguish between occupied and unoccupied beds, and may therefore assign staff to unoccupied beds. This gives rise to uneven and inefficient staff assignments. In this paper, the hospital admission-discharge-transfer (ADT) system is employed both as a data source and an assignment device to create staff assignments. When the patient data is newly added or modified, the ADT system updates the assignment software client with the relevant data. Based on the relevant data, the assignment software client is able to construct staff assignments in a more efficient way. © 2013 Elsevier Ltd. All rights reserved.

  16. Resonance Raman and quantum chemical studies of short polyene radical cations

    DEFF Research Database (Denmark)

    Keszthelyi, T.; Wilbrandt, R.; Bally, T.

    1997-01-01

    ,3,5-hexatriene have been studied. The radical cations were generated radiolytically in a glassy Freon matrix and investigated by optical absorption and resonance Raman spectroscopy. Ab initio and density functional molecular-orbital calculations have been carried out to predict equilibrium structures...... and to assist assignment of the resonance Raman spectra. A new and improved scaled quantum mechanical force field for the butadiene radical cation was also determined. The presence of more than one rotamer was observed in all the polyene radical cations we investigated. (C) 1997 Elsevier Science B.V....

  17. Application of a Dynamic Programming Algorithm for Weapon Target Assignment

    Science.gov (United States)

    2016-02-01

    evaluation and weapon assignment in maritime combat scenarios. Lloyd also acts as a liaison for the Weapons and Combat Systems Division with the ANZAC...positively identified a number of targets as threats, whether they are an enemy ship (i.e., specifically, its weapon launcher systems) or a directed

  18. Evaluation and analysis of nuclear resonance data

    International Nuclear Information System (INIS)

    Frohner, F.H.

    2000-01-01

    A probabilistic foundations of data evaluation are reviewed, with special emphasis on parameter estimation based on Bayes' theorem and a quadratic loss function, and on modern methods for the assignment of prior probabilities. The data reduction process leading from raw experimental data to evaluated computer files of nuclear reaction cross sections is outlined, with a discussion of systematic and statistical errors and their propagation and of the generalized least squares formalism including prior information and nonlinear theoretical models. It is explained how common errors induce correlations between data, what consequences they have for uncertainty propagation and sensitivity studies, and how evaluators can construct covariance matrices from the usual error information provided by experimentalists. New techniques for evaluation of inconsistent data are also presented. The general principles are then applied specifically to the analysis and evaluation of neutron resonance data in terms of theoretical models - R-matrix theory (and especially its practically used multi-level Breit-Wigner and Reich-Moore variants) in the resolved region, and resonance-averaged R-matrix theory (Hauser-Feshbach theory with width-fluctuation corrections) in the unresolved region. Complications arise because the measured transmission data, capture and fission yields, self-indication ratios and other observables are not yet the wanted cross sections. These are obtained only by means of parametrisation. The intervening effects - Doppler and resolution broadening, self-shielding, multiple scattering, backgrounds, sample impurities, energy-dependent detector efficiencies, inaccurate reference data etc - are therefore also discussed. (author)

  19. Optic Tract Edema: A Highly Specific Magnetic Resonance Imaging Finding for the Diagnosis of Craniopharyngiomas

    International Nuclear Information System (INIS)

    Hirunpat, S.; Tanomkiat, W.; Sriprung, H.; Chetpaophan, J.

    2005-01-01

    Purpose: To clarify the accuracy, sensitivity, and specificity of optic tract edema in the diagnosis of craniopharyngiomas. Material and Methods: Preoperative magnetic resonance images (MRIs) of 49 patients (between May 1996 and March 2003) who had a diagnosis of parasellar masses were blindly reviewed by two radiologists. The spread of edema surrounding the tumor on the coronal TSE T2-weighted images was analyzed. Sensitivity and specificity were calculated based on the numbers in this series and also pooled numbers from previous known reported series. Results: Edema along the optic tracts was detected in 7 of 1 craniopharyngiomas, giving a sensitivity of 63.6% (95% CI≅30.8-89.1) for our series and 66.7% (95% CI≅47.2-82.7) for the pooled numbers. The specificity was 00% (95% CI≅90.7-100.0) for our series and 93.9% (95% CI≅87.1-97.7) for the pooled numbers. None of the 28 pituitary macroadenomas, 4 meningiomas, 2 hypothalamic astrocytomas, 2 germinomas, mixed-germ cell tumor and arachnoid cyst in our study showed edema of the optic pathways. Conclusion: Optic tract edema, commonly seen in craniopharyngiomas, is a useful MR finding for distinguishing craniopharyngiomas from other parasellar tumors with considerable sensitivity and high specificity

  20. Optic Tract Edema: A Highly Specific Magnetic Resonance Imaging Finding for the Diagnosis of Craniopharyngiomas

    Energy Technology Data Exchange (ETDEWEB)

    Hirunpat, S.; Tanomkiat, W.; Sriprung, H.; Chetpaophan, J. [Prince of Songkla Univ., Hat Yai (Thailand). Dept. of Radiology and Epidemiology Unit

    2005-07-01

    Purpose: To clarify the accuracy, sensitivity, and specificity of optic tract edema in the diagnosis of craniopharyngiomas. Material and Methods: Preoperative magnetic resonance images (MRIs) of 49 patients (between May 1996 and March 2003) who had a diagnosis of parasellar masses were blindly reviewed by two radiologists. The spread of edema surrounding the tumor on the coronal TSE T2-weighted images was analyzed. Sensitivity and specificity were calculated based on the numbers in this series and also pooled numbers from previous known reported series. Results: Edema along the optic tracts was detected in 7 of 1 craniopharyngiomas, giving a sensitivity of 63.6% (95% CI{approx_equal}30.8-89.1) for our series and 66.7% (95% CI{approx_equal}47.2-82.7) for the pooled numbers. The specificity was 00% (95% CI{approx_equal}90.7-100.0) for our series and 93.9% (95% CI{approx_equal}87.1-97.7) for the pooled numbers. None of the 28 pituitary macroadenomas, 4 meningiomas, 2 hypothalamic astrocytomas, 2 germinomas, mixed-germ cell tumor and arachnoid cyst in our study showed edema of the optic pathways. Conclusion: Optic tract edema, commonly seen in craniopharyngiomas, is a useful MR finding for distinguishing craniopharyngiomas from other parasellar tumors with considerable sensitivity and high specificity.

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

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  2. Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts.

    Science.gov (United States)

    He, Zhe; Perl, Yehoshua; Elhanan, Gai; Chen, Yan; Geller, James; Bian, Jiang

    2017-11-01

    The Unified Medical Language System (UMLS) is an important terminological system. By the policy of its curators, each concept of the UMLS should be assigned the most specific Semantic Types (STs) in the UMLS Semantic Network (SN). Hence, the Semantic Types of most UMLS concepts are assigned at or near the bottom (leaves) of the UMLS Semantic Network. While most ST assignments are correct, some errors do occur. Therefore, Quality Assurance efforts of UMLS curators for ST assignments should concentrate on automatically detected sets of UMLS concepts with higher error rates than random sets. In this paper, we investigate the assignments of top-level semantic types in the UMLS semantic network to concepts, identify potential erroneous assignments, define four categories of errors, and thus provide assistance to curators of the UMLS to avoid these assignments errors. Human experts analyzed samples of concepts assigned 10 of the top-level semantic types and categorized the erroneous ST assignments into these four logical categories. Two thirds of the concepts assigned these 10 top-level semantic types are erroneous. Our results demonstrate that reviewing top-level semantic type assignments to concepts provides an effective way for UMLS quality assurance, comparing to reviewing a random selection of semantic type assignments.

  3. New Crystal Ball data on resonance formation by γγ-collisions

    International Nuclear Information System (INIS)

    Bienlein, J.K.

    1992-01-01

    The Crystal Ball detector at DORIS-II has observed a hitherto unknown (though expected) resonance at 1870 MeV/c 2 in the reaction γγ → ηπ o π o . Decay angular distributions and subsystem invariant masses favor the assignment η 2 (1870), a J PC = 2 -+ resonance. An efficient selection of the reaction γγ → π o π o yielded 7000 events. Angular distributions in narrow mass bins became possible and allowed the decomposition of the cross section into S- and D-wave contributions. Thus an f 0 (1250) resonance was found under the dominating f 2 (1270). The search for the channel γγ →ηη in the same selection yielded only (16 ± 6) events. (orig.)

  4. {sup 1}H HR-MAS NMR and S180 cells: metabolite assignment and evaluation of pulse sequence

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Aline L. de; Martinelli, Bruno César B.; Lião, Luciano M. [Universidade Federal de Goiás (UFG), Goiânia, GO (Brazil). Instituto de Química. Lab. de RMN; Pereira, Flávia C.; Silveira-Lacerda, Elisangela P. [Universidade Federal de Goiás (UFG), Goiânia, GO (Brazil). Instituto de Ciências Biológicas. Laboratório Genética Molecular e Citogenética; Alcantara, Glaucia B., E-mail: glaucia.alcantara@ufms.br [Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, MS (Brazil). Inst. de Química

    2014-07-01

    High resolution magic angle spinning {sup 1}H nuclear magnetic resonance spectroscopy (HR-MAS NMR) is a useful technique for evaluation of intact cells and tissues. However, optimal NMR parameters are crucial in obtaining reliable results. To identify the key steps for the optimization of HR-MAS NMR parameters, we assessed different pulse sequences and NMR parameters using sarcoma 180 (S180) cells. A complete assignment of the metabolites of S180 is given to assist future studies. (author)

  5. Complete NMR assignment of a bisecting hybrid-type oligosaccharide transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase.

    Science.gov (United States)

    Yamanoi, Takashi; Oda, Yoshiki; Katsuraya, Kaname; Inazu, Toshiyuki; Yamamoto, Kenji

    2016-06-02

    This study describes the complete nuclear magnetic resonance (NMR) spectral assignment of a bisecting hybrid-type oligosaccharide 1, transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase (Endo-M). Through (1)H- and (13)C-NMR, DQF-COSY, HSQC, HMBC, TOCSY, and NOESY experiments, we determine the structure of the glycoside linkage formed by the Endo-M transglycosylation, i.e., the connection between GlcNAc and GlcNAc in oligosaccharide 1. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. A note on ranking assignments using reoptimization

    DEFF Research Database (Denmark)

    Pedersen, Christian Roed; Nielsen, L.R.; Andersen, K.A.

    2005-01-01

    We consider the problem of ranking assignments according to cost in the classical linear assignment problem. An algorithm partitioning the set of possible assignments, as suggested by Murty, is presented where, for each partition, the optimal assignment is calculated using a new reoptimization...

  7. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-01-15

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

  9. Real life working shift assignment problem

    Science.gov (United States)

    Sze, San-Nah; Kwek, Yeek-Ling; Tiong, Wei-King; Chiew, Kang-Leng

    2017-07-01

    This study concerns about the working shift assignment in an outlet of Supermarket X in Eastern Mall, Kuching. The working shift assignment needs to be solved at least once in every month. Current approval process of working shifts is too troublesome and time-consuming. Furthermore, the management staff cannot have an overview of manpower and working shift schedule. Thus, the aim of this study is to develop working shift assignment simulation and propose a working shift assignment solution. The main objective for this study is to fulfill manpower demand at minimum operation cost. Besides, the day off and meal break policy should be fulfilled accordingly. Demand based heuristic is proposed to assign working shift and the quality of the solution is evaluated by using the real data.

  10. 24 CFR 221.770 - Assignment option.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Assignment option. 221.770 Section... § 221.770 Assignment option. A mortgagee holding a conditional or firm commitment issued on or before... mortgagee's approved underwriter on or before November 30, 1983) has the option to assign, transfer and...

  11. Parametric resonance in neutrino oscillations in matter

    Indian Academy of Sciences (India)

    Neutrino oscillations in matter can exhibit a specific resonance enhancement - parametric resonance, which is different from the MSW resonance. Oscillations of atmospheric and solar neutrinos inside the earth can undergo parametric enhancement when neutrino trajectories cross the core of the earth. In this paper we ...

  12. Geometrical optics model of Mie resonances

    Science.gov (United States)

    Roll; Schweiger

    2000-07-01

    The geometrical optics model of Mie resonances is presented. The ray path geometry is given and the resonance condition is discussed with special emphasis on the phase shift that the rays undergo at the surface of the dielectric sphere. On the basis of this model, approximate expressions for the positions of first-order resonances are given. Formulas for the cavity mode spacing are rederived in a simple manner. It is shown that the resonance linewidth can be calculated regarding the cavity losses. Formulas for the mode density of Mie resonances are given that account for the different width of resonances and thus may be adapted to specific experimental situations.

  13. Job Assignments under Moral Hazard

    DEFF Research Database (Denmark)

    Koch, Alexander; Nafziger, Julia

    Inefficient job assignments are usually explained with incomplete information about employees' abilities or contractual imperfections. We show that inefficient assignments arise even without uncertainty about the employee's ability and with complete contracts. Building on this result we provide...

  14. 24 CFR 221.255 - Assignment option.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Assignment option. 221.255 Section... Assignment option. (a) A mortgagee holding a mortgage insured pursuant to a conditional or firm commitment issued on or before November 30, 1983 has the option to assign, transfer and deliver to the Commissioner...

  15. Midwifery students' evaluation of team-based academic assignments involving peer-marking.

    Science.gov (United States)

    Parratt, Jenny A; Fahy, Kathleen M; Hastie, Carolyn R

    2014-03-01

    Midwives should be skilled team workers in maternity units and in group practices. Poor teamwork skills are a significant cause of adverse maternity care outcomes. Despite Australian and International regulatory requirements that all midwifery graduates are competent in teamwork, the systematic teaching and assessment of teamwork skills is lacking in higher education. How do midwifery students evaluate participation in team-based academic assignments, which include giving and receiving peer feedback? First and third year Bachelor of Midwifery students who volunteered (24 of 56 students). Participatory Action Research with data collection via anonymous online surveys. There was general agreement that team based assignments; (i) should have peer-marking, (ii) help clarify what is meant by teamwork, (iii) develop communication skills, (iv) promote student-to-student learning. Third year students strongly agreed that teams: (i) are valuable preparation for teamwork in practice, (ii) help meet Australian midwifery competency 8, and (iii) were enjoyable. The majority of third year students agreed with statements that their teams were effectively coordinated and team members shared responsibility for work equally; first year students strongly disagreed with these statements. Students' qualitative comments substantiated and expanded on these findings. The majority of students valued teacher feedback on well-developed drafts of the team's assignment prior to marking. Based on these findings we changed practice and created more clearly structured team-based assignments with specific marking criteria. We are developing supporting lessons to teach specific teamwork skills: together these resources are called "TeamUP". TeamUP should be implemented in all pre-registration Midwifery courses to foster students' teamwork skills and readiness for practice. Copyright © 2013 Australian College of Midwives. Published by Elsevier Ltd. All rights reserved.

  16. An algorithm for ranking assignments using reoptimization

    DEFF Research Database (Denmark)

    Pedersen, Christian Roed; Nielsen, Lars Relund; Andersen, Kim Allan

    2008-01-01

    We consider the problem of ranking assignments according to cost in the classical linear assignment problem. An algorithm partitioning the set of possible assignments, as suggested by Murty, is presented where, for each partition, the optimal assignment is calculated using a new reoptimization...... technique. Computational results for the new algorithm are presented...

  17. 48 CFR 42.602 - Assignment and location.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Assignment and location... Assignment and location. (a) A CACO may be assigned only when (1) the contractor has at least two locations..., or a full-time CACO may be assigned. In determining the location of the CACO, the responsible agency...

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  19. Calculation and measurement of radiation corrections for plasmon resonances in nanoparticles

    Science.gov (United States)

    Hung, L.; Lee, S. Y.; McGovern, O.; Rabin, O.; Mayergoyz, I.

    2013-08-01

    The problem of plasmon resonances in metallic nanoparticles can be formulated as an eigenvalue problem under the condition that the wavelengths of the incident radiation are much larger than the particle dimensions. As the nanoparticle size increases, the quasistatic condition is no longer valid. For this reason, the accuracy of the electrostatic approximation may be compromised and appropriate radiation corrections for the calculation of resonance permittivities and resonance wavelengths are needed. In this paper, we present the radiation corrections in the framework of the eigenvalue method for plasmon mode analysis and demonstrate that the computational results accurately match analytical solutions (for nanospheres) and experimental data (for nanorings and nanocubes). We also demonstrate that the optical spectra of silver nanocube suspensions can be fully assigned to dipole-type resonance modes when radiation corrections are introduced. Finally, our method is used to predict the resonance wavelengths for face-to-face silver nanocube dimers on glass substrates. These results may be useful for the indirect measurements of the gaps in the dimers from extinction cross-section observations.

  20. Prediction and Assignment of Function for a Divergent N-succinyl Amino Acid Racemase

    Energy Technology Data Exchange (ETDEWEB)

    Song,L.; Kalyanaraman, C.; Fedorov, A.; Fedorov, E.; Glasner, M.; Brown, S.; Imker, H.; Babbitt, P.; Almo, S.; et al.

    2007-01-01

    The protein databases contain many proteins with unknown function. A computational approach for predicting ligand specificity that requires only the sequence of the unknown protein would be valuable for directing experiment-based assignment of function. We focused on a family of unknown proteins in the mechanistically diverse enolase superfamily and used two approaches to assign function: (i) enzymatic assays using libraries of potential substrates, and (ii) in silico docking of the same libraries using a homology model based on the most similar (35% sequence identity) characterized protein. The results matched closely; an experimentally determined structure confirmed the predicted structure of the substrate-liganded complex. We assigned the N-succinyl arginine/lysine racemase function to the family, correcting the annotation (L-Ala-D/L-Glu epimerase) based on the function of the most similar characterized homolog. These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested.

  1. Resonance search on πN reaction

    International Nuclear Information System (INIS)

    Sugahara, Ryuhei

    1974-01-01

    Present status of the study on resonance state is reviewed. Among various problems on the resonance state, the inelastic decay of baryon resonance and boson resonance are described in this paper. Experimental data on N → N eta with bubble chambers are few. An experimental results by using a counter shows enhancement around 1.8 GeV in the relation between cross section and energy. Some bubble chamber experiment also shows enhancement around 1.6 GeV. The spin and parity analyses for 1000 events are required. Data on N → Nω show enhancement at 1.76 GeV. The effective mass distribution on N → delta ++ (1236)π + π - shows enhancement around 2.0 GeV. Study on the boson resonance has been made, but still ambiguity remains. Effective mass distribution on the reaction π + d → pspπ + π - π 0 shows a peak of ω 1664 . The assignment of spin and parity by Matthews et al. is not in agreement with that by Kenyon et al. therefore confirmation by other experiment is necessary. A few experiment show peaks at 1.4 and 1.7 GeV in the effective mass distribution of (rho 0 rho 0 ) in the reaction anti pp → 3π + π - . Confirmation is also required. Deviation was found in the effective mass distribution of (ωπ + π - ) in anti pp → 3π + π - π 0 reaction, and ωπ + π - decay was seen in π + d → psp2π + 2π - π 0 reaction. (Kato, T.)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-01

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

  3. Single-particle resonance levels in {sup 14}O examined by N13+p elastic resonance scattering

    Energy Technology Data Exchange (ETDEWEB)

    Teranishi, T. [Dept. of Physics, Kyushu Univ., 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581 (Japan)]. E-mail: teranishi@nucl.phys.kyushu-u.ac.jp; Kubono, S. [Center for Nuclear Study (CNS), Univ. of Tokyo, Wako Branch at RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Yamaguchi, H. [Center for Nuclear Study (CNS), Univ. of Tokyo, Wako Branch at RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); He, J.J. [Center for Nuclear Study (CNS), Univ. of Tokyo, Wako Branch at RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Saito, A. [Center for Nuclear Study (CNS), Univ. of Tokyo, Wako Branch at RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Fujikawa, H. [Center for Nuclear Study (CNS), Univ. of Tokyo, Wako Branch at RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Amadio, G. [Center for Nuclear Study (CNS), Univ. of Tokyo, Wako Branch at RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Niikura, M.; Shimoura, S. [Center for Nuclear Study (CNS), Univ. of Tokyo, Wako Branch at RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Wakabayashi, Y. [Dept. of Physics, Kyushu Univ., 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581 (Japan)]|[Center for Nuclear Study (CNS), Univ. of Tokyo, Wako Branch at RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Nishimura, S.; Nishimura, M. [RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Moon, J.Y.; Lee, C.S. [Dept. of Physics, Chung-Ang Univ., Seoul 156-756 (Korea, Republic of); Odahara, A. [Nishinippon Inst. of Technology, Kanda, Fukuoka 800-0394 (Japan); Sohler, D. [Inst. of Nuclear Research (ATOMKI), H-4001 Debrecen, P.O. Box 51 (Hungary); Khiem, L.H. [Inst. of Physics and Electronics (IOP), Vietnamese Academy for Science and Technology (VAST), 10 Daotan, Congvi, Badinh, P.O. Box 429-BOHO, Hanoi 10000 (Viet Nam); Li, Z.H.; Lian, G.; Liu, W.P. [China Inst. of Atomic Energy, P.O. Box 275(46), Beijing 102413 (China)

    2007-06-28

    Single-particle properties of low-lying resonance levels in {sup 14}O have been studied efficiently by utilizing a technique of proton elastic resonance scattering with a {sup 13}N secondary beam and a thick proton target. The excitation functions for the N13+p elastic scattering were measured over a wide energy range of E{sub CM}=0.4-3.3 MeV and fitted with an R-matrix calculation. A clear assignment of J{sup {pi}}=2{sup -} has been made for the level at E{sub x}=6.767(11) MeV in {sup 14}O for the first time. The excitation functions show a signature of a new 0{sup -} level at E{sub x}=5.71(2) MeV with {gamma}=400(100) keV. The excitation energies and widths of the {sup 14}O levels are discussed in conjunction with the spectroscopic structure of A=14 nuclei with T=1.

  4. Exogenous spatial attention influences figure-ground assignment.

    Science.gov (United States)

    Vecera, Shaun P; Flevaris, Anastasia V; Filapek, Joseph C

    2004-01-01

    In a hierarchical stage account of vision, figure-ground assignment is thought to be completed before the operation of focal spatial attention. Results of previous studies have supported this account by showing that unpredictive, exogenous spatial precues do not influence figure-ground assignment, although voluntary attention can influence figure-ground assignment. However, in these studies, attention was not summoned directly to a region in a figure-ground display. In three experiments, we addressed the relationship between figure-ground assignment and visuospatial attention. In Experiment 1, we replicated the finding that exogenous precues do not influence figure-ground assignment when they direct attention outside of a figure-ground stimulus. In Experiment 2, we demonstrated that exogenous attention can influence figure-ground assignment if it is directed to one of the regions in a figure-ground stimulus. In Experiment 3, we demonstrated that exogenous attention can influence figure-ground assignment in displays that contain a Gestalt figure-ground cue; this result suggests that figure-ground processes are not entirely completed prior to the operation of focal spatial attention. Exogenous spatial attention acts as a cue for figure-ground assignment and can affect the outcome of figure-ground processes.

  5. Chiral effects on the 13C resonances of α-tocopherol and related compounds. A novel illustration of Newman's rule of six

    International Nuclear Information System (INIS)

    Brownstein, S.; Burton, G.W.; Hughes, L.; Ingold, K.U.

    1989-01-01

    The 100-MHz 13 C NMR spectrum of (2R,4'R,8'R)-α-tocopherol (natural vitamin E) has been completely assigned with the aid of a number of selectively deuteriated (2R,4'R,8'R)-α-tocopherols. The 13 C NMR spectrum of (2RS,4'RS,8'RS)-α-tocopherol (all-racemic, synthetic vitamin E) has also been measured. Many of the individual carbons in this all-racemic mixture of eight α-tocopherol stereoisomers give more than one resonance with eight of the carbons (2-CH 3 , 2',3',4',4'-CH 3 , 5', 8', and 9') giving the maximum number of four resonances from each of the four enantiomeric pairs; these resonances have also been assigned. The structurally related 5'-hydroxy-2-(4',8',12'-trimethyltridecyl)-2,4,6,7-tetramethyl-2,3,-dihydrobenzofuran (HTDBF) has been synthesized for the first time in the 2R,4'R,8'R and 2S,4'R,8'R configurations and their 13 C resonances have been assigned. In its all-racemic form this compound also shows up to four resonances from a single carbon. Related observations have been made with phytol and isophytol. A careful examination of these chirally induced chemical shift differences for the individual carbon atoms, Δ, reveals a bond-alternation effect with maxima at a separation of one, three, and five bonds from the closest chiral center and with the maximum at a five-bond separation being greater than that at a three-bond separation. 32 references, 2 figures, 4 tables

  6. Statistical decay of the E1 giant resonance

    International Nuclear Information System (INIS)

    Teruya, N.; Dias, H.; Wolynec, E.

    1987-10-01

    Available esperimental data on neutron decay spectra from the E1 giant resonances in 208 Pb and 209 Bi are compared with the predicted spectra for statistical decay. The calculations are performed using the Hauser-Feshbach formalism with the experimental levels of the residual nuclei. The particle-vibrator model is used to assign spins and parities to experimental levels when those are unknown and also to predict the levels where there is not enough experimental information. (author) [pt

  7. Information on co-morbidities collected by history is useful for assigning Otitis Media risk to children.

    Science.gov (United States)

    Casselbrant, Margaretha L; Mandel, Ellen M; Doyle, William J

    2016-06-01

    Determine if a 2-Step multivariate analysis of historical symptom/sign data for comorbid diseases can abstract high-level constructs useful in assigning a child's "risk" for different Otitis Media expressions. Seventeen items related to the symptom/sign expression of hypothesized Otitis Media comorbidities were collected by history on 141 3-year-old children. Using established criteria, the children were assigned to 1 of 3 groups: Control (no significant past Otitis Media, n=45), Chronic Otitis Media with Effusion (n=45) and Recurrent Acute Otitis Media (n=51). Principal Component Analysis was used to identify factors representing the non-redundant shared information among related items and Discriminant Analysis operating on those factors was used to estimate the best predictor equation for pairwise group assignments. Six multivariate factors representing the assignable comorbidities of frequent colds, nasal allergy, gastroesophageal disease (specific and general), nasal congestion and asthma were identified and explained 81% of the variance in the 17 items. Discriminant Analysis showed that, for the Control-Chronic Otitis Media with Effusion comparison, a combination of 3 factors and, for the Control-Recurrent Acute Otitis Media comparison, a combination of 2 factors had assignment accuracies of 74% and 68%, respectively. For the contrast between the two disease expressions, a 2-factor combination had an assignment accuracy of 61%. These results show that this analytic methodology can abstract high-level constructs, comorbidities, from low-level data, symptom/sign scores, support a linkage between certain comorbidities and Otitis Media risk and suggest that specific comorbidity combinations contain information relevant to assigning the risk for different Otitis Media expressions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. Nonlinear resonance ultrasonic vibrations in Czochralski-silicon wafers

    Science.gov (United States)

    Ostapenko, S.; Tarasov, I.

    2000-04-01

    A resonance effect of generation of subharmonic acoustic vibrations is observed in as-grown, oxidized, and epitaxial silicon wafers. Ultrasonic vibrations were generated into a standard 200 mm Czochralski-silicon (Cz-Si) wafer using a circular ultrasound transducer with major frequency of the radial vibrations at about 26 kHz. By tuning frequency (f) of the transducer within a resonance curve, we observed a generation of intense f/2 subharmonic acoustic mode assigned as a "whistle." The whistle mode has a threshold amplitude behavior and narrow frequency band. The whistle is attributed to a nonlinear acoustic vibration of a silicon plate. It is demonstrated that characteristics of the whistle mode are sensitive to internal stress and can be used for quality control and in-line diagnostics of oxidized and epitaxial Cz-Si wafers.

  9. New results on exotic baryon resonances at LHCb

    CERN Document Server

    Zhang, Liming

    2016-01-01

    Observation of exotic resonant structures decaying into $J/\\psi p$ found in the LHCb experiment is discussed. Examination of the $J/\\psi p$ system in $\\Lambda^{0}_{b} \\to J/\\psi K^{-} p$ decays shows two states, each of which must be composed of at least $c \\bar{c} uud$ quarks, and are thus consistent with pentaquarks. The significance of each of these resonances is more than 9 standard deviations. Their masses are ($4 380 \\pm 8 \\pm 29$) MeV and ($4 449.8 \\pm 1.7 \\pm 2.5$) MeV, and their corresponding widths are ($205 \\pm 18 \\pm 86$) MeV, and ($39 \\pm 5 \\pm 19$) MeV. The preferred $J^{P}$ assignments are of opposite parity, with one state having spin 3/2 and the other 5/2.

  10. Laser-polarized xenon-129 magnetic resonance spectroscopy and imaging. The development of a method for in vivo perfusion measurement

    Science.gov (United States)

    Rosen, Matthew Scot

    2001-07-01

    This thesis presents in vivo nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) studies with laser-polarized 129Xe delivered to living rats by inhalation and transported to tissue via blood flow. The results presented herein include the observation, assignment, and dynamic measurement of 129Xe resonances in the brain and body, the first one- and two-dimensional chemical-shift-resolved images of 129Xe in blood, tissue, and gas in the thorax, and the first images of 129Xe in brain tissue. These results establish that laser-polarized 129Xe can be used as a magnetic resonance tracer in vivo. NMR resonances at 0, 191, 198, and 209 ppm relative to the 129 Xe gas resonance are observed in the rat thorax and assigned to 129Xe in gas, fat, tissue, and blood respectively. Resonances at 189, 192, 195, 198, and 209 ppm are observed in the brain, and the 195 and 209 ppm resonances are assigned to 129Xe in grey matter, and blood, respectively. The design and construction of a laser-polarized 129Xe production and delivery system is described. This system produces liter-volumes of laser- polarized 129Xe by spin-exchange optical- pumping. It represented an order of magnitude increase over previously reported production volumes of polarized 129Xe. At approximately 3-7% polarization, 157 cc-atm of xenon is produced and stored as ice every 5 minutes. This reliable, effective, and simple production method for large volumes of 129Xe can be applied to other areas of research involving the use of laser-polarized noble gases. A model of the in vivo transport of laser polarized 129Xe to tissue under realistic experimental NMR conditions is described. Appropriate control of the NMR parameters is shown to allow tissue perfasion and 129Xe tissue T1 to be extracted from measurement of the steady-state 129Xe tissue signal. In vivo rodent 129Xe NMR results are used to estimate the signal-to-noise ratio of this technique, and an inhaled 30% xenon/70% O2 mixture polarized to 5

  11. A sex-specific metabolite identified in a marine invertebrate utilizing phosphorus-31 nuclear magnetic resonance.

    Directory of Open Access Journals (Sweden)

    Robert A Kleps

    Full Text Available Hormone level differences are generally accepted as the primary cause for sexual dimorphism in animal and human development. Levels of low molecular weight metabolites also differ between men and women in circulating amino acids, lipids and carbohydrates and within brain tissue. While investigating the metabolism of blue crab tissues using Phosphorus-31 Nuclear Magnetic Resonance, we discovered that only the male blue crab (Callinectes sapidus contained a phosphorus compound with a chemical shift well separated from the expected phosphate compounds. Spectra obtained from male gills were readily differentiated from female gill spectra. Analysis from six years of data from male and female crabs documented that the sex-specificity of this metabolite was normal for this species. Microscopic analysis of male and female gills found no differences in their gill anatomy or the presence of parasites or bacteria that might produce this phosphorus compound. Analysis of a rare gynandromorph blue crab (laterally, half male and half female proved that this sex-specificity was an intrinsic biochemical process and was not caused by any variations in the diet or habitat of male versus female crabs. The existence of a sex-specific metabolite is a previously unrecognized, but potentially significant biochemical phenomenon. An entire enzyme system has been synthesized and activated only in one sex. Unless blue crabs are a unique species, sex-specific metabolites are likely to be present in other animals. Would the presence or absence of a sex-specific metabolite affect an animal's development, anatomy and biochemistry?

  12. WebAssign: Assessing Your Students' Understanding Continuously

    Science.gov (United States)

    Risley, John S.

    1999-11-01

    Motivating students to learn is a constant challenge for faculty. Technology can play a significant role. One such solution is WebAssign — a web-based homework system that offers new teaching and learning opportunities for educators and their students. WebAssign delivers, collects, grades, and records customized homework assignments over the Internet. Students get immediate feedback with credit and instructors can implement "Just-in-Time" teaching. In this talk, I will describe how assignments can be generated with different numerical values for each question, giving each student a unique problem to solve. This feature encourages independent thinking with the benefit of collaborative learning. Example assignments taken from textbook questions and intellectually engaging Java applet simulations will be shown. Studies and first-hand experience on the educational impact of using WebAssign will also be discussed.

  13. Coulomb and nuclear excitations of narrow resonances in 17Ne

    Directory of Open Access Journals (Sweden)

    J. Marganiec

    2016-08-01

    Full Text Available New experimental data for dissociation of relativistic 17Ne projectiles incident on targets of lead, carbon, and polyethylene targets at GSI are presented. Special attention is paid to the excitation and decay of narrow resonant states in 17Ne. Distributions of internal energy in the O15+p+p three-body system have been determined together with angular and partial-energy correlations between the decay products in different energy regions. The analysis was done using existing experimental data on 17Ne and its mirror nucleus 17N. The isobaric multiplet mass equation is used for assignment of observed resonances and their spins and parities. A combination of data from the heavy and light targets yielded cross sections and transition probabilities for the Coulomb excitations of the narrow resonant states. The resulting transition probabilities provide information relevant for a better understanding of the 17Ne structure.

  14. On the resonant behavior of the 16O + 15N reaction

    International Nuclear Information System (INIS)

    Aissaoui, N.; Haas, F.; Freeman, R.M.; Beck, C.; Morsad, A.; Djerroud, B.; Caplar, R.; Monnehan, G.A.; Hachem, A.; Youlal, M.

    1994-01-01

    The 16 O+ 15 N reaction products have been studied by the γ-ray detection method in the CM energy range 15.5 to 36.1 MeV and by the kinematical coincidence method at energies ranging from E CM =20.6 to 33.5 MeV. The γ-ray yield excitation function of the 16 O 3 - inelastic channel shows the existence of resonant structures. Two structures with ∼1.6 MeV width are observed in the large angle elastic, scattering excitation function, they are correlated with the resonances seen in the inelastic channel. Angular momentum assignments were made from the elastic backward angular distributions. (orig.)

  15. Sector-specific human capital and the distribution of earnings

    OpenAIRE

    Eric Smith

    2009-01-01

    This paper incorporates assignment frictions and sector-specific training into the Roy model of occupational choice. Assignment frictions represent the extent of the market whereas differences in sector-specific training reflect worker specialization. This framework thus captures Adam Smith's idea that the extent of the market determines the division of labor. The paper demonstrates the way in which the relationship between assignment frictions and specialization affects the level and composi...

  16. Resonance-enhanced multiphoton ionization photoelectron spectroscopy of even-parity autoionizing Rydberg states of atomic sulphur

    NARCIS (Netherlands)

    Woutersen, S.; de Milan, J.B.; de Lange, C.A.; Buma, W.J.

    1997-01-01

    Several previously unobserved Rydberg states of the sulphur atom above the lowest ionization threshold are identified and assigned using (2 + 1) resonance-enhanced multiphoton-ionization photoelectron spectroscopy. All states were accessed by two-photon transitions from either the 3P ground or the

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

    International Nuclear Information System (INIS)

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

    1987-01-01

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

  18. Solving the rectangular assignment problem and applications

    NARCIS (Netherlands)

    Bijsterbosch, J.; Volgenant, A.

    2010-01-01

    The rectangular assignment problem is a generalization of the linear assignment problem (LAP): one wants to assign a number of persons to a smaller number of jobs, minimizing the total corresponding costs. Applications are, e.g., in the fields of object recognition and scheduling. Further, we show

  19. 7 CFR 900.106 - Assignment of mediator.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Assignment of mediator. 900.106 Section 900.106 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing... Assignment of mediator. The Director of the Division shall assign a mediator, from the group designated by...

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

    Science.gov (United States)

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

    2011-11-01

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

  1. My Favorite Assignment.

    Science.gov (United States)

    ABCA Bulletin, 1983

    1983-01-01

    Describes three assignments for enticing business communication students to undertake library research: an analysis of a Fortune 500 company, a career choice report, and a report on an organization that offers potential employment. (AEA)

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

    International Nuclear Information System (INIS)

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

    1997-01-01

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

  3. Resonance ionization scheme development for europium

    Energy Technology Data Exchange (ETDEWEB)

    Chrysalidis, K., E-mail: katerina.chrysalidis@cern.ch; Goodacre, T. Day; Fedosseev, V. N.; Marsh, B. A. [CERN (Switzerland); Naubereit, P. [Johannes Gutenberg-Universität, Institiut für Physik (Germany); Rothe, S.; Seiffert, C. [CERN (Switzerland); Kron, T.; Wendt, K. [Johannes Gutenberg-Universität, Institiut für Physik (Germany)

    2017-11-15

    Odd-parity autoionizing states of europium have been investigated by resonance ionization spectroscopy via two-step, two-resonance excitations. The aim of this work was to establish ionization schemes specifically suited for europium ion beam production using the ISOLDE Resonance Ionization Laser Ion Source (RILIS). 13 new RILIS-compatible ionization schemes are proposed. The scheme development was the first application of the Photo Ionization Spectroscopy Apparatus (PISA) which has recently been integrated into the RILIS setup.

  4. H-1 and N-15 resonance assignment of the second fibronectin type III module of the neural cell adhesion molecule

    DEFF Research Database (Denmark)

    Kiselyov, Vladislav V; Berezin, Vladimir; Bock, Elisabeth

    2008-01-01

    We report here the NMR assignment of the second fibronectin type III module of the neural cell adhesion molecule (NCAM). This module has previously been shown to interact with the fibroblast growth factor receptor (FGFR), and the FGFR-binding site was mapped by NMR to the FG-loop region of the mo......We report here the NMR assignment of the second fibronectin type III module of the neural cell adhesion molecule (NCAM). This module has previously been shown to interact with the fibroblast growth factor receptor (FGFR), and the FGFR-binding site was mapped by NMR to the FG-loop region...... of the module. The FG-loop region also contains a putative nucleotide-binding motif, which was shown by NMR to interact with ATP. Furthermore, ATP was demonstrated to inhibit binding of the second F3 module of NCAM to FGFR....

  5. 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.

  6. Vibrational analysis of HOCl up to 98% of the dissociation energy with a Fermi resonance Hamiltonian

    International Nuclear Information System (INIS)

    Jost, R.; Joyeux, M.; Skokov, S.; Bowman, J.

    1999-01-01

    We have analyzed the vibrational energies and wave functions of HOCl obtained from previous ab initio calculations [J. Chem. Phys. 109, 2662 (1998); 109, 10273 (1998)]. Up to approximately 13 and h;000 cm -1 , the normal modes are nearly decoupled, so that the analysis is straightforward with a Dunham model. In contrast, above 13 and h;000 cm -1 the Dunham model is no longer valid for the levels with no quanta in the OH stretch (v 1 =0). In addition to v 1 , these levels can only be assigned a so-called polyad quantum number P=2v 2 +v 3 , where 2 and 3 denote, respectively, the bending and OCl stretching normal modes. In contrast, the levels with v 1 ≥2 remain assignable with three v i quantum numbers up to the dissociation (D 0 =19 and h;290 and h;cm -1 ). The interaction between the bending and the OCl stretch (ω 2 congruent 2ω 3 ) is well described with a simple, fitted Fermi resonance Hamiltonian. The energies and wave functions of this model Hamiltonian are compared with those obtained from ab initio calculations, which in turn enables the assignment of many additional ab initio vibrational levels. Globally, among the 809 bound levels calculated below dissociation, 790 have been assigned, the lowest unassigned level, No. 736, being located at 18 and h;885 cm -1 above the (0,0,0) ground level, that is, at about 98% of D 0 . In addition, 84 resonances located above D 0 have also been assigned. Our best Fermi resonance Hamiltonian has 29 parameters fitted with 725 ab initio levels, the rms deviation being of 5.3 cm -1 . This set of 725 fitted levels includes the full set of levels up to No. 702 at 18 and h;650 cm -1 . The ab initio levels, which are assigned but not included in the fit, are reasonably predicted by the model Hamiltonian, but with a typical error of the order of 20 cm -1 . The classical analysis of the periodic orbits of this Hamiltonian shows that two bifurcations occur at 13 and h;135 and 14 and h;059 cm -1 for levels with v 1 =0. Above each

  7. Ultra-small v-shaped gold split ring resonators for biosensing using fundamental magnetic resonance in the visible spectrum

    Science.gov (United States)

    Mauluidy Soehartono, Alana; Mueller, Aaron David; Tobing, Landobasa Yosef Mario; Chan, Kok Ken; Zhang, Dao Hua; Yong, Ken-Tye

    2017-10-01

    Strong light localization within metal nanostructures occurs by collective oscillations of plasmons in the form of electric and magnetic resonances. This so-called localized surface plasmon resonance (LSPR) has gained much interest in the development of low-cost sensing platforms in the visible spectrum. However, demonstrations of LSPR-based sensing are mostly limited to electric resonances due to the technological limitations for achieving magnetic resonances in the visible spectrum. In this work, we report the first demonstration of LSPR sensing based on fundamental magnetic resonance in the visible spectrum using ultrasmall gold v-shaped split ring resonators. Specifically, we show the ability for detecting adsorption of bovine serum albumin and cytochrome c biomolecules at monolayer levels, and the selective binding of protein A/G to immunoglobulin G.

  8. 1H NMR studies of human lysozyme: Spectral assignment and comparison with hen lysozyme

    International Nuclear Information System (INIS)

    Redfield, C.; Dobson, C.M.

    1990-01-01

    Complete main-chain (NH and αCH) 1 H NMR assignments are reported for the 130 residues of human lysozyme, along with extensive assignments for side-chain protons. Analysis of 2-D NOESY experiments shows that the regions of secondary structure for human lysozyme in solution are essentially identical with those found previously in a similar study of hen lysozyme and are in close accord with the structure of the protein reported previously from x-ray diffraction studies in the crystalline state. Comparison of the chemical shifts, spin-spin coupling constants, and hydrogen exchange behavior are also consistent with closely similar structures for the two proteins in solution. In a number of cases specific differences in the NMR parameters between hen and human lysozymes can be correlated with specific differences observed in the crystal structures

  9. Managing voluntary turnover through challenging assignments

    NARCIS (Netherlands)

    Preenen, P.T.Y.; de Pater, I.E.; van Vianen, A.E.M.; Keijzer, L.

    2011-01-01

    This study examines employees’ challenging assignments as manageable means to reduce turnover intentions, job search behaviors, and voluntary turnover. Results indicate that challenging assignments are negatively related to turnover intentions and job search behaviors and that these relationships

  10. Managing voluntary turnover through challenging assignments

    NARCIS (Netherlands)

    Preenen, P.T.Y.; Pater, I.E. de; Vianen, A.E.M. van; Keijzer, L.

    2011-01-01

    This study examines employees' challenging assignments as manageable means to reduce turnover intentions, job search behaviors, and voluntary turnover. Results indicate that challenging assignments are negatively related to turnover intentions and job search behaviors and that these relationships

  11. Application of a fast sorting algorithm to the assignment of mass spectrometric cross-linking data.

    Science.gov (United States)

    Petrotchenko, Evgeniy V; Borchers, Christoph H

    2014-09-01

    Cross-linking combined with MS involves enzymatic digestion of cross-linked proteins and identifying cross-linked peptides. Assignment of cross-linked peptide masses requires a search of all possible binary combinations of peptides from the cross-linked proteins' sequences, which becomes impractical with increasing complexity of the protein system and/or if digestion enzyme specificity is relaxed. Here, we describe the application of a fast sorting algorithm to search large sequence databases for cross-linked peptide assignments based on mass. This same algorithm has been used previously for assigning disulfide-bridged peptides (Choi et al., ), but has not previously been applied to cross-linking studies. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Automated Pre-processing for NMR Assignments with Reduced Tedium

    Energy Technology Data Exchange (ETDEWEB)

    2004-05-11

    An important rate-limiting step in the reasonance asignment process is accurate identification of resonance peaks in MNR spectra. NMR spectra are noisy. Hence, automatic peak-picking programs must navigate between the Scylla of reliable but incomplete picking, and the Charybdis of noisy but complete picking. Each of these extremes complicates the assignment process: incomplete peak-picking results in the loss of essential connectivities, while noisy picking conceals the true connectivities under a combinatiorial explosion of false positives. Intermediate processing can simplify the assignment process by preferentially removing false peaks from noisy peak lists. This is accomplished by requiring consensus between multiple NMR experiments, exploiting a priori information about NMR spectra, and drawing on empirical statistical distributions of chemical shift extracted from the BioMagResBank. Experienced NMR practitioners currently apply many of these techniques "by hand", which is tedious, and may appear arbitrary to the novice. To increase efficiency, we have created a systematic and automated approach to this process, known as APART. Automated pre-processing has three main advantages: reduced tedium, standardization, and pedagogy. In the hands of experienced spectroscopists, the main advantage is reduced tedium (a rapid increase in the ratio of true peaks to false peaks with minimal effort). When a project is passed from hand to hand, the main advantage is standardization. APART automatically documents the peak filtering process by archiving its original recommendations, the accompanying justifications, and whether a user accepted or overrode a given filtering recommendation. In the hands of a novice, this tool can reduce the stumbling block of learning to differentiate between real peaks and noise, by providing real-time examples of how such decisions are made.

  13. Statistical decay of giant monopole resonance in 208Pb

    International Nuclear Information System (INIS)

    Dias, H.; Wolynec, E.

    1984-01-01

    The neutron spectrum from the decay of the monopole giant resonance in 208 Pb is calculated using the known energy levels of 207 Pb. The particle vibrator model is used to assign spins parities to the measured 207 Pb levels, where these were not avaliable from experiments. The results of the Hauser-Feshbach calculation is in excellent agreement with the experimental spectrum, showing that the observed fast neutrons can be completely explained assuming a statistical decay. (Author) [pt

  14. Scaffolding students’ assignments

    DEFF Research Database (Denmark)

    Slot, Marie Falkesgaard

    2013-01-01

    This article discusses scaffolding in typical student assignments in mother tongue learning materials in upper secondary education in Denmark and the United Kingdom. It has been determined that assignments do not have sufficient scaffolding end features to help pupils understand concepts and build...... objects. The article presents the results of empirical research on tasks given in Danish and British learning materials. This work is based on a further development of my PhD thesis: “Learning materials in the subject of Danish” (Slot 2010). The main focus is how cognitive models (and subsidiary explicit...... learning goals) can help students structure their argumentative and communica-tive learning processes, and how various multimodal representations can give more open-ended learning possibilities for collaboration. The article presents a short introduction of the skills for 21st century learning and defines...

  15. Assignment of element and isotope factors

    International Nuclear Information System (INIS)

    Schneider, R.A.

    1984-01-01

    Element and isotope factors are assigned in the NICS internal accounting system at the Exxon Fuel Fabrication Facility on the basis of coded information included on the material transfer documents. This paper explains more fully the manner in which NICS assigns these factors

  16. Load characteristics of wireless power transfer system with different resonant types and resonator numbers

    Science.gov (United States)

    Zhang, Yiming; Zhao, Zhengming; Chen, Kainan; Fan, Jun

    2017-05-01

    Wireless Power Transfer (WPT) has been the research focus and applied in many fields. Normally power is transferred wirelessly to charge the battery, which requires specific load characteristics. The load characteristics are essential for the design and operation of the WPT system. This paper investigates the load characteristics of the WPT system with different resonant types and resonator numbers. It is found that in a WPT system with series or LCL resonance under a constant voltage source, the load characteristic is determined by the number of inductors. Even number of inductors results in a constant current characteristic and odd number constant voltage characteristic. Calculations, simulations, and experiments verify the analysis.

  17. NMR backbone resonance assignments of the prodomain variants of BDNF in the urea denatured state.

    Science.gov (United States)

    Wang, Jing; Bains, Henrietta; Anastasia, Agustin; Bracken, Clay

    2018-04-01

    Brain derived neurotrophic factor (BDNF) is a member of the neurotrophin family of proteins which plays a central role in neuronal survival, growth, plasticity and memory. A single Val66Met variant has been identified in the prodomain of human BDNF that is associated with anxiety, depression and memory disorders. The structural differences within the full-length prodomain Val66 and Met66 isoforms could shed light on the mechanism of action of the Met66 and its impact on the development of neuropsychiatric-associated disorders. In the present study, we report the backbone 1 H, 13 C, and 15 N NMR assignments of both full-length Val66 and Met66 prodomains in the presence of 2 M urea. These conditions were utilized to suppress residual structure and aid subsequent native state structural investigations aimed at mapping and identifying variant-dependent conformational differences under native-state conditions.

  18. Distribution functions for resonantly trapped orbits in the Galactic disc

    Science.gov (United States)

    Monari, Giacomo; Famaey, Benoit; Fouvry, Jean-Baptiste; Binney, James

    2017-11-01

    The present-day response of a Galactic disc stellar population to a non-axisymmetric perturbation of the potential has previously been computed through perturbation theory within the phase-space coordinates of the unperturbed axisymmetric system. Such an Eulerian linearized treatment, however, leads to singularities at resonances, which prevent quantitative comparisons with data. Here, we manage to capture the behaviour of the distribution function (DF) at a resonance in a Lagrangian approach, by averaging the Hamiltonian over fast angle variables and re-expressing the DF in terms of a new set of canonical actions and angles variables valid in the resonant region. We then follow the prescription of Binney, assigning to the resonant DF the time average along the orbits of the axisymmetric DF expressed in the new set of actions and angles. This boils down to phase-mixing the DF in terms of the new angles, such that the DF for trapped orbits depends only on the new set of actions. This opens the way to quantitatively fitting the effects of the bar and spirals to Gaia data in terms of DFs in action space.

  19. Common window resonance features in K and heavier alkaline atoms Rb and Cs

    International Nuclear Information System (INIS)

    Koide, Michi; Koike, Fumihiro; Nagata, Tetsuo

    2002-01-01

    A previous study of subvalence s-shell photoionization of potassium [Koide et al.: J. Phys. Soc. Jpn. 71 (2002) 1676] has been extended to the cases of heavier alkaline atoms Rb and Cs. We have measured the photoion time-of-flight spectra using monochromatized synchrotron radiation. Dual windows resonance structure previously observed in K was also found in Rb and Cs, suggesting that those structure are general features in alkaline atoms. We have observed also the Rydberg series of resonances that appear in dual windows. Our data analysis shows that the resonance widths are broad when compared with its rare gas neighbors. Based on multiconfiguration Dirac-Fock calculations, the Rydberg series of resonances were assigned to the 4s 1 4p 6 5s5p excitations embedded in the 4p 5 5s continua for Rb and to the 5s 1 5p 6 6s6p excitations embedded in the 5p 5 6s continua for Cs. (author)

  20. Method for assigning sites to projected generic nuclear power plants

    Energy Technology Data Exchange (ETDEWEB)

    Holter, G.M.; Purcell, W.L.; Shutz, M.E.; Young, J.R.

    1986-07-01

    Pacific Northwest Laboratory developed a method for forecasting potential locations and startup sequences of nuclear power plants that will be required in the future but have not yet been specifically identified by electric utilities. Use of the method results in numerical ratings for potential nuclear power plant sites located in each of the 10 federal energy regions. The rating for each potential site is obtained from numerical factors assigned to each of 5 primary siting characteristics: (1) cooling water availability, (2) site land area, (3) power transmission land area, (4) proximity to metropolitan areas, and (5) utility plans for the site. The sequence of plant startups in each federal energy region is obtained by use of the numerical ratings and the forecasts of generic nuclear power plant startups obtained from the EIA Middle Case electricity forecast. Sites are assigned to generic plants in chronological order according to startup date.

  1. Method for assigning sites to projected generic nuclear power plants

    International Nuclear Information System (INIS)

    Holter, G.M.; Purcell, W.L.; Shutz, M.E.; Young, J.R.

    1986-07-01

    Pacific Northwest Laboratory developed a method for forecasting potential locations and startup sequences of nuclear power plants that will be required in the future but have not yet been specifically identified by electric utilities. Use of the method results in numerical ratings for potential nuclear power plant sites located in each of the 10 federal energy regions. The rating for each potential site is obtained from numerical factors assigned to each of 5 primary siting characteristics: (1) cooling water availability, (2) site land area, (3) power transmission land area, (4) proximity to metropolitan areas, and (5) utility plans for the site. The sequence of plant startups in each federal energy region is obtained by use of the numerical ratings and the forecasts of generic nuclear power plant startups obtained from the EIA Middle Case electricity forecast. Sites are assigned to generic plants in chronological order according to startup date

  2. Coherence Phenomena in Coupled Optical Resonators

    Science.gov (United States)

    Smith, D. D.; Chang, H.

    2004-01-01

    We predict a variety of photonic coherence phenomena in passive and active coupled ring resonators. Specifically, the effective dispersive and absorptive steady-state response of coupled resonators is derived, and used to determine the conditions for coupled-resonator-induced transparency and absorption, lasing without gain, and cooperative cavity emission. These effects rely on coherent photon trapping, in direct analogy with coherent population trapping phenomena in atomic systems. We also demonstrate that the coupled-mode equations are formally identical to the two-level atom Schrodinger equation in the rotating-wave approximation, and use this result for the analysis of coupled-resonator photon dynamics. Notably, because these effects are predicted directly from coupled-mode theory, they are not unique to atoms, but rather are fundamental to systems of coherently coupled resonators.

  3. Frequency Assignment for Joint Aerial Layer Network High-Capacity Backbone

    Science.gov (United States)

    2017-08-11

    Two Frequency Assignment Problems (FAPs) are considered in this work, which are called MMC-FAP and MS-FAP. MMC-FAP is to minimize the frequency usage... minimize the frequency span in both frequency bands. By exploiting problem-specific properties, MMC-FAP can be formulated as a Mixed Integer Linear...considered for JALN HCB. The first FAP problem, called MMC- FAP, is to minimize the frequency usage of the most congested aerial platform in both

  4. Application of lanthanide-shift reagents in pulsed Fourier-transform nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Zektzer, A.S.

    1986-01-01

    The application of lanthanide-shift reagents (LSR's) to pulsed NMR is presented. Several areas were investigated in which the information content of the data was enhanced through the use of an LSR. The problem first investigated combines the ability of LSR's to influence both the shift and relaxation times of the substrate nuclei. Adamantan-2-ol which has a second-order proton spectra was simplified to first-order by the addition of Eu(fod) 3 at which time the T 1 -relaxation times of each resonance were measured at several ratios of [LSR]/[sub] in order to calculate the T 1 's of the bound species by multiple linear regression. The second application involved using LSR's to cause shift changes in compounds not usually accessible to LSR's. Sulfur heterocycles, which show little if any shift with LSR's, were found to exhibit large shifts when silver organic salts were used in combination with an LSR such as Dy(fod) 3 or Ho(fod) 3 . The last application was the assignment of the 1 H and 13 C resonances of a thieno-pyridine and the comparison of these assignments to those from high-field two-dimensional NMR techniques

  5. Resonance-enhanced multiphoton ionization (REMPI) spectroscopy of p-chlorofluorobenzene

    Science.gov (United States)

    Tuttle, William D.; Gardner, Adrian M.; Wright, Timothy G.

    2017-09-01

    The S1 ← S0 (A˜1 B2 ← X˜1 A1) electronic transition of para-chlorofluorobenzene has been investigated using resonance-enhanced multiphoton ionization (REMPI) spectroscopy. Assignment of the vibrational structure has been achieved by comparison with corresponding spectra of related molecules, via quantum chemical calculations, and via shifts in bands between the spectra of the 35Cl and 37Cl isotopologues. In addition, we have also partially reassigned a previously-published spectrum of para-dichlorobenzene.

  6. Defect states in hexagonal boron nitride: Assignments of observed properties and prediction of properties relevant to quantum computation

    Science.gov (United States)

    Sajid, A.; Reimers, Jeffrey R.; Ford, Michael J.

    2018-02-01

    Key properties of nine possible defect sites in hexagonal boron nitride (h-BN), VN,VN -1,CN,VNO2 B,VNNB,VNCB,VBCN,VBCNS iN , and VNCBS iB , are predicted using density-functional theory and are corrected by applying results from high-level ab initio calculations. Observed h-BN electron-paramagnetic resonance signals at 22.4, 20.83, and 352.70 MHz are assigned to VN,CN, and VNO2 B , respectively, while the observed photoemission at 1.95 eV is assigned to VNCB . Detailed consideration of the available excited states, allowed spin-orbit couplings, zero-field splitting, and optical transitions is made for the two related defects VNCB and VBCN . VNCB is proposed for realizing long-lived quantum memory in h-BN. VBCN is predicted to have a triplet ground state, implying that spin initialization by optical means is feasible and suitable optical excitations are identified, making this defect of interest for possible quantum-qubit operations.

  7. Significantly improving nuclear resonance fluorescence non-destructive assay by using the integral resonance transmission method and photofission

    International Nuclear Information System (INIS)

    Angell, Christopher T.; Hayakawa, Takehito; Shizuma, Toshiyuki; Hajima, Ryoichi

    2013-01-01

    Non-destructive assay (NDA) of 239 Pu in spent nuclear fuel or melted fuel using a γ-ray beam is possible using self absorption and the integral resonance transmission method. The method uses nuclear resonance absorption where resonances in 239 Pu remove photons from the beam, and the selective absorption is detected by measuring the decrease in scattering in a witness target placed in the beam after the fuel, consisting of the isotope of interest, namely 239 Pu. The method is isotope specific, and can use photofission or scattered γ-rays to assay the 239 Pu. It overcomes several problems related to NDA of melted fuel, including the radioactivity of the fuel, and the unknown composition and geometry. This talk will explain the general method, and how photofission can be used to assay specific isotopes, and present example calculations. (author)

  8. AgInS{sub 2}-ZnS nanocrystals: Evidence of bistable states using light-induced electron paramagnetic resonance and photoluminescence

    Energy Technology Data Exchange (ETDEWEB)

    Nobre, Sonia S.; Renard, Olivier; Chevallier, Theo; Le Blevennec, Gilles [Laboratoire d' Innovation pour les Technologies des Energies Nouvelles et les Nanomateriaux, Departement de Technologie des Nano-Materiaux, Service d' Elaboration de Nanomateriaux, Laboratoire de Synthese et Integration des Nanomateriaux, CEA-Grenoble (France); Lombard, Christian; Pepin-Donat, Brigitte [Laboratoire Structure et Proprietes d' Architecture Moleculaire (UMR 5819) CEA-CNRS - UJF/INAC/CEA-Grenoble (France)

    2014-04-15

    The precursor (AgIn){sub x} Zn{sub 2(1-x)}(S{sub 2}CN(C{sub 2}H{sub 5}){sub 2}){sub 4} was used to prepared AgInS{sub 2}-ZnS nanocrystals with different compositions (x = 0.4 and x = 0.7) and with different time of reaction (10 min and 75 min). The photoluminescence features of the nanocrystals were addressed by combining steady-state spectroscopy and light-induced electron paramagnetic resonance. Both techniques showed the contribution of at least two components for the emission, previously assigned to surface and intrinsic states. Light-induced electron paramagnetic resonance allowed detection of the photocreation both of irreversible paramagnetic species that are likely responsible for the nano-crystals degradation assigned to surface states and of reversible paramagnetic species assigned to intrinsic states. Moreover, reversible bistable paramagnetic states were observed. This Letter provides a scheme that might be useful in addressing the well-known problem of aging of the nanocrystals. (copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. 32 CFR 884.2 - Assigned responsibilities.

    Science.gov (United States)

    2010-07-01

    ... OF PERSONNEL TO UNITED STATES CIVILIAN AUTHORITIES FOR TRIAL § 884.2 Assigned responsibilities. (a... 32 National Defense 6 2010-07-01 2010-07-01 false Assigned responsibilities. 884.2 Section 884.2... requests for return of members to the United States for delivery to civilian authorities when the request...

  10. Is a neutral expression also a neutral stimulus? A study with functional magnetic resonance.

    Science.gov (United States)

    Carvajal, Fernando; Rubio, Sandra; Serrano, Juan M; Ríos-Lago, Marcos; Alvarez-Linera, Juan; Pacheco, Lara; Martín, Pilar

    2013-08-01

    Although neutral faces do not initially convey an explicit emotional message, it has been found that individuals tend to assign them an affective content. Moreover, previous research has shown that affective judgments are mediated by the task they have to perform. Using functional magnetic resonance imaging in 21 healthy participants, we focus this study on the cerebral activity patterns triggered by neutral and emotional faces in two different tasks (social or gender judgments). Results obtained, using conjunction analyses, indicated that viewing both emotional and neutral faces evokes activity in several similar brain areas indicating a common neural substrate. Moreover, neutral faces specifically elicit activation of cerebellum, frontal and temporal areas, while emotional faces involve the cuneus, anterior cingulated gyrus, medial orbitofrontal cortex, posterior superior temporal gyrus, precentral/postcentral gyrus and insula. The task selected was also found to influence brain activity, in that the social task recruited frontal areas while the gender task involved the posterior cingulated, inferior parietal lobule and middle temporal gyrus to a greater extent. Specifically, in the social task viewing neutral faces was associated with longer reaction times and increased activity of left dorsolateral frontal cortex compared with viewing facial expressions of emotions. In contrast, in the same task emotional expressions distinctively activated the left amygdale. The results are discussed taking into consideration the fact that, like other facial expressions, neutral expressions are usually assigned some emotional significance. However, neutral faces evoke a greater activation of circuits probably involved in more elaborate cognitive processing.

  11. Personnel dose assignment practices

    International Nuclear Information System (INIS)

    Fix, J.J.

    1993-04-01

    Implementation of DOE N 5480.6 Radiological Control Manual Article 511(3) requirements, to minimize the assignment of personnel dosimeters, should be done only under a broader context ensuring that capabilities are in place to monitor and record personnel exposure both for compliance and for potential litigation. As noted in NCRP Report No. 114, personnel dosimetry programs are conducted to meet four major objectives: radiation safety program control and evaluation; regulatory compliance; epidemiological research; and litigation. A change to Article 511(3) is proposed that would require that minimizing the assignment of personnel dosimeters take place only following full evaluation of overall capabilities (e.g., access control, area dosimetry, etc.) to meet the NCRP objectives

  12. Load characteristics of wireless power transfer system with different resonant types and resonator numbers

    Directory of Open Access Journals (Sweden)

    Yiming Zhang

    2017-05-01

    Full Text Available Wireless Power Transfer (WPT has been the research focus and applied in many fields. Normally power is transferred wirelessly to charge the battery, which requires specific load characteristics. The load characteristics are essential for the design and operation of the WPT system. This paper investigates the load characteristics of the WPT system with different resonant types and resonator numbers. It is found that in a WPT system with series or LCL resonance under a constant voltage source, the load characteristic is determined by the number of inductors. Even number of inductors results in a constant current characteristic and odd number constant voltage characteristic. Calculations, simulations, and experiments verify the analysis.

  13. Modeling of supermodes in coupled unstable resonators

    International Nuclear Information System (INIS)

    Townsend, S.S.

    1986-01-01

    A general formalism describing the supermodes of an array of N identical, circulantly coupled resonators is presented. The symmetry of the problem results in a reduction of the N coupled integral equations to N decoupled integral equations. Each independent integral equation defines a set of single-resonator modes derived for a hypothetical resonator whose geometry resembles a member of the real array with the exception that all coupling beams are replaced by feedback beams, each with a prescribed constant phase. A given array supermode consists of a single equivalent resonator mode appearing repetitively in each resonator with a prescribed relative phase between individual resonators. The specific array design chosen for example is that of N adjoint coupled confocal unstable resonators. The impact of coupling on the computer modeling of this system is discussed and computer results for the cases of two- and four-laser coupling are presented

  14. Computational Aspects of Assigning Agents to a Line

    DEFF Research Database (Denmark)

    Aziz, Haris; Hougaard, Jens Leth; Moreno-Ternero, Juan D.

    2017-01-01

    -egalitarian assignments. The approach relies on an algorithm which is shown to be faster than general purpose algorithms for the assignment problem. We also extend the approach to probabilistic assignments and explore the computational features of existing, as well as new, methods for this setting....

  15. Computational aspects of assigning agents to a line

    DEFF Research Database (Denmark)

    Aziz, Haris; Hougaard, Jens Leth; Moreno-Ternero, Juan D.

    2017-01-01

    -egalitarian assignments. The approach relies on an algorithm which is shown to be faster than general purpose algorithms for the assignment problem. We also extend the approach to probabilistic assignments and explore the computational features of existing, as well as new, methods for this setting....

  16. Neural correlates of temporal credit assignment in the parietal lobe.

    Directory of Open Access Journals (Sweden)

    Timothy M Gersch

    Full Text Available Empirical studies of decision making have typically assumed that value learning is governed by time, such that a reward prediction error arising at a specific time triggers temporally-discounted learning for all preceding actions. However, in natural behavior, goals must be acquired through multiple actions, and each action can have different significance for the final outcome. As is recognized in computational research, carrying out multi-step actions requires the use of credit assignment mechanisms that focus learning on specific steps, but little is known about the neural correlates of these mechanisms. To investigate this question we recorded neurons in the monkey lateral intraparietal area (LIP during a serial decision task where two consecutive eye movement decisions led to a final reward. The underlying decision trees were structured such that the two decisions had different relationships with the final reward, and the optimal strategy was to learn based on the final reward at one of the steps (the "F" step but ignore changes in this reward at the remaining step (the "I" step. In two distinct contexts, the F step was either the first or the second in the sequence, controlling for effects of temporal discounting. We show that LIP neurons had the strongest value learning and strongest post-decision responses during the transition after the F step regardless of the serial position of this step. Thus, the neurons encode correlates of temporal credit assignment mechanisms that allocate learning to specific steps independently of temporal discounting.

  17. Structures of peptide families by nuclear magnetic resonance spectroscopy and distance geometry

    Energy Technology Data Exchange (ETDEWEB)

    Pease, J.H.

    1989-12-01

    The three dimensional structures of several small peptides were determined using a combination of {sup 1}H nuclear magnetic resonance (NMR) and distance geometry calculations. These techniques were found to be particularly helpful for analyzing structural differences between related peptides since all of the peptides' {sup 1}H NMR spectra are very similar. The structures of peptides from two separate classes are presented. Peptides in the first class are related to apamin, an 18 amino acid peptide toxin from honey bee venom. The {sup 1}H NMR assignments and secondary structure determination of apamin were done previously. Quantitative NMR measurements and distance geometry calculations were done to calculate apamin's three dimensional structure. Peptides in the second class are 48 amino acid toxins from the sea anemone Radianthus paumotensis. The {sup 1}H NMR assignments of toxin II were done previously. The {sup 1}H NMR assignments of toxin III and the distance geometry calculations for both peptides are presented.

  18. Optimal density assignment to 2D diode array detector for different dose calculation algorithms in patient specific VMAT QA

    International Nuclear Information System (INIS)

    Park, So Yeon; Park, Jong Min; Choi, Chang Heon; Chun, MinSoo; Han, Ji Hye; Cho, Jin Dong; Kim, Jung In

    2017-01-01

    The purpose of this study is to assign an appropriate density to virtual phantom for 2D diode array detector with different dose calculation algorithms to guarantee the accuracy of patient-specific QA. Ten VMAT plans with 6 MV photon beam and ten VMAT plans with 15 MV photon beam were selected retrospectively. The computed tomography (CT) images of MapCHECK2 with MapPHAN were acquired to design the virtual phantom images. For all plans, dose distributions were calculated for the virtual phantoms with four different materials by AAA and AXB algorithms. The four materials were polystyrene, 455 HU, Jursinic phantom, and PVC. Passing rates for several gamma criteria were calculated by comparing the measured dose distribution with calculated dose distributions of four materials. For validation of AXB modeling in clinic, the mean percentages of agreement in the cases of dose difference criteria of 1.0% and 2.0% for 6 MV were 97.2%±2.3%, and 99.4%±1.1%, respectively while those for 15 MV were 98.5%±0.85% and 99.8%±0.2%, respectively. In the case of 2%/2 mm, all mean passing rates were more than 96.0% and 97.2% for 6 MV and 15 MV, respectively, regardless of the virtual phantoms of different materials and dose calculation algorithms. The passing rates in all criteria slightly increased for AXB as well as AAA when using 455 HU rather than polystyrene. The virtual phantom which had a 455 HU values showed high passing rates for all gamma criteria. To guarantee the accuracy of patent-specific VMAT QA, each institution should fine-tune the mass density or HU values of this device

  19. Optimal density assignment to 2D diode array detector for different dose calculation algorithms in patient specific VMAT QA

    Energy Technology Data Exchange (ETDEWEB)

    Park, So Yeon; Park, Jong Min; Choi, Chang Heon; Chun, MinSoo; Han, Ji Hye; Cho, Jin Dong; Kim, Jung In [Dept. of Radiation Oncology, Seoul National University Hospital, Seoul (Korea, Republic of)

    2017-03-15

    The purpose of this study is to assign an appropriate density to virtual phantom for 2D diode array detector with different dose calculation algorithms to guarantee the accuracy of patient-specific QA. Ten VMAT plans with 6 MV photon beam and ten VMAT plans with 15 MV photon beam were selected retrospectively. The computed tomography (CT) images of MapCHECK2 with MapPHAN were acquired to design the virtual phantom images. For all plans, dose distributions were calculated for the virtual phantoms with four different materials by AAA and AXB algorithms. The four materials were polystyrene, 455 HU, Jursinic phantom, and PVC. Passing rates for several gamma criteria were calculated by comparing the measured dose distribution with calculated dose distributions of four materials. For validation of AXB modeling in clinic, the mean percentages of agreement in the cases of dose difference criteria of 1.0% and 2.0% for 6 MV were 97.2%±2.3%, and 99.4%±1.1%, respectively while those for 15 MV were 98.5%±0.85% and 99.8%±0.2%, respectively. In the case of 2%/2 mm, all mean passing rates were more than 96.0% and 97.2% for 6 MV and 15 MV, respectively, regardless of the virtual phantoms of different materials and dose calculation algorithms. The passing rates in all criteria slightly increased for AXB as well as AAA when using 455 HU rather than polystyrene. The virtual phantom which had a 455 HU values showed high passing rates for all gamma criteria. To guarantee the accuracy of patent-specific VMAT QA, each institution should fine-tune the mass density or HU values of this device.

  20. A Computerized Approach to Trickle-Process, Random Assignment.

    Science.gov (United States)

    Braucht, G. Nicholas; Reichardt, Charles S.

    1993-01-01

    Procedures for implementing random assignment with trickle processing and ways they can be corrupted are described. A computerized method for implementing random assignment with trickle processing is presented as a desirable alternative in many situations and a way of protecting against threats to assignment validity. (SLD)

  1. Magnetic resonance imaging of breast implants.

    Science.gov (United States)

    Shah, Mala; Tanna, Neil; Margolies, Laurie

    2014-12-01

    Silicone breast implants have significantly evolved since their introduction half a century ago, yet implant rupture remains a common and expected complication, especially in patients with earlier-generation implants. Magnetic resonance imaging is the primary modality for assessing the integrity of silicone implants and has excellent sensitivity and specificity, and the Food and Drug Administration currently recommends periodic magnetic resonance imaging screening for silent silicone breast implant rupture. Familiarity with the types of silicone implants and potential complications is essential for the radiologist. Signs of intracapsular rupture include the noose, droplet, subcapsular line, and linguine signs. Signs of extracapsular rupture include herniation of silicone with a capsular defect and extruded silicone material. Specific sequences including water and silicone suppression are essential for distinguishing rupture from other pathologies and artifacts. Magnetic resonance imaging provides valuable information about the integrity of silicone implants and associated complications.

  2. NNΔ resonance and pd → 3He πo reaction

    International Nuclear Information System (INIS)

    Ueda, T.

    1988-01-01

    On the basis of the I = 1, JP = 2+ resonant NΔ interaction (the pp 1D2 dibaryon), one argues that in NNΔ system a three-body resonance is generated. With a clustering binding energy of a few 10 MeV between the N and the Δ making the dibaryon and another binding energy of about 10 MeV between the NΔ cluster and the spectator N due to the attractive interaction of the Δ exchange between the cluster and spectator, the NNΔ system is bound about 40 - 60 MeV below the NNΔ threshold. Because of the Δ decay width the NNΔ bound state is actually a resonant state. The case where the spins of all the particles align in the same direction is most favorable to be bound, since the driving term is largest here. Assigning the zero orbital angular momenta, the spin-parity of the NNΔ resonance is JP = (5/2)+ . The resonance couples with NNN system through NN(1D2)-NΔ(5S2). Thus the total spin of the NNN system which couples easily with the NNΔ resonance is 1/2. Namely the spin doublet pd channel creates the NNΔ resonance. Similar argument applies to NΔΔ system. Then one summarize: NNΔ resonance : M = 3.07 GeV, JP = (5/2)+. NΔΔ resonance : M = 3.36 GeV, JP = (7/2)+. Both are easy to couple with the spin-doublet pd channel. Assuming the NNΔ and NΔΔ resonance terms, combined with the background ones which are mild in the energy dependence, one analyses the differential cross section and the deuteron tensor polarization of pd → 3 He π o at deuteron incident energy 410 ∼ 2200 MeV at θ = 0 and π. The remarkable energy-dependent structure of the tensor polarization is fairly explained by the existence of the NNΔ and NΔΔ resonances. (author)

  3. Determination of the shear impedance of viscoelastic liquids using cylindrical piezoceramic resonators.

    Science.gov (United States)

    Kiełczyński, Piotr; Pajewski, Wincenty; Szalewski, Marek

    2003-03-01

    In this paper, a new method for determining the rheological parameters of viscoelastic liquids is presented. To this end, we used the perturbation method applied to shear vibrations of cylindrical piezoceramic resonators. The resonator was viscoelastically loaded on the outer cylindrical surface. Due to this loading, the resonant frequency and quality factor of the resonator changed. According to the perturbation method, the change in the complex resonant frequency deltaomega = deltaomega(re) + jdeltaomega(im) is directly proportional to the specific acoustic impedance for cylindrical waves Zc of a viscoelastic liquid surrounding the resonator, i.e., deltaomega is approximately equal to jZc, where j = (-1)1/2. Hence, the measurement of the real and imaginary parts of the complex resonant frequency deltaomega determines the real part, Rc, and imaginary part, Xc, of the complex acoustic impedance for cylindrical waves Zc of an investigated liquid. Furthermore, the specific impedance ZL for plane waves was related to the specific impedance Zc for cylindrical waves. Using theoretical formulas established and the results of the experiments performed, the shear storage modulus mu and the viscosity eta for various liquids (e.g., epoxy resins) were determined. Moreover, the authors derived for cylindrical resonators a formula that relates the shift in resonant frequency to the viscosity of the liquid. This formula is analogous to the Kanazawa-Gordon formula that was derived for planar resonators and Newtonian liquids.

  4. Specific proof of various stages of Osler's disease of the brain via high field magnetic resonance tomography (1. 5 Tesla)

    Energy Technology Data Exchange (ETDEWEB)

    Billet, F; Bluemm, R G; Beyer, H K

    1988-08-01

    MR is a sensitive noninvasive examination method for diagnosing parenchymatous cryptic arteriovenous malformations and sequels of cerebral haemorrhage. In a patient with recurring nosebleed and brain stem syndrome eleven so-called cryptic arteriovenous malformations or their haemorrhage sequels were diagnosed via magnetic resonance tomography. Basing on these specific findings, nosebleeding, and a positive family anamnesis, the findings could be classified as belonging to manifestations of Osler's disease (hereditary haemorrhagic telangiectasia). This rare disease is characterised by a triad of signs: telangiectasias, recurring bleeding, and heredity. In this article the specific MR image is compared with the CT pattern and the results are discussed against the background of literature on Osler's disease which is also known as Rendu-Osler-Weber disease.

  5. 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…

  6. Proton magnetic resonance spectroscopy and perfusion magnetic resonance imaging in the evaluation of musculoskeletal tumors

    International Nuclear Information System (INIS)

    Costa, Flavia Martins; Setti, Marcela; Vianna, Evandro Miguelote; Domingues, Romulo Cortes; Meohas, Walter; Rezende, Jose Francisco; Gasparetto, Emerson Leandro

    2009-01-01

    Objective: To assess the role of proton magnetic resonance spectroscopy and dynamic contrast-enhanced magnetic resonance imaging in the differentiation between malignant and benign musculoskeletal tumors. Materials And Methods: Fifty-five patients with musculoskeletal tumors (27 malignant and 28 benign) were studied. The examinations were performed in a 1.5 T magnetic resonance scanner with standard protocol, and single voxel proton magnetic resonance spectroscopy with 135 msec echo time. The dynamic contrast study was performed using T1-weighted gradient-echo sequence after intravenous gadolinium injection. Time signal intensity curves and slope values were calculated. The statistical analysis was performed with the Levene's test, followed by a Student's t-test, besides the Pearson's chi-squared and Fischer's exact tests. Results: Proton magnetic resonance spectroscopy sensitivity, specificity and accuracy were, respectively, 87.5%, 92.3% and 90.9% (p < 0.0001). Statistically significant difference was observed in the slope (%/min) between benign (mean, 27.5%/min) and malignant (mean, 110.9%/min) lesions (p < 0.0001). Conclusion: The time-intensity curve and slope values using dynamic-enhanced perfusion magnetic resonance imaging in association with the presence of choline peak demonstrated by single voxel magnetic resonance spectroscopy study are useful in the differentiation between malignant and benign musculoskeletal tumors. (author)

  7. Mannitol as a Potential Pitfall for Peak Assignment on Magnetic Resonance Spectra (MRS) for Brain Tumors: A Case Report

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jee Young; Ahn, Kook Jin; Yu, Won Jong; Kim, Bum Soo [Catholic University, Seoul (Korea, Republic of); Park, Ik Sung [Catholic University, Bucheon St. Mary' s Hospital, Bucheon (Korea, Republic of)

    2009-06-15

    Mannitol is a xenobiotic commonly used for the control of brain edema in patients with brain tumors. Although not typically identifiable with the use of routine proton magnetic resonance spectroscopy (MRS), we report a case where the mannitol peak was clearly visible on the MR spectra of a recurrent meningioma.

  8. Measurement of the Auger decay after resonance excitation of Xe 4d and Kr 3d resonance lines

    International Nuclear Information System (INIS)

    Eberhardt, W.; Kalkoffen, G.; Kunz, C.

    1978-03-01

    The Nsub(4,5) 0sub(2,3) 0sub(2,3) Auger spectra from Xe and the Msub(4,5) Nsub(2,3) Nsub(2,3) Auger spectra from Kr are investigated for different photon energies around threshold of ionization. When exciting at the resonance line (4d 9 5s 2 5p 6 6p for Xe and 3d 9 4s 2 4p 6 5p for Kr) we observe the usual Auger multiplet structure to be shifted to higher kinetic energies. Additionally, new lines appear which can be assigned to shake-up processes int he Xe + and Kr + ions. (orig.) [de

  9. Documents assignment to archival fonds in research institutions of the NAS of Ukraine

    Directory of Open Access Journals (Sweden)

    Sichova O.

    2015-01-01

    Full Text Available The article analyzes the main aspects of the assignment of the records of research institutions of the NAS of Ukraine to archival fonds, in particular, the records assignment to archival fonds according to certain characteristics, archival fonds creation in accordance with the scientific principles of provenance, continuity and archival fond integrity. Shown are the features of the internal systematization of the documents of research institutions of the NAS of Ukraine, caused by the specifics of the institutions functions. Illustrated are the examples of institutional archival fonds acquiring names and the conditions leading to their renaming. Analyzed is the procedure of a chronological scope fixation of a research institution of the NAS of Ukraine archival fond

  10. Selective ligand activity at Nur/retinoid X receptor complexes revealed by dimer-specific bioluminescence resonance energy transfer-based sensors

    Science.gov (United States)

    Giner, Xavier C; Cotnoir-White, David; Mader, Sylvie; Lévesque, Daniel

    2017-01-01

    Retinoid X receptors (RXR) play a role as master regulators due to their capacity to form heterodimers with other nuclear receptors. Accordingly, retinoid signaling is involved in multiple biological processes, including development, cell differentiation, metabolism and cell death. However, the role and functions of RXR in different heterodimer complexes remain unsolved, mainly because most RXR drugs (called rexinoids) are not selective to specific heterodimer complexes. This also strongly limits the use of rexinoids for specific therapeutic approaches. In order to better characterize rexinoids at specific nuclear receptor complexes, we have developed and optimized luciferase protein complementation-based Bioluminescence Resonance Energy Transfer (BRET) assays, which can directly measure recruitment of a co-activator motif fused to yellow fluorescent protein (YFP) by specific nuclear receptor dimers. To validate the assays, we compared rexinoid modulation of co-activator recruitment by RXR homodimer, and heterodimers Nur77/RXR and Nurr1/RXR. Results reveal that some rexinoids display selective co-activator recruitment activities with homo- or hetero-dimer complexes. In particular, SR11237 (BMS649) has increased potency for recruitment of co-activator motif and transcriptional activity with the Nur77/RXR heterodimer compared to other complexes. This technology should prove useful to identify new compounds with specificity for individual dimeric species formed by nuclear receptors. PMID:26148973

  11. Coherent control through near-resonant Raman transitions

    International Nuclear Information System (INIS)

    Dai Xingcan; Lerch, Eliza-Beth W.; Leone, Stephen R.

    2006-01-01

    The phase of an electronic wave function is shown to play an important role in coherent control experiments. By using a pulse shaping system with a femtosecond laser, we explore the phase relationships among resonant and off-resonant Raman transitions in Li 2 by measuring the phases of the resulting wave packets, or quantum beats. Specific pixels in a liquid-crystal spatial light modulator are used to isolate the resonant and off-resonant portions of the Raman transitions in Li 2 . The off-resonant Raman transitions have an approximately 90 degree sign phase shift with respect to the resonant Raman transition, and there is an approximately 180 degree sign phase shift between the blue-detuned and the red-detuned off-resonant Raman transitions. Calculations using second-order time-dependent perturbation theory for the electronic transitions agree with the experimental results for the laser pulse intensities used here. Interferences between the off-resonant Raman transitions as a function of detuning are used to demonstrate coherent control of the Raman quantum wave packet

  12. 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.

  13. First Trimester Fetal Gender Assignment by Ultrasound

    Directory of Open Access Journals (Sweden)

    Sabahattin Altunyurt

    2010-03-01

    Full Text Available Objective: To investigate the efficiency of genital tubercule angle on detecting fetal gender in first trimester by ultrasonography. Material-Method: Fetal sex assignment by ultrasound was carried out in 172 pregnancies at 11-13+6 weeks between 2007 June and 2007 December. Gestational age was determined by the measurement of crown-rump length (CRL. The ultrasound predictions were compared with actual sex at birth. Mid-sagittal planes of a section of the fetal genital tubercle were performed to identify the gender. Results: 155 of 172 patients’ data were achieved. The overall success rate was 92.3 % in sonographic assignment of fetal sex. The correct assignment rate in female fetuses was significantly higher than males (95.9 % - 88.8 % [p=0,001]. The correct identification of fetal sex improved with advancing gestational age from 89.3 % between 11-11+6 weeks, 92.5 % between 12-12+6 weeks and 93.4 % between 13-13+6 weeks (p=0,96. Conclusion: The fetal sex assignment by ultrasonography between 11-13+6 weeks had high success rate. The sensitivity of fetal sex assignment was not affected with fetus position and gestational age.

  14. NOESY-WaterControl: a new NOESY sequence for the observation of under-water protein resonances

    International Nuclear Information System (INIS)

    Torres, Allan M.; Zheng, Gang; Price, William S.

    2017-01-01

    Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω 2 ). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω 2 . The 2D NOESY maps obtained using the new sequence thus provide more information than the maps obtained with conventional water suppression, thereby lessening the number of experiments needed to complete resonance assignments of biomolecules. The 2D NOESY-WaterControl map of BPTI showed strong bound water and exchangeable proton signals in ω 1 but these signals were absent in ω 2 , indicating the possibility of using the new sequence to discriminate bound water and exchangeable proton resonances from non-labile proton resonances with similar chemical shifts to water.

  15. 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....

  16. HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids.

    KAUST Repository

    Mithani, Aziz; Belfield, Eric J; Brown, Carly; Jiang, Caifu; Leach, Lindsey J; Harberd, Nicholas P

    2013-01-01

    The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from which they are derived, and hinders the development of polyploid whole genome assemblies.We here present a next-generation sequencing (NGS)-based approach for assignment of subgenome-specific base-identity at sites containing homeolog-specific polymorphisms (HSPs): 'HSP base Assignment using NGS data through Diploid Similarity' (HANDS). We show that HANDS correctly predicts subgenome-specific base-identity at >90% of assayed HSPs in the hexaploid bread wheat (Triticum aestivum) transcriptome, thus providing a substantial increase in accuracy versus previous methods for homeolog-specific base assignment.We conclude that HANDS enables rapid and accurate genome-wide discovery of homeolog-specific base-identity, a capability having multiple applications in polyploid genomics.

  17. HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids.

    KAUST Repository

    Mithani, Aziz

    2013-09-24

    The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from which they are derived, and hinders the development of polyploid whole genome assemblies.We here present a next-generation sequencing (NGS)-based approach for assignment of subgenome-specific base-identity at sites containing homeolog-specific polymorphisms (HSPs): \\'HSP base Assignment using NGS data through Diploid Similarity\\' (HANDS). We show that HANDS correctly predicts subgenome-specific base-identity at >90% of assayed HSPs in the hexaploid bread wheat (Triticum aestivum) transcriptome, thus providing a substantial increase in accuracy versus previous methods for homeolog-specific base assignment.We conclude that HANDS enables rapid and accurate genome-wide discovery of homeolog-specific base-identity, a capability having multiple applications in polyploid genomics.

  18. Red-excitation resonance Raman analysis of the nu(Fe=O) mode of ferryl-oxo hemoproteins.

    Science.gov (United States)

    Ikemura, Kenichiro; Mukai, Masahiro; Shimada, Hideo; Tsukihara, Tomitake; Yamaguchi, Satoru; Shinzawa-Itoh, Kyoko; Yoshikawa, Shinya; Ogura, Takashi

    2008-11-05

    The Raman excitation profile of the nuFe O mode of horseradish peroxidase compound II exhibits a maximum at 580 nm. This maximum is located within an absorption band with a shoulder assignable to an oxygen-to-iron charge transfer band on the longer wavelength side of the alpha-band. Resonance Raman bands of the nuFe O mode of various ferryl-oxo type hemoproteins measured at 590 nm excitation indicate that many hemoproteins in the ferryl-oxo state have an oxygen-to-iron charge transfer band in the visible region. Since this red-excited resonance Raman technique causes much less photochemical damage in the proteins relative to blue-excited resonance Raman spectroscopy, it produces a higher signal-to-noise ratio and thus represents a powerful tool for investigations of ferryl-oxo intermediates of hemoproteins.

  19. SCRAED - Simple and Complex Random Assignment in Experimental Designs

    OpenAIRE

    Alferes, Valentim R.

    2009-01-01

    SCRAED is a package of 37 self-contained SPSS syntax files that performs simple and complex random assignment in experimental designs. For between-subjects designs, SCRAED includes simple random assignment (no restrictions, forced equal sizes, forced unequal sizes, and unequal probabilities), block random assignment (simple and generalized blocks), and stratified random assignment (no restrictions, forced equal sizes, forced unequal sizes, and unequal probabilities). For within-subject...

  20. Statistical issues in the estimation of assigned shares for carcinogenesis liability

    International Nuclear Information System (INIS)

    Cox, L.A. Jr.

    1987-01-01

    Congress is currently considering adopting a mathematical formula to assign shares in cancer causation to specific doses of radiation, for use in establishing liability and compensation awards. The proposed formula, if it were sound, would allow difficult problems in tort law and public policy to be resolved by reference to tabulated probabilities of causation. This article examines the statistical and conceptual bases for the proposed methodology. We find that the proposed formula is incorrect as an expression for probability and causation, that it implies hidden, debatable policy judgments in its treatment of factor interactions and uncertainties, and that it can not in general be quantified with sufficient precision to be useful. Three generic sources of statistical uncertainty are identified--sampling variability, population heterogeneity, and error propagation--that prevent accurate quantification of assigned shares. These uncertainties arise whenever aggregate epidemiological or risk data are used to draw causal inferences about individual cases

  1. Manual of functions, assignments, and responsibilities for nuclear safety: Revision 2

    Energy Technology Data Exchange (ETDEWEB)

    1994-10-15

    The FAR Manual is a convenient easy-to-use collection of the functions, assignments, and responsibilities (FARs) of DOE nuclear safety personnel. Current DOE directives, including Orders, Secretary of Energy Notices, and other assorted policy memoranda, are the source of this information and form the basis of the FAR Manual. Today, the majority of FARs for DOE personnel are contained in DOE`s nuclear safety Orders. As these Orders are converted to rules in the Code of Federal Regulations, the FAR Manual will become the sole source for information relating to the functions, assignments, responsibilities of DOE nuclear safety personnel. The FAR Manual identifies DOE directives that relate to nuclear safety and the specific DOE personnel who are responsible for implementing them. The manual includes only FARs that have been extracted from active directives that have been approved in accordance with the procedures contained in DOE Order 1321.1B.

  2. MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

    Directory of Open Access Journals (Sweden)

    Zhang Liqing

    2010-01-01

    Full Text Available Abstract Background Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (i.e., the random duplication model. However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (i.e., the tandem duplication model. Results In this paper, we develop MSOAR 2.0, an improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those that were duplicated after the speciation (i.e., the so-called inparalogs, using a simple phylogenetic tree reconciliation method. For each such set of tandemly duplicated inparalogs, all but one gene will be deleted from the concerned genome (because they cannot possibly appear in any one-to-one ortholog pairs, and MSOAR is invoked. Using both simulated and real data experiments, we show that MSOAR 2.0 is able to achieve a better sensitivity and specificity than MSOAR. In comparison with the well-known genome-scale ortholog assignment tool InParanoid, Ensembl ortholog database, and the orthology information extracted from the well-known whole-genome multiple alignment program MultiZ, MSOAR 2.0 shows the highest sensitivity. Although the specificity of MSOAR 2.0 is slightly worse than that of InParanoid in the real data experiments

  3. A Hybrid Model for Making Online Assignments Effective In a Traditional Classroom

    Directory of Open Access Journals (Sweden)

    Ronda Sturgill

    2011-04-01

    Full Text Available Today’s college student has grown up in a world filled with technology and many current college students routinely utilize the latest and most up to date forms of technology. The result is an ever-changing way of communicating between faculty members and students. Many faculty members, however, are intimidated by the use of the terms “technology”, “online” and “distance education.” This often results in a communication gap between faculty and students where faculty members will “lose” students on the first day of class. Advantages of incorporating online tools into the course structure include freeing up additional class time, enhancing classroom discussions, and allowing students to remain current with information in their field. This hybrid instructional model focuses on the integration of technology tools as a supplement to traditional classroom teaching. This paper will describe how to effectively incorporate and implement technology using online course tools in a traditional classroom setting. Specific examples of online assignments, discussions, and assessments from an allied health education program and class will be discussed. Lessons learned and challenges confronted when adapting to the utilization of specific online course assignments and tools will be discussed.

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

    International Nuclear Information System (INIS)

    Meksuriyen, D.

    1988-01-01

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

  5. BATMAN--an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model.

    Science.gov (United States)

    Hao, Jie; Astle, William; De Iorio, Maria; Ebbels, Timothy M D

    2012-08-01

    Nuclear Magnetic Resonance (NMR) spectra are widely used in metabolomics to obtain metabolite profiles in complex biological mixtures. Common methods used to assign and estimate concentrations of metabolites involve either an expert manual peak fitting or extra pre-processing steps, such as peak alignment and binning. Peak fitting is very time consuming and is subject to human error. Conversely, alignment and binning can introduce artefacts and limit immediate biological interpretation of models. We present the Bayesian automated metabolite analyser for NMR spectra (BATMAN), an R package that deconvolutes peaks from one-dimensional NMR spectra, automatically assigns them to specific metabolites from a target list and obtains concentration estimates. The Bayesian model incorporates information on characteristic peak patterns of metabolites and is able to account for shifts in the position of peaks commonly seen in NMR spectra of biological samples. It applies a Markov chain Monte Carlo algorithm to sample from a joint posterior distribution of the model parameters and obtains concentration estimates with reduced error compared with conventional numerical integration and comparable to manual deconvolution by experienced spectroscopists. http://www1.imperial.ac.uk/medicine/people/t.ebbels/ t.ebbels@imperial.ac.uk.

  6. GENERAL ISSUES CONCERNING THE ASSIGNMENT OF SOCIAL PARTS

    Directory of Open Access Journals (Sweden)

    Stela Mihăilescu

    2012-11-01

    Full Text Available By means of the present study, we try to offer a thorough image and an analysis concerning the assignment mode of social parts within a company having limited liability. The assignment of social parts is free and unrestricted except for the cases provided by article 202, paragraph 2 from Law no. 31/ 1990- the law of commercial companies with further modifications and completions and the ones provided in OUG no. 54/ 2010 concerning some measures for fighting fiscal evasion. By means of the assignment operation a transmission is made up by an assignment of social parts contract towards one or more already associated persons in the company or towards other individual or legal persons who are going to obtain the associate quality. The principle governing any assignment is the one of goods circulation freedom, a freedom restricted only by the public order and imperative judicial norms.

  7. How contrast situations affect the assignment of causality in symmetric physical settings.

    Science.gov (United States)

    Beller, Sieghard; Bender, Andrea

    2014-01-01

    In determining the prime cause of a physical event, people often weight one of two entities in a symmetric physical relation as more important for bringing about the causal effect than the other. In a broad survey (Bender and Beller, 2011), we documented such weighting effects for different kinds of physical events and found that their direction and strength depended on a variety of factors. Here, we focus on one of those: adding a contrast situation that-while being formally irrelevant-foregrounds one of the factors and thus frames the task in a specific way. In two experiments, we generalize and validate our previous findings by using different stimulus material (in Experiment 1), by applying a different response format to elicit causal assignments, an analog rating scale instead of a forced-choice decision (in Experiment 2), and by eliciting explanations for the physical events in question (in both Experiments). The results generally confirm the contrast effects for both response formats; however, the effects were more pronounced with the force-choice format than with the rating format. People tended to refer to the given contrast in their explanations, which validates our manipulation. Finally, people's causal assignments are reflected in the type of explanation given in that contrast and property explanations were associated with biased causal assignments, whereas relational explanations were associated with unbiased assignments. In the discussion, we pick up the normative questions of whether or not these contrast effects constitute a bias in causal reasoning.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  9. Transition of lasing modes in polymeric opal photonic crystal resonating cavity.

    Science.gov (United States)

    Shi, Lan-Ting; Zheng, Mei-Ling; Jin, Feng; Dong, Xian-Zi; Chen, Wei-Qiang; Zhao, Zhen-Sheng; Duan, Xuan-Ming

    2016-06-10

    We demonstrate the transition of lasing modes in the resonating cavity constructed by polystyrene opal photonic crystals and 7 wt. % tert-butyl Rhodamine B doped polymer film. Both single mode and multiple mode lasing emission are observed from the resonating cavity. The lasing threshold is determined to be 0.81  μJ/pulse for single mode lasing emission and 2.25  μJ/pulse for multiple mode lasing emission. The single mode lasing emission is attributed to photonic lasing resulting from the photonic bandgap effect of the opal photonic crystals, while the multiple mode lasing emission is assigned to random lasing due to the defects in the photonic crystals. The result would benefit the development of low threshold polymeric solid state photonic crystal lasers.

  10. Dynamic online peer evaluations to improve group assignments in nursing e-learning environment.

    Science.gov (United States)

    Adwan, Jehad

    2016-06-01

    The purpose of this research was to evaluate the use of online peer evaluation forms for online group activities in improving group project outcomes. The investigator developed and used a web-based Google Forms® self and peer evaluation form of 2 group assignments' rubric for junior and senior nursing students. The form covered elements of the assignments including: research activity, analysis of the literature, writing of report, participation in making of presentation, overall contribution to the project, and participation in the weekly group discussions. Items were rated from 1 (did not contribute) to 5 (outstanding contribution) in addition to NA when one activity did not apply. The self and peer evaluation process was conducted twice: once after group assignment 1 and once after group assignment 2. The group assignments final products were done in the form of VoiceThread online presentations that were shared with the rest of the class reflecting the groups' work on a health informatics topic of interest. Data collected as the students completed self and peer evaluations for group assignments 1 and 2. Also, optional comments regarding member performance were collected to add contextual information in addition to ratings. Students received credit for completing the peer evaluations and the grade for the particular assignment was affected by their performance based on peer evaluations of their contributions. Students' peer evaluations showed in a color-coded spreadsheet which enabled the course faculty to view real time results of students' ratings after each assignment. The faculty provided timely and tailored feedback to groups or individuals as needed, using positive feedback and commending high performance while urging struggling individual students and groups to improve lower ratings in specific areas. Comparing evaluations of both assignments, there were statistically significant improvements among all students. The mean scores of the entire sample were

  11. 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…

  12. On Resonance: A Critical Pluralistic Inquiry into Advertising Rhetoric.

    OpenAIRE

    McQuarrie, Edward F; Mick, David Glen

    1992-01-01

    Print ads exhibit resonance when they combine wordplay with a relevant picture to create ambiguity and incongruity. This article uses multiple perspectives and methods within a framework of critical pluralism to investigate advertising resonance. Semiotic text analyses, a content analysis of contemporary magazine ads, two experiments, and phenomenological interviews combine to yield insights into the operation, prevalence, impact and experience of resonance. Specifically, the two experiments ...

  13. Prebiopsy magnetic resonance spectroscopy and imaging in the diagnosis of prostate cancer

    International Nuclear Information System (INIS)

    Kumar, V.; Jagannathan, N.R.; Thulkar, S.; Kumar, R.

    2012-01-01

    Existing screening investigations for the diagnosis of early prostate cancer lack specificity, resulting in a high negative biopsy rate. There is increasing interest in the use of various magnetic resonance methods for improving the yield of transrectal ultrasound-guided biopsies of the prostate in men suspected to have prostate cancer. We review the existing status of such investigations. A literature search was carried out using the Pubmed database to identify articles related to magnetic resonance methods for diagnosing prostate cancer. References from these articles were also extracted and reviewed. Recent studies have focused on prebiopsy magnetic resonance investigations using conventional magnetic resonance imaging, dynamic contrast enhanced magnetic resonance imaging, diffusion weighted magnetic resonance imaging, magnetization transfer imaging and magnetic resonance spectroscopy of the prostate. This marks a shift from the earlier strategy of carrying out postbiopsy magnetic resonance investigations. Prebiopsy magnetic resonance investigations has been useful in identifying patients who are more likely to have a biopsy positive for malignancy. Prebiopsy magnetic resonance investigations has a potential role in increasing specificity of screening for early prostate cancer. It has a role in the targeting of biopsy sites, avoiding unnecessary biopsies and predicting the outcome of biopsies. (author)

  14. Distribution functions for orbits trapped at the resonances in the Galactic disc

    Science.gov (United States)

    Monari, G.

    2017-12-01

    The present-day response of a Galactic disc stellar population to a non-axisymmetric perturbation of the potential has previously been computed through perturbation theory within the phase-space coordinates of the unperturbed axisymmetric system. Such an Eulerian linearized treatment however leads to singularities at resonances, which prevent quantitative comparisons with data. Monari et al. manage to capture the behaviour of the distribution function (DF) at a resonance in a Lagrangian approach, by averaging the Hamiltonian over fast angle variables and re-expressing the DF in terms of a new set of canonical actions and angles variables valid in the resonant region. They then follow the prescription of Binney (2016), assigning to the resonant DF the time average along the orbits of the axisymmetric DF expressed in the new set of actions and angles. This boils down to phase-mixing the DF in terms of the new angles, such that the DF for trapped orbits only depends on the new set of actions. This opens the way to quantitatively fitting the effects of the bar and spirals to Gaia data in terms of distribution functions in action space.

  15. pH and temperature effects on the molecular conformation of the porcine pancreatic secretory trypsin inhibitor as detected by hydrogen-1 nuclear magnetic resonance

    International Nuclear Information System (INIS)

    De Marco, A.; Menegatti, E.; Guarneri, M.

    1982-01-01

    1 H NMR spectra of the porcine pancreatic secretory trypsin inhibitor (PSTI) have been recorded vs. pH and temperature. Of the two tyrosines, one titrates with a pK of 1.25, while the resonances from the other are pH insensitive in the investigated range 4.8 less than or equal to pH less than or equal to 12. This is consistent with PSTI having one Tyr solvent exposed (Try-20) and the other buried (Tyr-31). The resonances from the lysyl epsilon-CH 2 protons titrate with a pK of 10.95. The titration is accompanied by a pronounced line broadening, which starts near pH 8.5. Between pH 11.5 and pH 12 the epsilon-CH 2 resonances recover their low pH line width. Titration curves for the lysines and Tyr-20 reflect single proton ionization equilibria, suggesting that these residues do not interact among themselves. On the basis of double resonance experiments, combined with analysis of chemical shifts, spin-spin couplngs, and line widths, all methyl resonances are identified and followed as functions of pH and temperature. The γ-CH 3 doublet from the N-terminal Thr-1 is assigned by comparison between spectra of forms I and II of the inhibitor, the latter lacking the first four residues of form I. The β-CH 3 resonance from Ala-7 is also assigned. Proton resonance parameters of methyl groups are shown to afford useful NMR probes for the characterization of local nonbonded interactions, microenvironments, and mobilities

  16. Integer Linear Programming for Constrained Multi-Aspect Committee Review Assignment

    Science.gov (United States)

    Karimzadehgan, Maryam; Zhai, ChengXiang

    2011-01-01

    Automatic review assignment can significantly improve the productivity of many people such as conference organizers, journal editors and grant administrators. A general setup of the review assignment problem involves assigning a set of reviewers on a committee to a set of documents to be reviewed under the constraint of review quota so that the reviewers assigned to a document can collectively cover multiple topic aspects of the document. No previous work has addressed such a setup of committee review assignments while also considering matching multiple aspects of topics and expertise. In this paper, we tackle the problem of committee review assignment with multi-aspect expertise matching by casting it as an integer linear programming problem. The proposed algorithm can naturally accommodate any probabilistic or deterministic method for modeling multiple aspects to automate committee review assignments. Evaluation using a multi-aspect review assignment test set constructed using ACM SIGIR publications shows that the proposed algorithm is effective and efficient for committee review assignments based on multi-aspect expertise matching. PMID:22711970

  17. Resonant inelastic X-ray scattering of liquid water

    International Nuclear Information System (INIS)

    Nilsson, Anders; Tokushima, Takashi; Horikawa, Yuka; Harada, Yoshihisa; Ljungberg, Mathias P.; Shin, Shik; Pettersson, Lars G.M.

    2013-01-01

    Highlights: ► Two peaks are observed in the lone pair region of the XES spectrum of water assigned to tetrahedral and distorted hydrogen bonding configurations. ► The isotope effect observed as different relative peak heights is due to spectral line shape differences. ► The two different hydrogen bonding environments can be related to local structures mimicking either low density water or high density water. -- Abstract: We review recent studies using resonant inelastic X-ray scattering (RIXS) or also here denoted X-ray emission spectroscopy (XES) on liquid water and the assignment of the two sharp peaks in the lone-pair region. Using the excitation energy dependence we connect the two peaks to specific features in the X-ray absorption (XAS) spectrum which have independently been assigned to molecules in tetrahedral or distorted configurations. The polarization dependence shows that both peaks are of 1b 1 origin supporting an interpretation in terms of two structural species, tetrahedral or disordered, which is furthermore consistent with the temperature-dependence of the two peaks. We discuss effects of life-time vibrational interference and how this affects the two components differently and also leads to differences in the relative peak heights for H 2 O and D 2 O. We show furthermore that the inherent structure in molecular dynamics simulations contain the structural bimodality suggested by XES, but this is smeared out in the real structure when temperature is included. We present a discussion around alternative interpretations suggesting that the origin of the two peaks is related to ultrafast dissociation and show evidence that such a model is inconsistent with several experimental observations and theoretical concepts. We conclude that the peaks reflect a temperature-dependent balance in fluctuations between tetrahedral and disordered structures in the liquid. This is well-aligned with theories of water under supercooled conditions and higher pressures

  18. Resonant inelastic X-ray scattering of liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, Anders, E-mail: nilsson@slac.stanford.edu [SUNCAT Ctr Interface Sci and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 (Sweden); Tokushima, Takashi [RIKEN/Spring-8, Sayo-cho, Sayo, Hyogo 679-5148 (Japan); Horikawa, Yuka [RIKEN/Spring-8, Sayo-cho, Sayo, Hyogo 679-5148 (Japan); Institute for Solid State Physics (ISSP), The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); Harada, Yoshihisa [RIKEN/Spring-8, Sayo-cho, Sayo, Hyogo 679-5148 (Japan); Institute for Solid State Physics (ISSP), The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); Synchrotron Radiation Research Organization, The University of Tokyo, Sayo-cho, Sayo, Hyogo 679-5165 (Japan); Ljungberg, Mathias P. [Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 (Sweden); Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus UAB, E-08193 Bellaterra (Spain); Shin, Shik [RIKEN/Spring-8, Sayo-cho, Sayo, Hyogo 679-5148 (Japan); Institute for Solid State Physics (ISSP), The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); Synchrotron Radiation Research Organization, The University of Tokyo, Sayo-cho, Sayo, Hyogo 679-5165 (Japan); Pettersson, Lars G.M. [Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 (Sweden)

    2013-06-15

    Highlights: ► Two peaks are observed in the lone pair region of the XES spectrum of water assigned to tetrahedral and distorted hydrogen bonding configurations. ► The isotope effect observed as different relative peak heights is due to spectral line shape differences. ► The two different hydrogen bonding environments can be related to local structures mimicking either low density water or high density water. -- Abstract: We review recent studies using resonant inelastic X-ray scattering (RIXS) or also here denoted X-ray emission spectroscopy (XES) on liquid water and the assignment of the two sharp peaks in the lone-pair region. Using the excitation energy dependence we connect the two peaks to specific features in the X-ray absorption (XAS) spectrum which have independently been assigned to molecules in tetrahedral or distorted configurations. The polarization dependence shows that both peaks are of 1b{sub 1} origin supporting an interpretation in terms of two structural species, tetrahedral or disordered, which is furthermore consistent with the temperature-dependence of the two peaks. We discuss effects of life-time vibrational interference and how this affects the two components differently and also leads to differences in the relative peak heights for H{sub 2}O and D{sub 2}O. We show furthermore that the inherent structure in molecular dynamics simulations contain the structural bimodality suggested by XES, but this is smeared out in the real structure when temperature is included. We present a discussion around alternative interpretations suggesting that the origin of the two peaks is related to ultrafast dissociation and show evidence that such a model is inconsistent with several experimental observations and theoretical concepts. We conclude that the peaks reflect a temperature-dependent balance in fluctuations between tetrahedral and disordered structures in the liquid. This is well-aligned with theories of water under supercooled conditions and

  19. Ring-Resonator/Sol-Gel Interferometric Immunosensor

    Science.gov (United States)

    Bearman, Gregory; Cohen, David

    2007-01-01

    A proposed biosensing system would be based on a combination of (1) a sensing volume containing antibodies immobilized in a sol-gel matrix and (2) an optical interferometer having a ring resonator configuration. The antibodies would be specific to an antigen species that one seeks to detect. In the ring resonator of the proposed system, light would make multiple passes through the sensing volume, affording greater interaction length and, hence, greater antibody- detection sensitivity.

  20. 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...

  1. Statistical aspects of optimal treatment assignment

    OpenAIRE

    van der Linden, Willem J.

    1980-01-01

    The issues of treatment assignment is ordinarily dealt with within the framework of testing aptitude treatment interaction (ATI) hypothesis. ATI research mostly uses linear regression techniques, and an ATI exists when the aptitude treatment (AT) regression lines cross each other within the relevant interval of the aptitude variable. Consistent with this approach is the use of the points of interaction of AT regression lines as treatment-assignment rule. The replacement of such rules by monot...

  2. One of My Favorite Assignments: Automated Teller Machine Simulation.

    Science.gov (United States)

    Oberman, Paul S.

    2001-01-01

    Describes an assignment for an introductory computer science class that requires the student to write a software program that simulates an automated teller machine. Highlights include an algorithm for the assignment; sample file contents; language features used; assignment variations; and discussion points. (LRW)

  3. Improved switching using Fano resonances in photonic crystal structures

    DEFF Research Database (Denmark)

    Heuck, Mikkel; Kristensen, Philip Trøst; Elesin, Yuriy

    2013-01-01

    difference time domain simulations taking into account the signal bandwidth. The results suggest a significant energy reduction by employing Fano resonances compared to more well established Lorentzian resonance structures. A specific example of a Kerr nonlinearity shows an order of magnitude energy...

  4. Moessbauer, electron paramagnetic resonance and magnetic susceptibility studies of photosensitive nitrile hydratase from Rhodococcus sp. N-771

    International Nuclear Information System (INIS)

    Nagamune, Teruyuki; Honda, Jun; Kobayashi, Yoshio; Sasabe, Hiroyuki; Endo, Isao; Ambe, Fumitoshi; Teratani, Yoshitaka; Hirata, Akira

    1992-01-01

    Moessbauer, magnetic susceptibility and electron paramagnetic resonance (EPR) studies of inactive and photoactivated NHase enzymes were performed to elucidate the electronic change of non-heme two-iron atom center of the enzyme by photoactivation. These spectroscopic investigations revealed that both the two iron atoms of the active NHase could be assigned to low-spin ferric state, and those of the inactive NHase could each be assigned to low-spin ferric and low-spin ferrous ones. From these results, it was concluded that one of the non-heme iron atoms is oxidized in the inactive NHase during photoactivation. (orig.)

  5. 7 CFR 1900.5 - Assignment of cases.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 12 2010-01-01 2010-01-01 false Assignment of cases. 1900.5 Section 1900.5 Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS... REGULATIONS GENERAL Delegations of Authority § 1900.5 Assignment of cases. The State Director may, in writing...

  6. Children's (Pediatric) Magnetic Resonance Imaging

    Medline Plus

    Full Text Available ... MRI) exam. View full size with caption Pediatric Content Some imaging tests and treatments have special pediatric considerations. The teddy bear denotes child-specific content. Related Articles and Media Catheter Angiography Magnetic Resonance, ...

  7. METHOD FOR SOLVING FUZZY ASSIGNMENT PROBLEM USING MAGNITUDE RANKING TECHNIQUE

    OpenAIRE

    D. Selvi; R. Queen Mary; G. Velammal

    2017-01-01

    Assignment problems have various applications in the real world because of their wide applicability in industry, commerce, management science, etc. Traditional classical assignment problems cannot be successfully used for real life problem, hence the use of fuzzy assignment problems is more appropriate. In this paper, the fuzzy assignment problem is formulated to crisp assignment problem using Magnitude Ranking technique and Hungarian method has been applied to find an optimal solution. The N...

  8. A systematic analysis of backbone amide assignments achieved via combinatorial selective labelling of amino acids

    Energy Technology Data Exchange (ETDEWEB)

    Jeremy Craven, C. [University of Sheffield, Department of Biotechnology and Molecular Biology (United Kingdom); Al-Owais, Moza; Parker, Martin J. [University of Leeds, Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology (United Kingdom)], E-mail: m.j.parker@leeds.ac.uk

    2007-06-15

    With the advent of high-yield cell-free expressions systems, many researchers are exploiting selective isotope labelling of amino acids to increase the efficiency and accuracy of the NMR assignment process. We developed recently a combinatorial selective labelling (CSL) method capable of yielding large numbers of residue-type and sequence-specific backbone amide assignments, which involves comparing cross-peak intensities in {sup 1}H-{sup 15}N HSQC and 2D {sup 1}H-{sup 15}N HNCO spectra collected for five samples containing different combinations of {sup 13}C- and {sup 15}N-labelled amino acids [Parker MJ, Aulton-Jones M, Hounslow A, Craven C J (2004) J Am Chem Soc 126:5020-5021]. In this paper we develop a robust method for establishing the reliability of these assignments. We have performed a detailed statistical analysis of the CSL data collected for a model system (the B1 domain of protein G from Streptococcus), developing a scoring method which allows the confidence in assignments to be assessed, and which enables the effects of overlap on assignment fidelity to be predicted. To further test the scoring method and also to assess the performance of CSL in relation to sample quality, we have applied the method to the CSL data collected for GFP in our previous study.

  9. Testing the Effectiveness of Online Assignments in Theory of Finance

    Science.gov (United States)

    Batu, Michael; Bower, Nancy; Lun, Esmond; Sadanand, Asha

    2018-01-01

    The authors investigated the effectiveness of online versus paper assignments using final examination scores in three cohorts of theory of finance. In particular, two cohorts were exposed to online assignments while another cohort was exposed to traditional assignments. The central result is that exposure to online assignments robustly leads to…

  10. Gravitoelectromagnetic resonances

    International Nuclear Information System (INIS)

    Tsagas, Christos G.

    2011-01-01

    The interaction between gravitational and electromagnetic radiation has a rather long research history. It is well known, in particular, that gravity-wave distortions can drive propagating electromagnetic signals. Since forced oscillations provide the natural stage for resonances to occur, gravitoelectromagnetic resonances have been investigated as a means of more efficient gravity-wave detection methods. In this report, we consider the coupling between the Weyl and the Maxwell fields on a Minkowski background, which also applies to astrophysical environments where gravity is weak, at the second perturbative level. We use covariant methods that describe gravitational waves via the transverse component of the shear, instead of pure-tensor metric perturbations. The aim is to calculate the properties of the electromagnetic signal, which emerges from the interaction of its linear counterpart with an incoming gravitational wave. Our analysis shows how the wavelength and the amplitude of the gravitationally driven electromagnetic wave vary with the initial conditions. More specifically, for certain initial data, the amplitude of the induced electromagnetic signal is found to diverge. Analogous, diverging, gravitoelectromagnetic resonances were also reported in cosmology. Given that, we extend our Minkowski space study to cosmology and discuss analogies and differences in the physics and in the phenomenology of the Weyl-Maxwell coupling between the aforementioned two physical environments.

  11. The Monte Carlo Quiz: Encouraging Punctual Completion and Deep Processing of Assigned Readings

    Science.gov (United States)

    Fernald, Peter S.

    2004-01-01

    The Monte Carlo Quiz (MCQ), a single-item quiz, is so named because chance, with the roll of a die, determines (a) whether the quiz is administered; (b) the specific article, chapter, or section of the assigned reading that the quiz covers; and (c) the particular question that makes up the quiz. The MCQ encourages both punctual completion and deep…

  12. Dynamic study of pelvic floor in patients with constipation: dynamic magnetic resonance vs defecography

    International Nuclear Information System (INIS)

    Gonzalez Vasquez, Carlos Mario; Pulgarin, Ricardo Luis German; Melo Arango, Catalina; Delgado de Bedout, Jorge Andres; Llano Serna, Juan Fernando; Restrepo Restrepo, Jose Ignacio

    2007-01-01

    Purpose: to compare the concordance between defecography and magnetic resonance in patients with constipation. Materials and methods: we did a prospective and descriptive assay to determine the concordance of a diagnostic test with 17 patients. The evaluation of the studies was double blind. Results: the 17 patients were females, age range 31 - 77 year the symptoms were present between 3 to 120 months. Anterior rectocele was the most common diagnosis (11 patients) and magnetic resonance had sensibility 100%, specificity 50%, positive predictive value 78, 57% and negative predictive value 100%. 7 patients had pelvic floor descent and magnetic resonance had sensibility 71.4%, specificity 20% positive predictive value 38.46% and negative predictive value 50%. Defecography found patients with enterocele and magnetic resonance had sensibility 0% and specificity 100 anismus was present in 2 patients and magnetic resonance didn't find them. Conclusion defecography is still the gold standard for patients with eonstipation. Magnetic resonance are a promise for those patients but has to improve

  13. Children's (Pediatric) Magnetic Resonance Imaging

    Medline Plus

    Full Text Available ... or thyroid problems. Any of these conditions may influence the decision on whether contrast material will be ... bear denotes child-specific content. Related Articles and Media Catheter Angiography Magnetic Resonance, Functional (fMRI) - Brain Children's ( ...

  14. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... bear denotes child-specific content. Related Articles and Media MR Angiography (MRA) Magnetic Resonance, Functional (fMRI) - Brain ... the web pages found at these links. About Us | Contact Us | FAQ | Privacy | Terms of Use | Links | ...

  15. Children's (Pediatric) Magnetic Resonance Imaging

    Medline Plus

    Full Text Available ... bear denotes child-specific content. Related Articles and Media Catheter Angiography Magnetic Resonance, Functional (fMRI) - Brain Children's ( ... the web pages found at these links. About Us | Contact Us | FAQ | Privacy | Terms of Use | Links | ...

  16. Accuracy of magnetic resonance in identifying traumatic intraarticular knee lesions

    International Nuclear Information System (INIS)

    Vaz, Carlos Eduardo Sanches; Camargo, Olavo Pires de; Santana, Paulo Jose de; Valezi, Antonio Carlos

    2005-01-01

    Purpose: To evaluate the diagnostic accuracy of magnetic resonance imaging of the knee in identifying traumatic intraarticular knee lesions. Method: 300 patients with a clinical diagnosis of traumatic intraarticular knee lesions underwent prearthoscopic magnetic resonance imaging. The sensitivity, specificity, positive predictive value, negative predictive value, likelihood ratio for a positive test, likelihood ratio for a negative test, and accuracy of magnetic resonance imaging were calculated relative to the findings during arthroscopy in the studied structures of the knee (medial meniscus, lateral meniscus, anterior cruciate ligament, posterior cruciate ligament, and articular cartilage). Results: Magnetic resonance imaging produced the following results regarding detection of lesions: medial meniscus: sensitivity 97.5%, specificity 92.9%, positive predictive value 93.9%, positive negative value 97%, likelihood positive ratio 13.7, likelihood negative ratio 0.02, and accuracy 95.3%; lateral meniscus: sensitivity 91.9%, specificity 93.6%, positive predictive value 92.7%, positive negative value 92.9%, likelihood positive ratio 14.3, likelihood negative ratio 0.08, and accuracy 93.6%; anterior cruciate ligament: sensitivity 99.0%, specificity 95.9%, positive predictive value 91.9%, positive negative value 99.5%, likelihood positive ratio 21.5, likelihood negative ratio 0.01, and accuracy 96.6%; posterior cruciate ligament: sensitivity 100%, specificity 99%, positive predictive value 80.0%, positive negative value 100%, likelihood positive ratio 100, likelihood negative ratio 0.01, and accuracy 99.6%; articular cartilage: sensitivity 76.1%, specificity 94.9%, positive predictive value 94.7%, positive negative value 76.9%, likelihood positive ratio 14.9, likelihood negative ratio 0.25, and accuracy 84.6%. Conclusion: Magnetic resonance imaging is a satisfactory diagnostic tool for evaluating meniscal and ligamentous lesions of the knee, but it is unable to clearly

  17. Accuracy of magnetic resonance in identifying traumatic intraarticular knee lesions

    Directory of Open Access Journals (Sweden)

    Vaz Carlos Eduardo Sanches

    2005-01-01

    Full Text Available PURPOSE: To evaluate the diagnostic accuracy of magnetic resonance imaging of the knee in identifying traumatic intraarticular knee lesions. METHOD: 300 patients with a clinical diagnosis of traumatic intraarticular knee lesions underwent prearthoscopic magnetic resonance imaging. The sensitivity, specificity, positive predictive value, negative predictive value, likelihood ratio for a positive test, likelihood ratio for a negative test, and accuracy of magnetic resonance imaging were calculated relative to the findings during arthroscopy in the studied structures of the knee (medial meniscus, lateral meniscus, anterior cruciate ligament, posterior cruciate ligament, and articular cartilage. RESULTS: Magnetic resonance imaging produced the following results regarding detection of lesions: medial meniscus: sensitivity 97.5%, specificity 92.9%, positive predictive value 93.9%, positive negative value 97%, likelihood positive ratio 13.7, likelihood negative ratio 0.02, and accuracy 95.3%; lateral meniscus: sensitivity 91.9%, specificity 93.6%, positive predictive value 92.7%, positive negative value 92.9%, likelihood positive ratio 14.3, likelihood negative ratio 0.08, and accuracy 93.6%; anterior cruciate ligament: sensitivity 99.0%, specificity 95.9%, positive predictive value 91.9%, positive negative value 99.5%, likelihood positive ratio 21.5, likelihood negative ratio 0.01, and accuracy 96.6%; posterior cruciate ligament: sensitivity 100%, specificity 99%, positive predictive value 80.0%, positive negative value 100%, likelihood positive ratio 100, likelihood negative ratio 0.01, and accuracy 99.6%; articular cartilage: sensitivity 76.1%, specificity 94.9%, positive predictive value 94.7%, positive negative value 76.9%, likelihood positive ratio 14.9, likelihood negative ratio 0.25, and accuracy 84.6%. CONCLUSION: Magnetic resonance imaging is a satisfactory diagnostic tool for evaluating meniscal and ligamentous lesions of the knee, but it is

  18. Integrated assignment and path planning

    Science.gov (United States)

    Murphey, Robert A.

    2005-11-01

    A surge of interest in unmanned systems has exposed many new and challenging research problems across many fields of engineering and mathematics. These systems have the potential of transforming our society by replacing dangerous and dirty jobs with networks of moving machines. This vision is fundamentally separate from the modern view of robotics in that sophisticated behavior is realizable not by increasing individual vehicle complexity, but instead through collaborative teaming that relies on collective perception, abstraction, decision making, and manipulation. Obvious examples where collective robotics will make an impact include planetary exploration, space structure assembly, remote and undersea mining, hazardous material handling and clean-up, and search and rescue. Nonetheless, the phenomenon driving this technology trend is the increasing reliance of the US military on unmanned vehicles, specifically, aircraft. Only a few years ago, following years of resistance to the use of unmanned systems, the military and civilian leadership in the United States reversed itself and have recently demonstrated surprisingly broad acceptance of increasingly pervasive use of unmanned platforms in defense surveillance, and even attack. However, as rapidly as unmanned systems have gained acceptance, the defense research community has discovered the technical pitfalls that lie ahead, especially for operating collective groups of unmanned platforms. A great deal of talent and energy has been devoted to solving these technical problems, which tend to fall into two categories: resource allocation of vehicles to objectives, and path planning of vehicle trajectories. An extensive amount of research has been conducted in each direction, yet, surprisingly, very little work has considered the integrated problem of assignment and path planning. This dissertation presents a framework for studying integrated assignment and path planning and then moves on to suggest an exact

  19. 12 CFR 563e.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Assigned ratings. 563e.28 Section 563e.28 Banks... for Assessing Performance § 563e.28 Assigned ratings. (a) Ratings in general. Subject to paragraphs (b... performance under the lending, investment and service tests, the community development test, the small savings...

  20. How contrast situations affect the assignment of causality in symmetric physical settings

    Directory of Open Access Journals (Sweden)

    Sieghard eBeller

    2015-01-01

    Full Text Available In determining the prime cause of a physical event, people often weight one of two entities in a symmetric physical relation as more important for bringing about the causal effect than the other. In a broad survey (Bender and Beller, 2011, we documented such weighting effects for different kinds of physical events and found that their direction and strength depended on a variety of factors. Here, we focus on one of those: adding a contrast situation that—while being formally irrelevant—foregrounds one of the factors and thus frames the task in a specific way. In two experiments, we generalize and validate our previous findings by using different stimulus material (in Experiment 1, by applying a different response format to elicit causal assignments, an analogue rating scale instead of a forced-choice decision (in Experiment 2, and by eliciting explanations for the physical events in question (in both experiments. The results generally confirm the contrast effects for both response formats; however, the effects were more pronounced with the force-choice format than with the rating format. People tended to refer to the given contrast in their explanations, which validates our manipulation. Finally, people’s causal assignments are reflected in the type of explanation given in that contrast and property explanations were associated with biased causal assignments, whereas relational explanations were associated with unbiased assignments. In the discussion, we pick up the normative questions of whether or not these contrast effects constitute a bias in causal reasoning.

  1. Privacy-Preserving Task Assignment in Spatial Crowdsourcing

    KAUST Repository

    Liu, An

    2017-09-20

    With the progress of mobile devices and wireless networks, spatial crowdsourcing (SC) is emerging as a promising approach for problem solving. In SC, spatial tasks are assigned to and performed by a set of human workers. To enable effective task assignment, however, both workers and task requesters are required to disclose their locations to untrusted SC systems. In this paper, we study the problem of assigning workers to tasks in a way that location privacy for both workers and task requesters is preserved. We first combine the Paillier cryptosystem with Yao’s garbled circuits to construct a secure protocol that assigns the nearest worker to a task. Considering that this protocol cannot scale to a large number of workers, we then make use of Geohash, a hierarchical spatial index to design a more efficient protocol that can securely find approximate nearest workers. We theoretically show that these two protocols are secure against semi-honest adversaries. Through extensive experiments on two real-world datasets, we demonstrate the efficiency and effectiveness of our protocols.

  2. Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring

    DEFF Research Database (Denmark)

    Bekkevold, Dorte; Helyar, Sarah J.; Limborg, Morten T.

    2015-01-01

    , there are relatively few examples in marine fish displaying accurate origin assignment. We synthesize data for 156 single-nucleotide polymorphisms typed in 1039 herring, Clupea harengus L., spanning the Northeast Atlantic to develop a tool that allows assignment of individual herring to their regional origin. We show......Regulations on the exploitation of populations of commercially important fish species and the ensuing consumer interest in sustainable products have increased the need to accurately identify the population of origin of fish and fish products. Although genomics-based tools have proven highly useful...... the method's suitability to address specific biological questions, as well as management applications. We analyse temporally replicated collections from two areas, the Skagerrak (n = 81, 84, 66) and the western Baltic (n = 52, 52). Both areas harbour heavily fished mixed-origin stocks, complicating...

  3. Investigation of the Pygmy Dipole Resonance in {sup 60}Ni

    Energy Technology Data Exchange (ETDEWEB)

    Fritzsche, Matthias; Pietralla, Norbert; Romig, Christopher; Savran, Deniz; Sonnabend, Kerstin [Institut fuer Kernphysik, Technische Universitaet, Darmstadt (Germany); Rusev, Gencho; Tonchev, Anton P.; Tornow, Werner; Weller, Henry R. [Triangle Universities Nuclear Laboratory, Duke University, Durham, NC (United States); Zilges, Andreas [Institut fuer Kernphysik, Universitaet Koeln (Germany)

    2009-07-01

    At the High Intensity Photon Setup (HIPS) at S-DALINAC in Darmstadt {sup 60}Ni was investigated with unpolarized bremsstrahlung with energies up to 8.0 MeV and 9.9 MeV, respectively. Determination of spin and parity quantum numbers and absolute transition strengths was possible, using HPGe detectors placed under different angles. To assign also parity quantum numbers, the polarized photon beam of the High Intensity Gamma Source (HI{gamma}S) at Duke University was used. With the combined results, evidence of the Pygmy Dipole Resonance in {sup 60}Ni was found.

  4. Optical and magnetic resonance measurements of a segmented poly(ester urethane)

    International Nuclear Information System (INIS)

    Cooke, D.W.; Muenchausen, R.E.; Bennett, B.L.; Orler, E.B.; Wrobleski, D.A.; Smith, M.E.; Jahan, M.S.; Thomas, D.E.

    1999-01-01

    X-ray-induced damage in Estane(registered trademark)5703 has been studied by luminescence, optical absorption and electron spin resonance techniques in the temperature interval ∼10-300 K. Molecular motion of the polymer soft segment, as determined by viscoelastic measurements, is correlated with features in the glow curve, indicating charge detrapping via thermal destruction of cavity traps. Spectral emission is characterized by four Lorentzian bands with maxima at 2.38, 2.55, 2.74 and 2.93 eV, which are attributed to triplet-to-singlet electronic transitions of the phenyl group in the polymer hard segment. Absorption peaks at 3.97, 4.29 and 4.46 eV are also assigned to transitions within this group. Several radicals with overlapping resonances are induced at 35 K, which, with increasing temperature, evolve into the relatively stable peroxy free-radical at room temperature

  5. Environmental Light and Its Relationship with Electromagnetic Resonances of Biomolecular Interactions, as Predicted by the Resonant Recognition Model

    Directory of Open Access Journals (Sweden)

    Irena Cosic

    2016-06-01

    Full Text Available The meaning and influence of light to biomolecular interactions, and consequently to health, has been analyzed using the Resonant Recognition Model (RRM. The RRM proposes that biological processes/interactions are based on electromagnetic resonances between interacting biomolecules at specific electromagnetic frequencies within the infra-red, visible and ultra-violet frequency ranges, where each interaction can be identified by the certain frequency critical for resonant activation of specific biological activities of proteins and DNA. We found that: (1 the various biological interactions could be grouped according to their resonant frequency into super families of these functions, enabling simpler analyses of these interactions and consequently analyses of influence of electromagnetic frequencies to health; (2 the RRM spectrum of all analyzed biological functions/interactions is the same as the spectrum of the sun light on the Earth, which is in accordance with fact that life is sustained by the sun light; (3 the water is transparent to RRM frequencies, enabling proteins and DNA to interact without loss of energy; (4 the spectrum of some artificial sources of light, as opposed to the sun light, do not cover the whole RRM spectrum, causing concerns for disturbance to some biological functions and consequently we speculate that it can influence health.

  6. Evidence of demyelination in mild cognitive impairment and dementia using a direct and specific magnetic resonance imaging measure of myelin content.

    Science.gov (United States)

    Bouhrara, Mustapha; Reiter, David A; Bergeron, Christopher M; Zukley, Linda M; Ferrucci, Luigi; Resnick, Susan M; Spencer, Richard G

    2018-04-18

    We investigated brain demyelination in aging, mild cognitive impairment (MCI), and dementia using magnetic resonance imaging of myelin. Brains of young and old controls and old subjects with MCI, Alzheimer's disease, or vascular dementia were scanned using our recently developed myelin water fraction (MWF) mapping technique, which provides greatly improved accuracy over previous comparable methods. Maps of MWF, a direct and specific myelin measure, and relaxation times and magnetization transfer ratio, indirect and nonspecific measures, were constructed. MCI subjects showed decreased MWF compared with old controls. Demyelination was greater in Alzheimer's disease or vascular dementia. As expected, decreased MWF was accompanied by decreased magnetization transfer ratio and increased relaxation times. The young subjects showed greater myelin content than the old subjects. We believe this to be the first demonstration of myelin loss in MCI, Alzheimer's disease, and vascular dementia using a method that provides a quantitative magnetic resonance imaging-based measure of myelin. Our findings add to the emerging evidence that myelination may represent an important biomarker for the pathology of MCI and dementia. This study supports the investigation of the role of myelination in MCI and dementia through use of this quantitative magnetic resonance imaging approach in clinical studies of disease progression, relationship of functional status to myelination status, and therapeutics. Furthermore, mapping MWF may permit myelin to serve as a therapeutic target in clinical trials. Copyright © 2018. Published by Elsevier Inc.

  7. NOESY-WaterControl: a new NOESY sequence for the observation of under-water protein resonances

    Energy Technology Data Exchange (ETDEWEB)

    Torres, Allan M.; Zheng, Gang, E-mail: g.zheng@westernsydney.edu.au; Price, William S. [Western Sydney University, Nanoscale Organisation and Dynamics Group, School of Science and Health (Australia)

    2017-03-15

    Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω{sub 2}). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω{sub 2}. The 2D NOESY maps obtained using the new sequence thus provide more information than the maps obtained with conventional water suppression, thereby lessening the number of experiments needed to complete resonance assignments of biomolecules. The 2D NOESY-WaterControl map of BPTI showed strong bound water and exchangeable proton signals in ω{sub 1} but these signals were absent in ω{sub 2}, indicating the possibility of using the new sequence to discriminate bound water and exchangeable proton resonances from non-labile proton resonances with similar chemical shifts to water.

  8. Incorporating breeding abundance into spatial assignments on continuous surfaces.

    Science.gov (United States)

    Rushing, Clark S; Marra, Peter P; Studds, Colin E

    2017-06-01

    Determining the geographic connections between breeding and nonbreeding populations, termed migratory connectivity, is critical to advancing our understanding of the ecology and conservation of migratory species. Assignment models based on stable isotopes historically have been an important tool for studying migratory connectivity of small-bodied species, but the low resolution of these assignments has generated interest into combining isotopes with other sources in information. Abundance is one of the most appealing data sources to include in isotope-based assignments, but there are currently no statistical methods or guidelines for optimizing the contribution of stable isotopes and abundance for inferring migratory connectivity. Using known-origin stable-hydrogen isotope samples of six Neotropical migratory bird species, we rigorously assessed the performance of assignment models that differentially weight the contribution of the isotope and abundance data. For two species with adequate sample sizes, we used Pareto optimality to determine the set of models that simultaneously minimized both assignment error rate and assignment area. We then assessed the ability of the top models from these two species to improve assignments of the remaining four species compared to assignments based on isotopes alone. We show that the increased precision of models that include abundance is often offset by a large increase in assignment error. However, models that optimally weigh the abundance data relative to the isotope data can result in higher precision and, in some cases, lower error than models based on isotopes alone. The top models, however, depended on the distribution of relative breeding abundance, with patchier distributions requiring stronger downweighting of abundance, and we present general guidelines for future studies. These results confirm that breeding abundance can be an important source of information for studies investigating broad-scale movements of

  9. Magnetic resonance spectral characterization of the heme active site of Coprinus cinereus peroxidase

    International Nuclear Information System (INIS)

    Lukat, G.S.; Rodgers, K.R.; Jabro, M.N.; Goff, H.M.

    1989-01-01

    Examination of the peroxidase isolated from the inkcap Basidiomycete Coprinus cinereus shows that the 42,000-dalton enzyme contains a protoheme IX prosthetic group. Reactivity assays and the electronic absorption spectra of native Coprinus peroxidase and several of its ligand complexes indicate that this enzyme has characteristics similar to those reported for horseradish peroxidase. In this paper, the authors characterize the H 2 O 2 -oxidized forms of Coprinus peroxidase compounds I, II, and III by electronic absorption and magnetic resonance spectroscopies. Electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) studies of this Coprinus peroxidase indicate the presence of high-spin Fe(III) in the native protein and a number of differences between the heme site of Coprinus peroxidase and horseradish peroxidase. Carbon-13 (of the ferrous CO adduct) and nitrogen-15 (of the cyanide complex) NMR studies together with proton NMR studies of the native and cyanide-complexed Caprinus peroxidase are consistent with coordination of a proximal histidine ligand. The EPR spectrum of the ferrous NO complex is also reported. Protein reconstitution with deuterated hemin has facilitated the assignment of the heme methyl resonances in the proton NMR spectrum

  10. Entangling distant resonant exchange qubits via circuit quantum electrodynamics

    Science.gov (United States)

    Srinivasa, V.; Taylor, J. M.; Tahan, Charles

    2016-11-01

    We investigate a hybrid quantum system consisting of spatially separated resonant exchange qubits, defined in three-electron semiconductor triple quantum dots, that are coupled via a superconducting transmission line resonator. Drawing on methods from circuit quantum electrodynamics and Hartmann-Hahn double resonance techniques, we analyze three specific approaches for implementing resonator-mediated two-qubit entangling gates in both dispersive and resonant regimes of interaction. We calculate entangling gate fidelities as well as the rate of relaxation via phonons for resonant exchange qubits in silicon triple dots and show that such an implementation is particularly well suited to achieving the strong coupling regime. Our approach combines the favorable coherence properties of encoded spin qubits in silicon with the rapid and robust long-range entanglement provided by circuit QED systems.

  11. Enhancement of Otolith Specific Ocular Responses Using Vestibular Stochastic Resonance

    Science.gov (United States)

    Fiedler, Matthew; De Dios, Yiri E.; Esteves, Julie; Galvan, Raquel; Wood, Scott; Bloomberg, Jacob; Mulavara, Ajitkumar

    2011-01-01

    Introduction: Astronauts experience disturbances in sensorimotor function after spaceflight during the initial introduction to a gravitational environment, especially after long-duration missions. Our goal is to develop a countermeasure based on vestibular stochastic resonance (SR) that could improve central interpretation of vestibular input and mitigate these risks. SR is a mechanism by which noise can assist and enhance the response of neural systems to relevant, imperceptible sensory signals. We have previously shown that imperceptible electrical stimulation of the vestibular system enhances balance performance while standing on an unstable surface. Methods: Eye movement data were collected from 10 subjects during variable radius centrifugation (VRC). Subjects performed 11 trials of VRC that provided equivalent tilt stimuli from otolith and other graviceptor input without the normal concordant canal cues. Bipolar stochastic electrical stimulation, in the range of 0-1500 microamperes, was applied to the vestibular system using a constant current stimulator through electrodes placed over the mastoid process behind the ears. In the VRC paradigm, subjects were accelerated to 216 deg./s. After the subjects no longer sensed rotation, the chair oscillated along a track at 0.1 Hz to provide tilt stimuli of 10 deg. Eye movements were recorded for 6 cycles while subjects fixated on a target in darkness. Ocular counter roll (OCR) movement was calculated from the eye movement data during periods of chair oscillations. Results: Preliminary analysis of the data revealed that 9 of 10 subjects showed an average increase of 28% in the magnitude of OCR responses to the equivalent tilt stimuli while experiencing vestibular SR. The signal amplitude at which performance was maximized was in the range of 100-900 microamperes. Discussion: These results indicate that stochastic electrical stimulation of the vestibular system can improve otolith specific responses. This will have a

  12. Dual earners’ willingness to accept an international assignment.

    NARCIS (Netherlands)

    van der Velde, E.G.; Bossink, C.J.H.; Jansen, P.G.W.

    2005-01-01

    Multinational organisations experience difficulties in finding managers willing to accept international assignments. This study has therefore focused on factors that can predict males' and females' willingness to accept international assignments, or to follow their partners on international

  13. Task assignment and coaching

    NARCIS (Netherlands)

    Dominguez-Martinez, S.

    2009-01-01

    An important task of a manager is to motivate her subordinates. One way in which a manager can give incentives to junior employees is through the assignment of tasks. How a manager allocates tasks in an organization, provides information to the junior employees about his ability. Without coaching

  14. Resonance Raman Spectrum of the Transient (SCN)2 Free Radical Anion

    DEFF Research Database (Denmark)

    Wilbrandt, Robert Walter; Jensen, N. H.; Pagsberg, Palle Bjørn

    1979-01-01

    The resonance Raman spectrum of the transient species (λmax = 475 nm, τ½ = 1.6 μs) formed by pulse radiolysis of aqueous solutions of thiocyanate, SCN2−, is reported. The spectrum is discussed in terms of the previous assignment of this transient to the radical anion, (SCN)−2. The observed...... vibrational frequencies of the radical anion are consistent with substantial weakening of the S---S and the Ctriple bond; length as m-dashN bonds are compared with neutral thiocyanogen....

  15. SimPhospho: a software tool enabling confident phosphosite assignment.

    Science.gov (United States)

    Suni, Veronika; Suomi, Tomi; Tsubosaka, Tomoya; Imanishi, Susumu Y; Elo, Laura L; Corthals, Garry L

    2018-03-27

    Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. SimPhospho is available for Windows, Linux and Mac operating systems at https://sourceforge.net/projects/simphospho/. It is open source and implemented in C ++. A user's manual with detailed description of data analysis using SimPhospho as well as test data can be found as supplementary material of this article. Supplementary data are available at https://www.btk.fi/research/ computational-biomedicine/software/.

  16. Specific proof of various stages of Osler's disease of the brain via high field magnetic resonance tomography (1. 5 Tesla)

    Energy Technology Data Exchange (ETDEWEB)

    Billet, F.; Bluemm, R.G.; Beyer, H.K.

    1988-08-01

    MR is a sensitive noninvasive examination method for diagnosing parenchymatous cryptic arteriovenous malformations and sequels of cerebral haemorrhage. In a patient with recurring nosebleed and brain stem syndrome eleven so-called cryptic arteriovenous malformations or their haemorrhage sequels were diagnosed via magnetic resonance tomography. Basing on these specific findings, nosebleeding, and a positive family anamnesis, the findings could be classified as belonging to manifestations of Osler's disease (hereditary haemorrhagic telangiectasia). This rare disease is characterised by a triad of signs: telangiectasias, recurring bleeding, and heredity. In this article the specific MR image is compared with the CT pattern and the results are discussed against the background of literature on Osler's disease which is also known as Rendu-Osler-Weber disease.

  17. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested that prot......The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...

  18. Age- and gender-specific differences in left and right ventricular cardiac function and mass determined by cine magnetic resonance imaging

    International Nuclear Information System (INIS)

    Sandstede, J.; Lipke, C.; Beer, M.; Hofmann, S.; Pabst, T.; Kenn, W.; Hahn, D.; Neubauer, S.

    2000-01-01

    We examined possible age- and gender-specific differences in the function and mass of left (LV) and right (RV) ventricles in 36 healthy volunteers using cine gradient-recalled echo magnetic resonance imaging. Subjects were divided into four groups (nine men and nine women in each): men aged under 45 years (32 ± 7), women aged under 45 (27 ± 6), men aged over 45 (59 ± 8), and women aged over 45 (57 ± 9). Functional analysis of cardiac volume and mass and of LV wall motion was performed by manual segmentation of the endocardial and epicardial borders of the end-diastolic and end-systolic frame; both absolute and normalized (per square meter body surface area) values were evaluated. With age there was a significant decrease in both absolute and normalized LV and RV chamber volumes (EDV, ESV), while LV and RV masses remained unchanged. Gender-specific differences were found in cardiac mass and volume (for men and women, respectively: LV mass, 155 ± 18 and 110 ± 16 g; LV EDV, 118 ± 27 and 96 ± 21 ml; LV ESV, 40 ± 13 and 29 ± 9 ml; RV mass, 52 ± 10 and 39 ± 5 g; RV EDV, 131 ± 28 and 100 ± 23 ml; RV ESV, 53 ± 17 and 33 ± 15 ml). Normalization to body surface area eliminated differences in LV volumes but not those in LV mass, RV mass, or RV function. Functional parameters such as cardiac output and LV ejection fraction showed nonsignificant or only slight differences and were thus largely independent of age and gender. Intra- and interobserver variability ranged between 1.4 % and 5.9 % for all parameters. Cine magnetic resonance imaging thus shows age- and gender-specific differences in cardiac function, and therefore the evaluation of cardiac function in patients should consider age- and gender-matched normative values. (orig.)

  19. Testing resonating vector strength: Auditory system, electric fish, and noise

    Science.gov (United States)

    Leo van Hemmen, J.; Longtin, André; Vollmayr, Andreas N.

    2011-12-01

    Quite often a response to some input with a specific frequency ν○ can be described through a sequence of discrete events. Here, we study the synchrony vector, whose length stands for the vector strength, and in doing so focus on neuronal response in terms of spike times. The latter are supposed to be given by experiment. Instead of singling out the stimulus frequency ν○ we study the synchrony vector as a function of the real frequency variable ν. Its length turns out to be a resonating vector strength in that it shows clear maxima in the neighborhood of ν○ and multiples thereof, hence, allowing an easy way of determining response frequencies. We study this "resonating" vector strength for two concrete but rather different cases, viz., a specific midbrain neuron in the auditory system of cat and a primary detector neuron belonging to the electric sense of the wave-type electric fish Apteronotus leptorhynchus. We show that the resonating vector strength always performs a clear resonance correlated with the phase locking that it quantifies. We analyze the influence of noise and demonstrate how well the resonance associated with maximal vector strength indicates the dominant stimulus frequency. Furthermore, we exhibit how one can obtain a specific phase associated with, for instance, a delay in auditory analysis.

  20. Authentication Sensing System Using Resonance Evaluation Spectroscopy (ASSURES)

    Science.gov (United States)

    Trolinger, James D.; Dioumaev, Andrei K.; Lal, Amit K.; Dimas, Dave

    2017-08-01

    This paper describes an ongoing instrument development project to distinguish genuine manufactured components from counterfeit components; we call the instrument ASSURES (Authentication Sensing System Using Resonance Evaluation Spectroscopy). The system combines Laser Doppler Vibrometry with acoustical resonance spectroscopy, augmented with finite element analysis. Vibrational properties of components, such as resonant modes, damping, and spectral frequency response to various forcing functions depend strongly upon the mechanical properties of the material, including its size, shape, internal hardness, tensile strength, alloy/composite compositions, flaws, defects, and other internal material properties. Although acoustic resonant spectroscopy has seen limited application, the information rich signals in the vibrational spectra of objects provide a pathway to many new applications. Components with the same shape but made of different materials, different fatigue histories, damage, tampering, or heat treatment, will respond differently to high frequency stimulation. Laser Doppler Vibrometry offers high sensitivity and frequency bandwidth to measure the component's frequency spectrum, and overcomes many issues that limit conventional acoustical resonance spectroscopy, since the sensor laser beam can be aimed anywhere along the part as well as to multiple locations on a part in a non-contact way. ASSURES is especially promising for use in additive manufacturing technology by providing signatures as digital codes that are unique to specific objects and even to specific locations on objects. We believe that such signatures can be employed to address many important issues in the manufacturing industry. These include insuring the part meets the often very rigid specifications of the customer and being able to detect non-visible internal manufacturing defects or non-visible damage that has occurred after manufacturing.

  1. 56Fe resonance parameters for neutron energies up to 850 keV

    International Nuclear Information System (INIS)

    Perey, C.M.; Perey, F.G.; Harvey, J.A.; Hill, N.W.; Larson, N.M.

    1990-12-01

    High-resolution neutron measurements for 56 Fe-enriched iron targets were made at the Oak Ridge Electron Linear Accelerator (ORELA) in transmission below 20 MeV and in differential elastic scattering below 5 MeV. Transmission measurements were also performed with a natural iron target below 160 keV. The transmission data were analyzed from 5 to 850 keV with the multilevel R-matrix code SAMMY which uses Bayes' theorem for the fitting process. This code provides energies and neutron widths of the resonances inside the 5- to 850-keV energy region, as well as possible parameterization for resonances external to the analyzed region to describe the smooth cross section from a few eV to 850 keV. The resulting set of resonance parameters yields the accepted values for the thermal total and capture cross sections. The differential elastic-scattering data at several scattering angles were compared to theoretical calculations from 40 to 850 keV using the R-matrix code RFUNC based on the Blatt-Biedenharn formalism. Various combinations of spin and parity were tried to predict cross sections for the well defined ell > 0 resonances; comparison of these predictions with the data allowed us to determine the most likely spin and parity assignments for these resonances. The results of a capture data analysis by Corvi et al. (COR84), from 2 to 350 keV, were combined with our results to obtain the radiation widths of the resonances below 350 keV observed in transmission, capture, and differential elastic-scattering experiments

  2. Packets of resonant modes in the Fermi–Pasta–Ulam system

    International Nuclear Information System (INIS)

    Genta, Tommaso; Giorgilli, Antonio; Paleari, Simone; Penati, Tiziano

    2012-01-01

    We reconsider the phenomenon of localization of energy in low frequency modes in the FPU system, exploiting the resonances in the lower part of the spectrum. Using the resonant normal form of Birkhoff we construct some candidates of approximate first integrals which we put in correspondence to packets of low frequency modes. By numerical calculation we show that the packet associated to the best quasi-integral involves all modes up to a frequency ω ⁎ (ε), where ε is the specific energy. The phenomenon disappears when the specific energy is bigger than a threshold value. The dependence of the relevant quantities on the number N of particles is also investigated. A final section is devoted to a first comparison with the Toda model. -- Highlights: ► We study the role of resonances for energy localization and metastability in the FPU model. ► We construct an approximated first integral associated to the metastable state. ► We propose to identify the metastable state as a packet of resonant modes. ► The packet extend up to a frequency ω ⁎ (ε), which depends only on the specific energy ε.

  3. Packets of resonant modes in the Fermi–Pasta–Ulam system

    Energy Technology Data Exchange (ETDEWEB)

    Genta, Tommaso, E-mail: tomgenta@gmail.com [Università degli Studi di Milano, Corso di Laurea in Matematica, Via C. Saldini 50, 20133 Milano (Italy); Giorgilli, Antonio, E-mail: antonio.giorgilli@unimi.it [Università degli Studi di Milano, Dipartimento di Matematica, Via C. Saldini 50, 20133 Milano (Italy); Paleari, Simone, E-mail: simone.paleari@unimi.it [Università degli Studi di Milano, Dipartimento di Matematica, Via C. Saldini 50, 20133 Milano (Italy); Penati, Tiziano, E-mail: tiziano.penati@unimi.it [Università degli Studi di Milano, Dipartimento di Matematica, Via C. Saldini 50, 20133 Milano (Italy)

    2012-06-04

    We reconsider the phenomenon of localization of energy in low frequency modes in the FPU system, exploiting the resonances in the lower part of the spectrum. Using the resonant normal form of Birkhoff we construct some candidates of approximate first integrals which we put in correspondence to packets of low frequency modes. By numerical calculation we show that the packet associated to the best quasi-integral involves all modes up to a frequency ω{sup ⁎}(ε), where ε is the specific energy. The phenomenon disappears when the specific energy is bigger than a threshold value. The dependence of the relevant quantities on the number N of particles is also investigated. A final section is devoted to a first comparison with the Toda model. -- Highlights: ► We study the role of resonances for energy localization and metastability in the FPU model. ► We construct an approximated first integral associated to the metastable state. ► We propose to identify the metastable state as a packet of resonant modes. ► The packet extend up to a frequency ω{sup ⁎}(ε), which depends only on the specific energy ε.

  4. Calibrated peer review assignments for the earth sciences

    Science.gov (United States)

    Rudd, J.A.; Wang, V.Z.; Cervato, C.; Ridky, R.W.

    2009-01-01

    Calibrated Peer Review ??? (CPR), a web-based instructional tool developed as part of the National Science Foundation reform initiatives in undergraduate science education, allows instructors to incorporate multiple writing assignments in large courses without overwhelming the instructor. This study reports successful implementation of CPR in a large, introductory geology course and student learning of geoscience content. For each CPR assignment in this study, students studied web-based and paper resources, wrote an essay, and reviewed seven essays (three from the instructor, three from peers, and their own) on the topic. Although many students expressed negative attitudes and concerns, particularly about the peer review process of this innovative instructional approach, they also recognized the learning potential of completing CPR assignments. Comparing instruction on earthquakes and plate boundaries using a CPR assignment vs. an instructional video lecture and homework essay with extensive instructor feedback, students mastered more content via CPR instruction.

  5. Subcarrier Group Assignment for MC-CDMA Wireless Networks

    Directory of Open Access Journals (Sweden)

    Le-Ngoc Tho

    2007-01-01

    Full Text Available Two interference-based subcarrier group assignment strategies in dynamic resource allocation are proposed for MC-CDMA wireless systems to achieve high throughput in a multicell environment. Least interfered group assignment (LIGA selects for each session the subcarrier group on which the user receives the minimum interference, while best channel ratio group assignment (BCRGA chooses the subcarrier group with the largest channel response-to-interference ratio. Both analytical framework and simulation model are developed for evaluation of throughput distribution of the proposed schemes. An iterative approach is devised to handle the complex interdependency between multicell interference profiles in the throughput analysis. Illustrative results show significant throughput improvement offered by the interference-based assignment schemes for MC-CDMA multicell wireless systems. In particular, under low loading conditions, LIGA renders the best performance. However, as the load increases BCRGA tends to offer superior performance.

  6. Subcarrier Group Assignment for MC-CDMA Wireless Networks

    Directory of Open Access Journals (Sweden)

    Tho Le-Ngoc

    2007-12-01

    Full Text Available Two interference-based subcarrier group assignment strategies in dynamic resource allocation are proposed for MC-CDMA wireless systems to achieve high throughput in a multicell environment. Least interfered group assignment (LIGA selects for each session the subcarrier group on which the user receives the minimum interference, while best channel ratio group assignment (BCRGA chooses the subcarrier group with the largest channel response-to-interference ratio. Both analytical framework and simulation model are developed for evaluation of throughput distribution of the proposed schemes. An iterative approach is devised to handle the complex interdependency between multicell interference profiles in the throughput analysis. Illustrative results show significant throughput improvement offered by the interference-based assignment schemes for MC-CDMA multicell wireless systems. In particular, under low loading conditions, LIGA renders the best performance. However, as the load increases BCRGA tends to offer superior performance.

  7. Identifying inter-residue resonances in crowded 2D {sup 13}C-{sup 13}C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Miao Yimin; Cross, Timothy A. [Florida State University, Department of Chemistry and Biochemistry (United States); Fu Riqiang, E-mail: rfu@magnet.fsu.edu [National High Magnet Field Lab (United States)

    2013-07-15

    The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially enhanced resolution in crowded two-dimensional {sup 13}C-{sup 13}C chemical shift correlation spectra is presented. With the analyses of {sup 13}C-{sup 13}C spin diffusion in simple spin systems, difference spectroscopy is proposed to partially separate the spin diffusion resonances of relatively short intra-residue distances from the longer inter-residue distances, leading to a better identification of the inter-residue resonances. Here solid-state magic-angle-spinning NMR spectra of the full length M2 protein embedded in synthetic lipid bilayers have been used to illustrate the resolution enhancement in the difference spectra. The integral membrane M2 protein of Influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Based on known amino acid resonance assignments from amino acid specific labeled samples of truncated M2 sequences or from time-consuming 3D experiments of uniformly labeled samples, some inter-residue resonances of the full length M2 protein can be identified in the difference spectra of uniformly {sup 13}C labeled protein that are consistent with the high resolution structure of the M2 (22-62) protein (Sharma et al., Science 330(6003):509-512, 2010)

  8. Interactive visual exploration and refinement of cluster assignments.

    Science.gov (United States)

    Kern, Michael; Lex, Alexander; Gehlenborg, Nils; Johnson, Chris R

    2017-09-12

    With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don't properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear. While there are metrics and visualization techniques that allow analysts to compare clusterings or to judge cluster quality, there is no comprehensive method that allows analysts to evaluate, compare, and refine cluster assignments based on the source data, derived scores, and contextual data. In this paper, we introduce a method that explicitly visualizes the quality of cluster assignments, allows comparisons of clustering results and enables analysts to manually curate and refine cluster assignments. Our methods are applicable to matrix data clustered with partitional, hierarchical, and fuzzy clustering algorithms. Furthermore, we enable analysts to explore clustering results in context of other data, for example, to observe whether a clustering of genomic data results in a meaningful differentiation in phenotypes. Our methods are integrated into Caleydo StratomeX, a popular, web-based, disease subtype analysis tool. We show in a usage scenario that our approach can reveal ambiguities in cluster assignments and produce improved clusterings that better differentiate genotypes and phenotypes.

  9. Student generated assignments about electrical circuits in a computer simulation

    NARCIS (Netherlands)

    Vreman-de Olde, Cornelise; de Jong, Anthonius J.M.

    2004-01-01

    In this study we investigated the design of assignments by students as a knowledge-generating activity. Students were required to design assignments for 'other students' in a computer simulation environment about electrical circuits. Assignments consisted of a question, alternatives, and feedback on

  10. Three-dimensional imaging of the aortic vessel wall using an elastin-specific magnetic resonance contrast agent.

    Science.gov (United States)

    Makowski, Marcus R; Preissel, Anne; von Bary, Christian; Warley, Alice; Schachoff, Sylvia; Keithan, Alexandra; Cesati, Richard R; Onthank, David C; Schwaiger, Markus; Robinson, Simon P; Botnar, René M

    2012-07-01

    The aim of this study was to demonstrate the feasibility of high-resolution 3-dimensional aortic vessel wall imaging using a novel elastin-specific magnetic resonance contrast agent (ESMA) in a large animal model. The thoracic aortic vessel wall of 6 Landrace pigs was imaged using a novel ESMA and a nonspecific control agent. On day 1, imaging was performed before and after the administration of a nonspecific control agent, gadolinium diethylenetriamine pentaacetic acid (Gd-DTPA; Bayer Schering AG, Berlin, Germany). On day 3, identical scans were repeated before and after the administration of a novel ESMA (Lantheus Medical Imaging, North Billerica, Massachusetts). Three-dimensional inversion recovery gradient echo delayed-enhancement imaging and magnetic resonance (MR) angiography of the thoracic aortic vessel wall were performed on a 1.5-T MR scanner (Achieva; Philips Medical Systems, the Netherlands). The signal-to-noise ratio and the contrast-to-noise ratio of arterial wall enhancement, including the time course of enhancement, were assessed for ESMA and Gd-DTPA. After the completion of imaging sessions, histology, electron microscopy, and inductively coupled plasma mass spectroscopy were performed to localize and quantify the gadolinium bound to the arterial vessel wall. Administration of ESMA resulted in a strong enhancement of the aortic vessel wall on delayed-enhancement imaging, whereas no significant enhancement could be measured with Gd-DTPA. Ninety to 100 minutes after the administration of ESMA, significantly higher signal-to-noise ratio and contrast-to-noise ratio could be measured compared with the administration of Gd-DTPA (45.7 ± 9.6 vs 13.2 ± 3.5, P wall imaging using a novel ESMA in a large animal model under conditions resembling a clinical setting. Such an approach could be useful for the fast 3-dimensional assessment of the arterial vessel wall in the context of atherosclerosis, aortic aneurysms, and hypertension.

  11. 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

  12. Optimizing and accelerating the assignation of lineages in Mycobacterium tuberculosis using novel alternative single-tube assays.

    Directory of Open Access Journals (Sweden)

    María Carcelén

    Full Text Available The assignation of lineages in Mycobacterium tuberculosis (MTB provides valuable information for evolutionary and phylogeographic studies and makes for more accurate knowledge of the distribution of this pathogen worldwide. Differences in virulence have also been found for certain lineages. MTB isolates were initially assigned to lineages based on data obtained from genotyping techniques, such as spoligotyping or MIRU-VNTR analysis, some of which are more suitable for molecular epidemiology studies. However, since these methods are subject to a certain degree of homoplasy, other criteria have been chosen to assign lineages. These are based on targeting robust and specific SNPs for each lineage. Here, we propose two newly designed multiplex targeting methods-both of which are single-tube tests-to optimize the assignation of the six main lineages in MTB. The first method is based on ASO-PCR and offers an inexpensive and easy-to-implement assay for laboratories with limited resources. The other, which is based on SNaPshot, enables more refined standardized assignation of lineages for laboratories with better resources. Both methods performed well when assigning lineages from cultured isolates from a control panel, a test panel, and a problem panel from an unrelated population, Mexico, which included isolates in which standard genotyping was not able to classify lineages. Both tests were also able to assign lineages from stored isolates, without the need for subculture or purification of DNA, and even directly from clinical specimens with a medium-high bacilli burden. Our assays could broaden the contexts where information on lineages can be acquired, thus enabling us to quickly update data from retrospective collections and to merge data with those obtained at the time of diagnosis of a new TB case.

  13. Personnel shift assignment: Existence conditions and network models

    NARCIS (Netherlands)

    van den Berg, Jeroen P.; van den Berg, J.P.; Panton, David M.

    1994-01-01

    The personnel scheduling problem is known to be a five-stage process in which the final stage involves the assignment of shifts to the days worked in the schedule. This paper discusses the existence conditions for both continuous and forward rotating shift assignments and heuristic network

  14. Electron spin resonance signal from a tetra-interstitial defect in silicon

    CERN Document Server

    Mchedlidze, T

    2003-01-01

    The Si-B3 electron spin resonance (ESR) signal from agglomerates of self-interstitials was detected for the first time in hydrogen-doped float-zone-grown silicon samples subjected to annealing after electron irradiation. Previously this signal had been detected only in neutron- or proton-irradiated silicon samples. The absence of obscuring ESR peaks for the investigated samples at applied measurement conditions allowed an investigation of the hyperfine structure of the Si-B3 spectra. The analysis supports assignment of a tetra-interstitial defect as the origin of the signal.

  15. 75 FR 55355 - Delegation of Authority and Assignment of Responsibility

    Science.gov (United States)

    2010-09-10

    ... DEPARTMENT OF LABOR Office of the Secretary Delegation of Authority and Assignment of Responsibility Secretary's Order 4-2010 Subject: Delegation of Authority and Assignment of Responsibility to the... delegations and assignments in full force and effect, except as expressly modified herein. 4. Delegation of...

  16. Resonant-cantilever bio/chemical sensors with an integrated heater for both resonance exciting optimization and sensing repeatability enhancement

    International Nuclear Information System (INIS)

    Yu Haitao; Li Xinxin; Gan Xiaohua; Liu Yongjing; Liu Xiang; Xu Pengcheng; Li Jungang; Liu Min

    2009-01-01

    With an integrated resonance exciting heater and a self-sensing piezoresistor, resonant micro-cantilever bio/chemical sensors are optimally designed and fabricated by micromachining techniques. This study is emphasized on the optimization of the integrated heating resistor. Previous research has put the heater at either the cantilever clamp end, the midpoint or the free end. Aiming at sufficiently high and stable resonant amplitude, our research indicates that the optimized location of the thermal-electric exciting resistor is the clamp end instead of other positions. By both theoretical analysis and resonance experiments where three heating resistors are placed at the three locations of the fabricated cantilever, it is clarified that the clamp end heating provides the most efficient resonance excitation in terms of resonant amplitude, Q-factor and resonance stability. Besides, the optimized combination of dc bias and ac voltage is determined by both analysis and experimental verification. With the optimized heating excitation, the resonant cantilever is used for biotin–avidin-specific detection, resulting in a ±0.1 Hz ultra-low noise floor of the frequency signal and a 130 fg mass resolution. In addition to resonance excitation, the heater is used to heat up the cantilever for speed-up desorption after detection that helps rapid and repeated sensing to chemical vapor. The clamp end is determined (by simulation) as the optimal heating location for uniform temperature distribution on the cantilever. Using the resonant cantilever, a rapid and repeated sensing experiment on dimethyl methylphosphonate (DMMP) vapor shows that a short-period heating at the detection interval significantly quickens the signal recovery and enhances the sensing repeatability

  17. Backbone and side-chain 1H, 15N and 13C resonance assignments of two Sac10b family members Mvo10b and Mth10bTQQA from archaea.

    Science.gov (United States)

    Xuan, Jinsong; Yao, Hongwei; Feng, Yingang; Wang, Jinfeng

    2017-10-01

    The Sac10b family proteins, also named as Alba, are small, basic, nucleic acid-binding proteins widely distributed in archaea. They possess divergent physiological functions such as binding to both DNA and RNA with a high affinity and involving in genomic DNA compaction, RNA transactions and transcriptional regulations. The structures of many Sac10b family proteins from hyperthermophilic archaea have been reported, while those from thermophilic and mesophilic archaea are largely unknown. As was pointed out, the homologous members from thermophilic and mesophilic archaea may have functions different from the hyperthermophilic members. Therefore, comparison of these homologous members can provide biophysical and structural insight into the functional diversity and thermal adaptation mechanism. The present work mainly focused on the NMR study of two Sac10b family members, Mvo10b and Mth10b, from the mesophilic and thermophilic archaea, respectively. To overcome the difficulties caused by the oligomerization and conformation heterogeneity of Mth10b, a M13T/L17Q/I20Q/P56A mutant Mth10b (Mth10bTQQA) was constructed and used together with Mvo10b for multi-dimensional NMR experiments. The resonance assignments of Mvo10b and Mth10bTQQA are reported for further structural determination which is a basis for understanding the functional diversity and their thermal adaption mechanisms.

  18. Staff assignment practices in nursing homes: review of the literature.

    Science.gov (United States)

    Rahman, Anna; Straker, Jane K; Manning, Lydia

    2009-01-01

    Consistent assignment, whereby nursing home staff members, particularly certified nurse aides, are assigned to the same residents on most shifts, is increasingly viewed as a cornerstone of culture change in nursing homes. It has been advocated as a best-care model that increases residents' quality of life while contributing to a more stable frontline staff. Given these potential benefits, consistent assignment is now widely viewed as superior to rotating assignment, an alternative staffing model that aims to distribute care burden more fairly among staff and ensure that workers are familiar with most residents. Despite favorable anecdotal reports about the benefits of consistent assignment, the research literature reports mixed and sometimes contradictory findings for this staffing practice. This article reviews the research pertaining to staff assignment practices in nursing homes. Reviewed here are 13 reports on experimental trials (6 reports), evaluation research (4 reports), and nursing home surveys (3 reports). The review reveals broad diversity in staffing practices and raises questions that challenge popular assumptions about consistent assignment. The article closes with a discussion of the research, policy, and practice implications of the research findings.

  19. Fingerprinting analysis of Saposhnikovia divaricata using 1H nuclear magnetic resonance spectroscopy and high performance liquid chromatography.

    Science.gov (United States)

    Xin, Yue-Yang; Deng, An-Jun; Du, Guan-Hua; Zhang, Jin-Lan; Qin, Hai-Lin

    2010-09-01

    The (1)H nuclear magnetic resonance ((1)H NMR) fingerprints of fractionated non-polar and polar extracts (control substance for plant drug [CSPD] A and B) from the roots of 12 specimens of Saposhnikovia divaricata (Turcz.) Schischk were achieved with Fourier Transform (FT)-NMR spectrometer and assigned by comparison to each other and to the (1)H NMR spectra of the isolated individual compounds. These fingerprints were found to be uniform in terms of the specificity for the implication of all 12 specimens being systematically of the same origin. The uniformity was further affirmed by high performance liquid chromatography (HPLC), which also revealed exactly identical specificity for the identified S. divaricata species with the (1)H NMR appearances of corresponding CSPD on the part of the composition of characteristic constituents when comparing to corresponding individual compounds. This investigation unambiguously shows that the specific signals from the chemotaxonomically significant compounds of chromones and coumarins in S. divaricata are exhibited distinctively in the composite features of both (1)H NMR fingerprints and HPLC profiles. The (1)H NMR and HPLC profiles established can successfully be used as reference for the authentication of the origin of S. divaricata species as well as for chemotaxonomic studies.

  20. 75 FR 55354 - Delegation of Authority and Assignment of Responsibilities

    Science.gov (United States)

    2010-09-10

    ... DEPARTMENT OF LABOR Office of the Secretary Delegation of Authority and Assignment of Responsibilities Secretary's Order 3-2010 Subject: Delegation of Authority and Assignment of Responsibilities to... Secretary to enforce sections 18A and 18B of the FLSA. 4. Delegation of Authority and Assignment of...

  1. Quality Control Test for Sequence-Phenotype Assignments

    Science.gov (United States)

    Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

    2015-01-01

    Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10–20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

  2. 25 CFR 225.33 - Assignment of minerals agreements.

    Science.gov (United States)

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Assignment of minerals agreements. 225.33 Section 225.33 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS OIL AND GAS, GEOTHERMAL, AND SOLID MINERALS AGREEMENTS Minerals Agreements § 225.33 Assignment of minerals agreements. An...

  3. Automating Formative and Summative Feedback for Individualised Assignments

    Science.gov (United States)

    Hamilton, Ian Robert

    2009-01-01

    Purpose: The purpose of this paper is to report on the rationale behind the use of a unique paper-based individualised accounting assignment, which automated the provision to students of immediate formative and timely summative feedback. Design/methodology/approach: As students worked towards completing their assignment, the package provided…

  4. submission of art studio-based assignments: students experience

    African Journals Online (AJOL)

    PUBLICATIONS1

    are reluctant to complete their studio assignments on time are critically ... tative and qualitative data, derived from survey and interviews were used to ... is therefore exploratory and studio based. It ... mogenous group of students who report pro- ... Assignment management .... The analyses in this study are based on data.

  5. E1 Gap of Wurtzite InAs Single Nanowires Measured by Means of Resonant Raman Spectroscopy

    International Nuclear Information System (INIS)

    Moeller, M.; Lima, M. M. Jr. de; Cantarero, A.; Dacal, L. C. O.; Iikawa, F.; Chiaramonte, T.; Cotta, M. A.

    2011-01-01

    Indium arsenide nanowires were synthesized with an intermixing of wurtzite and zincblende structure by chemical beam epitaxy with the vapor-liquid-solid mechanism. Resonant Raman spectroscopy of the transverse optical phonon mode at 215 cm -1 reveals an E 1 gap of 2.47 eV which is assigned to the electronic band gap at the A point in the indium arsenide wurtzite phase.

  6. E1 Gap of Wurtzite InAs Single Nanowires Measured by Means of Resonant Raman Spectroscopy

    Science.gov (United States)

    Möller, M.; Dacal, L. C. O.; de Lima, M. M.; Iikawa, F.; Chiaramonte, T.; Cotta, M. A.; Cantarero, A.

    2011-12-01

    Indium arsenide nanowires were synthesized with an intermixing of wurtzite and zincblende structure by chemical beam epitaxy with the vapor-liquid-solid mechanism. Resonant Raman spectroscopy of the transverse optical phonon mode at 215 cm-1 reveals an E1 gap of 2.47 eV which is assigned to the electronic band gap at the A point in the indium arsenide wurtzite phase.

  7. Heuristic for Task-Worker Assignment with Varying Learning Slopes

    Directory of Open Access Journals (Sweden)

    Wipawee Tharmmaphornphilas

    2010-04-01

    Full Text Available Fashion industry has variety products, so the multi-skilled workers are required to improve flexibility in production and assignment. Generally the supervisor will assign task to the workers based on skill and skill levels of worker. Since in fashion industry new product styles are launched more frequently and the order size tends to be smaller, the workers always learn when the raw material and the production process changes. Consequently they require less time to produce the succeeding units of a task based on their learning ability. Since the workers have both experience and inexperience workers, so each worker has different skill level and learning ability. Consequently, the assignment which assumed constant skill level is not proper to use. This paper proposes a task-worker assignment considering worker skill levels and learning abilities. Processing time of each worker changes along production period due to a worker learning ability. We focus on a task-worker assignment in a fashion industry where tasks are ordered in series; the number of tasks is greater than the number of workers. Therefore, workers can perform multiple assignments followed the precedence restriction as an assembly line balancing problem. The problem is formulated in an integer linear programming model with objective to minimize makespan. A heuristic is proposed to determine the lower bound (LB and the upper bound (UB of the problem and the best assignment is determined. The performance of the heuristic method is tested by comparing quality of solution and computational time to optimal solutions.

  8. Element-resolved x-ray ferrimagnetic and ferromagnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    Boero, G; Mouaziz, S; Rusponi, S; Bencok, P; Nolting, F; Stepanow, S; Gambardella, P

    2008-01-01

    We report on the measurement of element-specific magnetic resonance spectra at gigahertz frequencies using x-ray magnetic circular dichroism (XMCD). We investigate the ferrimagnetic precession of Gd and Fe ions in Gd-substituted yttrium iron garnet, showing that the resonant field and linewidth of Gd precisely coincide with Fe up to the nonlinear regime of parametric excitations. The opposite sign of the Gd x-ray magnetic resonance signal with respect to Fe is consistent with dynamic antiferromagnetic alignment of the two ionic species. Further, we investigate a bilayer metal film, Ni 80 Fe 20 (5 nm)/Ni(50 nm), where the coupled resonance modes of Ni and Ni 80 Fe 20 are separately resolved, revealing shifts in the resonance fields of individual layers but no mutual driving effects. Energy-dependent dynamic XMCD measurements are introduced, combining x-ray absorption and magnetic resonance spectroscopies

  9. Search for new resonances with boosted signatures at CMS

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    The LHC and its experiments are ideally suited to search for these new resonances in order to validate or constrain the corresponding theories. At resonance masses well above 1 TeV, these searches face specific challenges. The decay products have large Lorentz boosts, resulting in very collimated final state topologies. Jet substructure methods and the use of non-isolate...

  10. Elucidation of reactive wavepackets by two-dimensional resonance Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Zhenkun; Molesky, Brian P.; Cheshire, Thomas P.; Moran, Andrew M., E-mail: ammoran@email.unc.edu [Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 (United States)

    2015-09-28

    Traditional second-order kinetic theories fail to describe sub-picosecond photochemical reactions when solvation and vibrational dephasing undermine the assumption of equilibrium initial conditions. Four-wave mixing spectroscopies may reveal insights into such non-equilibrium processes but are limited by the single “population time” available in these types of experiments. Here, we use two-dimensional resonance Raman (2DRR) spectroscopy to expose correlations between coherent nuclear motions of the reactant and product in the photodissociation reaction of triiodide. It is shown that the transition of a nuclear wavepacket from the reactant (triiodide) to product (diiodide) states gives rise to a unique pattern of 2DRR resonances. Peaks associated with this coherent reaction mechanism are readily assigned, because they are isolated in particular quadrants of the 2DRR spectrum. A theoretical model in which the chemical reaction is treated as a vibronic coherence transfer transition from triiodide to diiodide reproduces the patterns of 2DRR resonances detected in experiments. These signal components reveal correlation between the nonequilibrium geometry of triiodide and the vibrational coherence frequency of diiodide. The 2DRR signatures of coherent reaction mechanisms established in this work may generalize to studies of ultrafast energy and charge transfer processes.

  11. Quantum heat engine with coupled superconducting resonators

    DEFF Research Database (Denmark)

    Hardal, Ali Ümit Cemal; Aslan, Nur; Wilson, C. M.

    2017-01-01

    the differences between the quantum and classical descriptions of our system by solving the quantum master equation and classical Langevin equations. Specifically, we calculate the mean number of excitations, second-order coherence, as well as the entropy, temperature, power, and mean energy to reveal......We propose a quantum heat engine composed of two superconducting transmission line resonators interacting with each other via an optomechanical-like coupling. One resonator is periodically excited by a thermal pump. The incoherently driven resonator induces coherent oscillations in the other one...... the signatures of quantum behavior in the statistical and thermodynamic properties of the system. We find evidence of a quantum enhancement in the power output of the engine at low temperatures....

  12. Assignment Procedures in the Air Force Procurement Management Information System.

    Science.gov (United States)

    Ward, Joe H., Jr.; And Others

    An overview is presented of the procedure for offering jobs in the Air Force Procurement Management Information System (PROMIS), an assignment system which makes possible the use of human resources research findings to improve individual personnel assignments. A general framework for viewing personnel assignment systems is presented; then job…

  13. A property of assignment type mixed integer linear programming problems

    NARCIS (Netherlands)

    Benders, J.F.; van Nunen, J.A.E.E.

    1982-01-01

    In this paper we will proof that rather tight upper bounds can be given for the number of non-unique assignments that are achieved after solving the linear programming relaxation of some types of mixed integer linear assignment problems. Since in these cases the number of splitted assignments is

  14. 41 CFR 105-8.152 - Program accessibility: Assignment of space.

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Program accessibility: Assignment of space. 105-8.152 Section 105-8.152 Public Contracts and Property Management Federal Property...-8.152 Program accessibility: Assignment of space. (a) When GSA assigns or reassigns space to an...

  15. Interaction between doubly-excited 4p4nln'l' resonances in KrI

    International Nuclear Information System (INIS)

    Sukhorukov, V L; Petrov, I D; Demekhin, Ph V; Schmoranzer, H; Mickat, S; Kammer, S; Schartner, K-H; Klumpp, S; Werner, L; Ehresmann, A

    2007-01-01

    Photoionization cross sections for the 4p 4 ( 3 P)5s 4 P 5/2,3/2,1/2 satellites and 4s → εl, 4p → εl main lines of Kr II were measured using the photon-induced fluorescence spectroscopy in the exciting-photon energy range between 27.80 eV and 29.44 eV with extremely narrow bandwidth (1.7 meV at 28.55 eV) of the monochromatized synchrotron radiation. The observed resonances were assigned to the 4p 4 5s( 4 P 1/2 )np and 4p 4 5s( 2 P 3/2 )np Rydberg series on the basis of the calculations including core relaxation and interaction between many resonances and many continua. The calculation shows that the resonance structure in the photoionization channels exists due to the 4p 4 ( 1 D)5s 2 D 5/2 6p 3/2 and 4p 4 ( 1 D)5s 2 D 3/2 6p 3/2,1/2 promoter states which strongly perturb the above Rydberg series

  16. Combining M-FISH and Quantum Dot technology for fast chromosomal assignment of transgenic insertions

    Directory of Open Access Journals (Sweden)

    Yusuf Mohammed

    2011-12-01

    Full Text Available Abstract Background Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH is a reliable and cost-effective technique. Chromosomal assignment is commonly achieved either by concurrent G-banding or by a multi-color FISH approach consisting of iteratively co-hybridizing the transgenic sequence of interest with one or more chromosome-specific probes at a time, until the location of the transgenic insertion is identified. Results Here we report a technical development for fast chromosomal assignment of transgenic insertions at the single cell level in mouse and rat models. This comprises a simplified 'single denaturation mixed hybridization' procedure that combines multi-color karyotyping by Multiplex FISH (M-FISH, for simultaneous and unambiguous identification of all chromosomes at once, and the use of a Quantum Dot (QD conjugate for the transgene detection. Conclusions Although the exploitation of the unique optical properties of QD nanocrystals, such as photo-stability and brightness, to improve FISH performance generally has been previously investigated, to our knowledge this is the first report of a purpose-designed molecular cytogenetic protocol in which the combined use of QDs and standard organic fluorophores is specifically tailored to assist gene transfer technology.

  17. Scaffolding Assignments and Activities for Undergraduate Research Methods

    Science.gov (United States)

    Fisher, Sarah; Justwan, Florian

    2018-01-01

    This article details assignments and lessons created for and tested in research methods courses at two different universities, a large state school and a small liberal arts college. Each assignment or activity utilized scaffolding. Students were asked to push beyond their comfort zone while utilizing concrete and/or creative examples,…

  18. Correlation of probability scores of placenta accreta on magnetic resonance imaging with hemorrhagic morbidity.

    Science.gov (United States)

    Lim, Grace; Horowitz, Jeanne M; Berggruen, Senta; Ernst, Linda M; Linn, Rebecca L; Hewlett, Bradley; Kim, Jennifer; Chalifoux, Laurie A; McCarthy, Robert J

    2016-11-01

    To evaluate the hypothesis that assigning grades to magnetic resonance imaging (MRI) findings of suspected placenta accreta will correlate with hemorrhagic outcomes. We chose a single-center, retrospective, observational design. Nulliparous or multiparous women who had antenatal placental MRI performed at a tertiary level academic hospital were included. Cases with antenatal placental MRI were included and compared with cases without MRI performed. Two radiologists assigned a probability score for accreta to each study. Estimated blood loss and transfusion requirements were compared among groups by the Kruskal-Wallis H test. Thirty-five cases had placental MRI performed. MRI performance was associated with higher blood loss compared with the non-MRI group (2600 [1400-4500]mL vs 900[600-1500]mL, Paccreta, probability scores for antenatal placental MRI may not be associated with increasing degrees of hemorrhage. Continued research is warranted to determine the effectiveness of assigning probability scores for antenatal accreta imaging studies, combined with clinical indices of suspicion, in assisting with antenatal multidisciplinary team planning for operative management of this morbid condition. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. First observation of laser-induced resonant annihilation in metastable antiprotonic helium atoms

    International Nuclear Information System (INIS)

    Morita, N.; Kumakura, M.; Yamazaki, T.

    1993-11-01

    We have observed the first laser-induced resonant transitions in antiprotonic helium atoms. These occur between metastable states and Auger dominated short lived states, and show that the anomalous longevity of antiprotons previously observed in helium media results from the formation of high-n high-l atomic states of p-barHe + . The observed transition with vacuum wavelength 597.259 ± 0.002 nm and lower-state lifetime 15 ± 1 ns is tentatively assigned to (n,l) = (39,35) → (38,34). (author)

  20. Socially-assigned race, healthcare discrimination and preventive healthcare services.

    Directory of Open Access Journals (Sweden)

    Tracy Macintosh

    Full Text Available Race and ethnicity, typically defined as how individuals self-identify, are complex social constructs. Self-identified racial/ethnic minorities are less likely to receive preventive care and more likely to report healthcare discrimination than self-identified non-Hispanic whites. However, beyond self-identification, these outcomes may vary depending on whether racial/ethnic minorities are perceived by others as being minority or white; this perception is referred to as socially-assigned race.To examine the associations between socially-assigned race and healthcare discrimination and receipt of selected preventive services.Cross-sectional analysis of the 2004 Behavioral Risk Factor Surveillance System "Reactions to Race" module. Respondents from seven states and the District of Columbia were categorized into 3 groups, defined by a composite of self-identified race/socially-assigned race: Minority/Minority (M/M, n = 6,837, Minority/White (M/W, n = 929, and White/White (W/W, n = 25,913. Respondents were 18 years or older, with 61.7% under age 60; 51.8% of respondents were female. Measures included reported healthcare discrimination and receipt of vaccinations and cancer screenings.Racial/ethnic minorities who reported being socially-assigned as minority (M/M were more likely to report healthcare discrimination compared with those who reported being socially-assigned as white (M/W (8.9% vs. 5.0%, p = 0.002. Those reporting being socially-assigned as white (M/W and W/W had similar rates for past-year influenza (73.1% vs. 74.3% and pneumococcal (69.3% vs. 58.6% vaccinations; however, rates were significantly lower among M/M respondents (56.2% and 47.6%, respectively, p-values<0.05. There were no significant differences between the M/M and M/W groups in the receipt of cancer screenings.Racial/ethnic minorities who reported being socially-assigned as white are more likely to receive preventive vaccinations and less likely to report

  1. A Novel Magnetic Resonance Imaging (MRI) Approach for Measuring Weak Electric Currents Inside the Human Brain

    DEFF Research Database (Denmark)

    Göksu, Cihan

    of individual ohmic conductivity values may open up the possibility of creating more realistic and accurate head models, which may ameliorate the simulations and practical use of NIBS techniques. Magnetic resonance current density imaging (MRCDI) and magnetic resonance electrical impedance tomography (MREIT......Knowing the electrical conductivity and current density distribution inside the human brain will be useful in various biomedical applications, i.e. for improving the efficiency of non-invasive brain stimulation (NIBS) techniques, the accuracy of electroencephalography (EEG......) and magnetoencephalography (MEG) source localization, or localization of pathological tissues. For example, the accuracy of electric field simulations for NIBS techniques is currently reduced by assigning inaccurate ohmic conductivity values taken from literature to different brain tissues. Therefore, the knowledge...

  2. The Presentation Assignment: Creating Learning Opportunities for Diverse Student Populations.

    Science.gov (United States)

    Spencer, Brenda H.; Bartle-Angus, Kathryn

    2000-01-01

    Finds the presentation assignment to be an effective method of providing students with the opportunity to apply the literacy skills they are learning in ways that are personally meaningful. Describes the presentation assignment framework and provides an example of an assignment that required students to analyze and interpret works of literature…

  3. Triage level assignment and nurse characteristics and experience.

    Science.gov (United States)

    Gómez-Angelats, Elisenda; Miró, Òscar; Bragulat Baur, Ernesto; Antolín Santaliestra, Alberto; Sánchez Sánchez, Miquel

    2018-06-01

    To study the relation between nursing staff demographics and experience and their assignment of triage level in the emergency department. One-year retrospective observational study in the triage area of a tertiary care urban university hospital that applies the Andorran-Spanish triage model. Variables studied were age, gender, nursing experience, triage experience, shift, usual level of emergency work the nurse undertakes, number of triage decisions made, and percentage of patients assigned to each level. Fifty nurses (5 men, 45 women) with a mean (SD) age of 45 (9) years triaged 67 803 patients during the year. Nurses classified more patients in level 5 on the morning shift (7.9%) than on the afternoon shift (5.5%) (P=.003). The difference in the rate of level-5 triage classification became significant when nurses were older (β = 0.092, P=.037) and experience was greater (β = 0.103, P=.017). The number of triages recorded by a nurse was significantly and directly related to the percentage of patients assigned to level 3 (β = 0.003, P=.006) and inversely related to the percentages assigned to level 4 (β = -0.002, P=.008) and level 5 (β = -0.001, P=.017). We found that triage level assignments were related to age, experience, shift, and total number of patients triaged by a nurse.

  4. Visual words assignment via information-theoretic manifold embedding.

    Science.gov (United States)

    Deng, Yue; Li, Yipeng; Qian, Yanjun; Ji, Xiangyang; Dai, Qionghai

    2014-10-01

    Codebook-based learning provides a flexible way to extract the contents of an image in a data-driven manner for visual recognition. One central task in such frameworks is codeword assignment, which allocates local image descriptors to the most similar codewords in the dictionary to generate histogram for categorization. Nevertheless, existing assignment approaches, e.g., nearest neighbors strategy (hard assignment) and Gaussian similarity (soft assignment), suffer from two problems: 1) too strong Euclidean assumption and 2) neglecting the label information of the local descriptors. To address the aforementioned two challenges, we propose a graph assignment method with maximal mutual information (GAMI) regularization. GAMI takes the power of manifold structure to better reveal the relationship of massive number of local features by nonlinear graph metric. Meanwhile, the mutual information of descriptor-label pairs is ultimately optimized in the embedding space for the sake of enhancing the discriminant property of the selected codewords. According to such objective, two optimization models, i.e., inexact-GAMI and exact-GAMI, are respectively proposed in this paper. The inexact model can be efficiently solved with a closed-from solution. The stricter exact-GAMI nonparametrically estimates the entropy of descriptor-label pairs in the embedding space and thus leads to a relatively complicated but still trackable optimization. The effectiveness of GAMI models are verified on both the public and our own datasets.

  5. Resonance effects in elastic cross sections for electron scattering on pyrimidine: Experiment and theory.

    Science.gov (United States)

    Regeta, Khrystyna; Allan, Michael; Winstead, Carl; McKoy, Vincent; Mašín, Zdeněk; Gorfinkiel, Jimena D

    2016-01-14

    We measured differential cross sections for elastic (rotationally integrated) electron scattering on pyrimidine, both as a function of angle up to 180(∘) at electron energies of 1, 5, 10, and 20 eV and as a function of electron energy in the range 0.1-14 eV. The experimental results are compared to the results of the fixed-nuclei Schwinger variational and R-matrix theoretical methods, which reproduce satisfactorily the magnitudes and shapes of the experimental cross sections. The emphasis of the present work is on recording detailed excitation functions revealing resonances in the excitation process. Resonant structures are observed at 0.2, 0.7, and 4.35 eV and calculations for different symmetries confirm their assignment as the X̃(2)A2, Ã(2)B1, and B̃(2)B1 shape resonances. As a consequence of superposition of coherent resonant amplitudes with background scattering the B̃(2)B1 shape resonance appears as a peak, a dip, or a step function in the cross sections recorded as a function of energy at different scattering angles and this effect is satisfactorily reproduced by theory. The dip and peak contributions at different scattering angles partially compensate, making the resonance nearly invisible in the integral cross section. Vibrationally integrated cross sections were also measured at 1, 5, 10 and 20 eV and the question of whether the fixed-nuclei cross sections should be compared to vibrationally elastic or vibrationally integrated cross section is discussed.

  6. Specific magnetic resonance imaging findings in patient with progressive supranuciear palsy

    International Nuclear Information System (INIS)

    Vuchkova, R.; Zlatareva, D.

    2013-01-01

    Progressive supranuclear palsy (PSP) is a progressive neurodegenerative disease. The clinical symptoms are vertical supranuclear palsy, gait and postural instability, cognitive deficit, Parkinsonism. It is not always possible to differentiate clinically PSP from other atypical Parkinsonian syndromes and from Parkinson disease. We present a case of 56-years old women with clinically suspected PSP. The typical magnetic resonance findings were of most importance in diagnosis. For diagnosing the disease by means of neuroimaging it is necessary to analyze the sagittal MR images what is achievable in daily routine practice without additional software and post processing. (authors)

  7. 28 CFR 545.23 - Inmate work/program assignment.

    Science.gov (United States)

    2010-07-01

    ... community living area, unless the pretrial inmate has signed a waiver of his or her right not to work (see... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Inmate work/program assignment. 545.23... WORK AND COMPENSATION Inmate Work and Performance Pay Program § 545.23 Inmate work/program assignment...

  8. 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...... and in general is a substantial support in decision making....

  9. PARETO OPTIMAL SOLUTIONS FOR MULTI-OBJECTIVE GENERALIZED ASSIGNMENT PROBLEM

    Directory of Open Access Journals (Sweden)

    S. Prakash

    2012-01-01

    Full Text Available

    ENGLISH ABSTRACT: The Multi-Objective Generalized Assignment Problem (MGAP with two objectives, where one objective is linear and the other one is non-linear, has been considered, with the constraints that a job is assigned to only one worker – though he may be assigned more than one job, depending upon the time available to him. An algorithm is proposed to find the set of Pareto optimal solutions of the problem, determining assignments of jobs to workers with two objectives without setting priorities for them. The two objectives are to minimise the total cost of the assignment and to reduce the time taken to complete all the jobs.

    AFRIKAANSE OPSOMMING: ‘n Multi-doelwit veralgemeende toekenningsprobleem (“multi-objective generalised assignment problem – MGAP” met twee doelwitte, waar die een lineêr en die ander nielineêr is nie, word bestudeer, met die randvoorwaarde dat ‘n taak slegs toegedeel word aan een werker – alhoewel meer as een taak aan hom toegedeel kan word sou die tyd beskikbaar wees. ‘n Algoritme word voorgestel om die stel Pareto-optimale oplossings te vind wat die taaktoedelings aan werkers onderhewig aan die twee doelwitte doen sonder dat prioriteite toegeken word. Die twee doelwitte is om die totale koste van die opdrag te minimiseer en om die tyd te verminder om al die take te voltooi.

  10. Evaluation of toroidal torque by non-resonant magnetic perturbations in tokamaks for resonant transport regimes using a Hamiltonian approach

    Energy Technology Data Exchange (ETDEWEB)

    Albert, Christopher G.; Heyn, Martin F.; Kapper, Gernot; Kernbichler, Winfried; Martitsch, Andreas F. [Fusion@ÖAW, Institut für Theoretische Physik - Computational Physics, Technische Universität Graz, Petersgasse 16, 8010 Graz (Austria); Kasilov, Sergei V. [Fusion@ÖAW, Institut für Theoretische Physik - Computational Physics, Technische Universität Graz, Petersgasse 16, 8010 Graz (Austria); Institute of Plasma Physics, National Science Center “Kharkov Institute of Physics and Technology,” ul. Akademicheskaya 1, 61108 Kharkov (Ukraine)

    2016-08-15

    Toroidal torque generated by neoclassical viscosity caused by external non-resonant, non-axisymmetric perturbations has a significant influence on toroidal plasma rotation in tokamaks. In this article, a derivation for the expressions of toroidal torque and radial transport in resonant regimes is provided within quasilinear theory in canonical action-angle variables. The proposed approach treats all low-collisional quasilinear resonant neoclassical toroidal viscosity regimes including superbanana-plateau and drift-orbit resonances in a unified way and allows for magnetic drift in all regimes. It is valid for perturbations on toroidally symmetric flux surfaces of the unperturbed equilibrium without specific assumptions on geometry or aspect ratio. The resulting expressions are shown to match the existing analytical results in the large aspect ratio limit. Numerical results from the newly developed code NEO-RT are compared to calculations by the quasilinear version of the code NEO-2 at low collisionalities. The importance of the magnetic shear term in the magnetic drift frequency and a significant effect of the magnetic drift on drift-orbit resonances are demonstrated.

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

    KAUST Repository

    Jang, Richard; Gao, Xin; Li, Ming

    2012-01-01

    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.

  12. 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.

  13. Game theory and traffic assignment.

    Science.gov (United States)

    2013-09-01

    Traffic assignment is used to determine the number of users on roadway links in a network. While this problem has : been widely studied in transportation literature, its use of the concept of equilibrium has attracted considerable interest : in the f...

  14. Resonances, resonance functions and spectral deformations

    International Nuclear Information System (INIS)

    Balslev, E.

    1984-01-01

    The present paper is aimed at an analysis of resonances and resonance states from a mathematical point of view. Resonances are characterized as singular points of the analytically continued Lippman-Schwinger equation, as complex eigenvalues of the Hamiltonian with a purely outgoing, exponentially growing eigenfunction, and as poles of the S-matrix. (orig./HSI)

  15. Optically Detected Magnetic Resonance Studies on π-conjugated semiconductor systems

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Ying [Iowa State Univ., Ames, IA (United States)

    2011-01-01

    Optically Detected Magnetic Resonance (ODMR) techniques were used to investigate the dynamics of excitons and charge carriers in π-conjugated organic semiconductors. Degradation behavior of the negative spin-1/2 electroluminescence-detected magnetic resonance (ELDMR) was observed in Alq3 devices. The increase in the resonance amplitude implies an increasing bipolaron formation during degradation, which might be the result of growth of charge traps in the device. The same behavior of the negative spin-1/2 ELDMR was observed in 2wt% Rubrene doped Tris(8-hydroxyquinolinato)aluminium (Alq3) devices. However, with increasing injection current, a positive spin-1/2 ELDMR, together with positive spin 1 triplet powder patterns at ΔmS=±1 and ΔmS=±2, emerges. Due to the similarities in the frequency dependences of single and double modulated ELDMR and the photoluminescence-detected magnetic resonance (PLDMR) results in poly[2-methoxy-5-(2 -ethyl-hexyloxy)-1,4-phenyl ene vinylene] (MEH-PPV) films, the mechanism for this positive spin-1/2 ELDMR was assigned to enhanced triplet-polaron quenching under resonance conditions. The ELDMR in rubrene doped Alq3 devices provides a path to investigate charge distribution in the device under operational conditions. Combining the results of several devices with different carrier blocking properties and the results from transient EL, it was concluded trions not only exist near buffer layer but also exist in the electron transport layer. This TPQ model can also be used to explain the positive spin-1/2 PLDMR in poly(3-hexylthiophene) (P3HT) films at low temperature and in MEH-PPV films at various temperatures up to room temperature. Through quantitative analysis, TE-polaron quenching (TPQ) model is shown having the ability to explain most behaviors of the positive spin-1/2 resonance. Photocurrent detected magnetic resonance (PCDMR) studies on MEH-PPV devices revealed a novel transient resonance signal. The signal

  16. Simulated annealing algorithm for solving chambering student-case assignment problem

    Science.gov (United States)

    Ghazali, Saadiah; Abdul-Rahman, Syariza

    2015-12-01

    The problem related to project assignment problem is one of popular practical problem that appear nowadays. The challenge of solving the problem raise whenever the complexity related to preferences, the existence of real-world constraints and problem size increased. This study focuses on solving a chambering student-case assignment problem by using a simulated annealing algorithm where this problem is classified under project assignment problem. The project assignment problem is considered as hard combinatorial optimization problem and solving it using a metaheuristic approach is an advantage because it could return a good solution in a reasonable time. The problem of assigning chambering students to cases has never been addressed in the literature before. For the proposed problem, it is essential for law graduates to peruse in chambers before they are qualified to become legal counselor. Thus, assigning the chambering students to cases is a critically needed especially when involving many preferences. Hence, this study presents a preliminary study of the proposed project assignment problem. The objective of the study is to minimize the total completion time for all students in solving the given cases. This study employed a minimum cost greedy heuristic in order to construct a feasible initial solution. The search then is preceded with a simulated annealing algorithm for further improvement of solution quality. The analysis of the obtained result has shown that the proposed simulated annealing algorithm has greatly improved the solution constructed by the minimum cost greedy heuristic. Hence, this research has demonstrated the advantages of solving project assignment problem by using metaheuristic techniques.

  17. Efficient Mechanisms to Allocate Assignment Incentives in the Navy

    National Research Council Canada - National Science Library

    Nimon, R. W; Hall, Ricky D; Zaki, Hossam

    2005-01-01

    .... All assignments, however, may not necessarily be voluntary. These assignments (jobs) have been labeled as "hard to fill" by Navy leadership, and the Navy has implemented market-based, cash stipends to attract Sailors to these jobs...

  18. Ant Colony Algorithm and Simulation for Robust Airport Gate Assignment

    Directory of Open Access Journals (Sweden)

    Hui Zhao

    2014-01-01

    Full Text Available Airport gate assignment is core task for airport ground operations. Due to the fact that the departure and arrival time of flights may be influenced by many random factors, the airport gate assignment scheme may encounter gate conflict and many other problems. This paper aims at finding a robust solution for airport gate assignment problem. A mixed integer model is proposed to formulate the problem, and colony algorithm is designed to solve this model. Simulation result shows that, in consideration of robustness, the ability of antidisturbance for airport gate assignment scheme has much improved.

  19. Giant quadrupole resonance in 24Mg, 27Al, and 28Si

    International Nuclear Information System (INIS)

    Youngblood, D.H.; Rozsa, C.M.; Moss, J.M.; Brown, D.R.; Bronson, J.D.

    1977-01-01

    The giant-resonance region of 24 Mg, 27 Al, and 28 Si was studied by inelastic scattering of 126-MeV α particles. In contrast to results at 96 MeV, considerable clustering of E2 strength was observed for 27 Al at E/sub x/ approx. 20.1 MeV with GAMMA approx. 7.6 MeV exhausting about 35% of the E2 energy weighted sum rule. E2 strength was also located in 24 Mg in two clusters of states at E-bar/sub x/ approx. 18.2, 24.4 MeV; however, contributions from other multipoles cannot be neglected. In 28 Si a multipeaked group was observed at E/sub x/ approx. 19.4 MeV with GAMMA approx. 4 MeV but no L assignment was made. The energy dependence of the cross section for the giant quadrupole resonance was found to be consistent with distorted-wave Born approximation predictions

  20. Protein structure analysis using the resonant recognition model and wavelet transforms

    International Nuclear Information System (INIS)

    Fang, Q.; Cosic, I.

    1998-01-01

    An approach based on the resonant recognition model and the discrete wavelet transform is introduced here for characterising proteins' biological function. The protein sequence is converted into a numerical series by assigning the electron-ion interaction potential to each amino acid from N-terminal to C-terminal. A set of peaks is found after performing a wavelet transform onto a numerical series representing a group of homologous proteins. These peaks are related to protein structural and functional properties and named characteristic vector of that protein group. Further more, the amino acids contributing mostly to a protein's biological functions, the so-called 'hot spots' amino acids, are predicted by the continuous wavelet transform. It is found that the hot spots are clustered around the protein's cleft structure. The wavelets approach provides a novel methods for amino acid sequence analysis as well as an expansion for the newly established macromolecular interaction model: the resonant recognition model. Copyright (1998) Australasian Physical and Engineering Sciences in Medicine

  1. Characterization of human breast disease using phosphorus magnetic resonance spectroscopy and proton magnetic resonance imaging

    International Nuclear Information System (INIS)

    Merchant, T.E.

    1992-01-01

    This thesis provides the fundamental characterization and differentiation of breast tissues using in vivo and ex vivo MR techniques in the hope that these techniques and experimental findings will be used on a larger scale and in a predictive manner in order to improve the specificity of diagnosis and treatment of breast cancer. In this dissertation, clinical studies were performed using proton magnetic resonance imaging and phosphorus magnetic resonance spectro-scopy ( 31 P MRS) to characterize and differentiate malignant breast tumors, benign breast tumors and normal breast tissues in vivo. These studies were carried out following the methodical characterization of chemical extracts of malignant breast tumor, benign breast tumor and normal breast parenchymal surgical tissue specimens using high resolution 31 P MRS. Alterations in breast tissue metabolism, as a result of pathological processes, were postulated to be responsible for measurable differences between malignant breast tumors, benign breast tumors and normal breast tissues using magnetic resonance techniques. (author). 365 refs.; 37 figs.; 25 tabs

  2. Resonant photoluminescence studies of carrier localisation in c-plane InGaN/GaN quantum well structures

    Science.gov (United States)

    Blenkhorn, W. E.; Schulz, S.; Tanner, D. S. P.; Oliver, R. A.; Kappers, M. J.; Humphreys, C. J.; Dawson, P.

    2018-05-01

    In this paper we report on changes in the form of the low temperature (12 K) photoluminescence spectra of an InGaN/GaN quantum well structure as a function of excitation photon energy. As the photon energy is progressively reduced we observe at a critical energy a change in the form of the spectra from one which is determined by the occupation of the complete distribution of hole localisation centres to one which is determined by the resonant excitation of specific localisation sites. This change is governed by an effective mobility edge whereby the photo-excited holes remain localised at their initial energy and are prevented from scattering to other localisation sites. This assignment is confirmed by the results of atomistic tight binding calculations which show that the wave function overlap of the lowest lying localised holes with other hole states is low compared with the overlap of higher lying hole states with other higher lying hole states.

  3. The diagnostic accuracy of acetabular labral tears using magnetic resonance imaging and magnetic resonance arthrography: a meta-analysis

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Toby O. [University of East Anglia, Faculty of Health, Queen' s Building, Norwich (United Kingdom); Hilton, Gemma [Norfolk and Norwich University Hospital, Norwich (United Kingdom); Toms, Andoni P.; Donell, Simon T. [Norfolk and Norwich University Hospital, University of East Anglia, Norwich (United Kingdom); Hing, Caroline B. [St. George' s Hospital, London (United Kingdom)

    2011-04-15

    Magnetic resonance imaging (MRI) and magnetic resonance arthrography (MRA) have been advocated for the diagnosis of acetabular labral tears. The purpose of this study was to determine the sensitivity and specificity of MRI and MRA in diagnosing acetabular labral tears using meta-analysis. Pertinent published and unpublished literature databases were reviewed. A two-by-two table was constructed to calculate the sensitivity and specificity of MRI or MRA investigations against surgical outcomes. Pooled sensitivity and specificity and Receiver Operating Characteristic curve (ROC) evaluations were performed. Methodological quality of each study was assessed using the QUADAS (Quality Assessment of Diagnostic Accuracy Studies) tool. Nineteen papers assessing 881 hips were reviewed. Conventional MRI was assessed in 13 studies and MRA was assessed in 16 studies. Whilst both MRI (0.5-3T) and MRA (0.5-3T) presented with a moderate sensitivity and specificity (sensitivity 66%, 87%; specificity 79%, 64%), diagnostic accuracy of MRA appeared to be superior to MRI in detecting acetabular labral tears on ROC curve interpretation. The literature poorly described population characteristics, assessor blinding, with limited sample sizes. MRI and MRA may be useful adjuncts in the diagnosis of acetabular labral tears in adults. MRA appears to be superior to conventional MRI. (orig.)

  4. Evaluation of nuclear magnetic resonance spectroscopy variability

    Energy Technology Data Exchange (ETDEWEB)

    Barreto, Felipe Rodrigues; Salmon, Carlos Ernesto Garrido, E-mail: garrido@ffclrp.usp.br [Universidade de Sao Paulo (FFCLRP/USP), Ribeirao Preto, SP (Brazil). Fac. de Filisofia, Ciencias e Letras; Otaduy, Maria Concepcion Garcia [Universidade de Sao Paulo (FAMUS/USP), Sao Paulo, SP (Brazil). Fac. de Medicina. Departamento de Radiologia

    2014-11-01

    Introduction: the intrinsically high sensitivity of Magnetic Resonance Spectroscopy (MRS) causes considerable variability in metabolite quantification. In this study, we evaluated the variability of MRS in two research centers using the same model of magnetic resonance image scanner. Methods: two metabolic phantoms were created to simulate magnetic resonance spectra from in vivo hippocampus. The phantoms were filled with the same basic solution containing the following metabolites: N-acetyl-aspartate, creatine, choline, glutamate, glutamine and inositol. Spectra were acquired over 15 months on 26 acquisition dates, resulting in a total of 130 spectra per center. Results: the phantoms did not undergo any physical changes during the 15-month period. Temporal analysis from both centers showed mean metabolic variations of 3.7% in acquisitions on the same day and of 8.7% over the 15-month period. Conclusion: The low deviations demonstrated here, combined with the high specificity of Magnetic Resonance Spectroscopy, confirm that it is feasible to use this technique in multicenter studies in neuroscience research. (author)

  5. Development of Novel Piezoelectric Biosensor Using PZT Ceramic Resonator for Detection of Cancer Markers.

    Science.gov (United States)

    Su, Li; Fong, Chi-Chun; Cheung, Pik-Yuan; Yang, Mengsu

    2017-01-01

    A novel biosensor based on piezoelectric ceramic resonator was developed for direct detection of cancer markers in the study. For the first time, a commercially available PZT ceramic resonator with high resonance frequency was utilized as transducer for a piezoelectric biosensor. A dual ceramic resonators scheme was designed wherein two ceramic resonators were connected in parallel: one resonator was used as the sensing unit and the other as the control unit. This arrangement minimizes environmental influences including temperature fluctuation, while achieving the required frequency stability for biosensing applications. The detection of the cancer markers Prostate Specific Antigen (PSA) and α-Fetoprotein (AFP) was carried out through frequency change measurement. The device showed high sensitivity (0.25 ng/ml) and fast detection (within 30 min) with small samples (1 μl), which is compatible with the requirements of clinical measurements. The results also showed that the ceramic resonator-based piezoelectric biosensor platform could be utilized with different chemical interfaces, and had the potential to be further developed into biosensor arrays with different specificities for simultaneous detection of multiple analytes.

  6. Bony vibration stimulation test combined with magnetic resonance imaging. Can discography be replaced?

    Science.gov (United States)

    Yrjämä, M; Tervonen, O; Kurunlahti, M; Vanharanta, H

    1997-04-01

    The results of two noninvasive methods, magnetic resonance imaging and a bony vibration test, were compared with discographic pain provocation findings. To evaluate whether the combination of magnetic resonance imaging and vibration pain provocation tests could be used to replace discography in low back pain diagnostics. Magnetic resonance imaging gives a wealth of visual information on anatomic changes of the spine with often unknown clinical significance. Discographic examination of the spine is still the only widely accepted diagnostic method that can relate the pathoanatomic changes to the patient's clinical pain. Internal anular rupture has been shown to be one of the sources of back pain. The bony vibration test of the spinal processes has been shown correlate well with discographic pain provocation tests in cases of internal anular rupture. The three lowest lumbar discs of 33 patients with back pain were examined by means of magnetic resonance imaging and a bony vibration stimulation test, and the results were compared with those from computed tomography-discography. In cases of intradiscal magnetic resonance imaging findings, the vibration provocation test showed a sensitivity of 0.88 and a specificity of 0.50 compared with the discographic pain provocation test. If the patients with previous back surgery were excluded, the specificity was 0.75. In the cases of total anular rupture, the sensitivity was 0.50, and the specificity was 0.33. The combination of the two noninvasive methods, vibration stimulation and magnetic resonance imaging, gives more information on the origin of the back pain than magnetic resonance imaging alone. The pathoanatomic changes seen in magnetic resonance imaging can be correlated with the patient's disorder more reliably using the vibration provocation test in the cases of partial anular ruptures. The use of discography can be limited mostly to cases with total anular ruptures detected by magnetic resonance imaging.

  7. 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....

  8. NbF5 and TaF5: Assignment of 19F NMR resonances and chemical bond analysis from GIPAW calculations

    International Nuclear Information System (INIS)

    Biswal, Mamata; Body, Monique; Legein, Christophe; Sadoc, Aymeric; Boucher, Florent

    2013-01-01

    The 19 F isotropic chemical shifts (δ iso ) of two isomorphic compounds, NbF 5 and TaF 5 , which involve six nonequivalent fluorine sites, have been experimentally determined from the reconstruction of 1D 19 F MAS NMR spectra. In parallel, the corresponding 19 F chemical shielding tensors have been calculated using the GIPAW method for both experimental and DFT-optimized structures. Furthermore, the [M 4 F 20 ] units of NbF 5 and TaF 5 being held together by van der Waals interactions, the relevance of Grimme corrections to the DFT optimization processes has been evaluated. However, the semi-empirical dispersion correction term introduced by such a method does not show any significant improvement. Nonetheless, a complete and convincing assignment of the 19 F NMR lines of NbF 5 and TaF 5 is obtained, ensured by the linearity between experimental 19 F δ iso values and calculated 19 F isotropic chemical shielding σ iso values. The effects of the geometry optimizations have been carefully analyzed, confirming among other matters, the inaccuracy of the experimental structure of NbF 5 . The relationships between the fluorine chemical shifts, the nature of the fluorine atoms (bridging or terminal), the position of the terminal ones (opposite or perpendicular to the bridging ones), the fluorine charges, the ionicity and the length of the M–F bonds have been established. Additionally, for three of the 19 F NMR lines of NbF 5 , distorted multiplets, arising from 1 J-coupling and residual dipolar coupling between the 19 F and 93 Nb nuclei, were simulated yielding to values of 93 Nb– 19 F 1 J-coupling for the corresponding fluorine sites. - Graphical abstract: The complete assignment of the 19 F NMR lines of NbF 5 and TaF 5 allow establishing relationships between the 19 F δ iso values, the nature of the fluorine atoms (bridging or terminal), the position of the terminal ones (opposite or perpendicular to the bridging ones), the fluorine charges, the ionicity and the

  9. The ICAP (Interactive Course Assignment Pages Publishing System

    Directory of Open Access Journals (Sweden)

    Kim Griggs

    2008-03-01

    Full Text Available The ICAP publishing system is an open source custom content management system that enables librarians to easily and quickly create and manage library help pages for course assignments (ICAPs, without requiring knowledge of HTML or other web technologies. The system's unique features include an emphasis on collaboration and content reuse and an easy-to-use interface that includes in-line help, simple forms and drag and drop functionality. The system generates dynamic, attractive course assignment pages that blend Web 2.0 features with traditional library resources, and makes the pages easier to find by providing a central web page for the course assignment pages. As of December 2007, the code is available as free, open-source software under the GNU General Public License.

  10. Graph-Based Specification and Simulation of Featherweight Java with Around Advice

    NARCIS (Netherlands)

    Staijen, T.; Rensink, Arend

    In this paper we specify an operational run-time semantics of Assignment Featherweight Java -- a minimal subset of Java with assignments -- with around advice, using graph transformations. We introduce a notion of correctness of our specification with respect to an existing semantics and claim a

  11. Photoabsorption and S 2p photoionization of the SF6 molecule: resonances in the excitation energy range of 200-280 eV.

    Science.gov (United States)

    Stener, M; Bolognesi, P; Coreno, M; O'Keeffe, P; Feyer, V; Fronzoni, G; Decleva, P; Avaldi, L; Kivimäki, A

    2011-05-07

    Photoabsorption and S 2p photoionization of the SF(6) molecule have been studied experimentally and theoretically in the excitation energy range up to 100 eV above the S 2p ionization potentials. In addition to the well-known 2t(2g) and 4e(g) shape resonances, the spin-orbit-resolved S 2p photoionization cross sections display two weak resonances between 200 and 210 eV, a wide resonance around 217 eV, a Fano-type resonance around 240 eV, and a second wide resonance around 260 eV. Calculations based on time-dependent density functional theory allow us to assign the 217-eV and 260-eV features to the shape resonances in S 2p photoionization. The Fano resonance is caused by the interference between the direct S 2p photoionization channel and the resonant channel that results from the participator decay of the S 2s(-1)6t(1u) excited state. The weak resonances below 210-eV photon energy, not predicted by theory, are tentatively suggested to originate from the coupling between S 2p shake-up photoionization and S 2p single-hole photoionization. The experimental and calculated angular anisotropy parameters for S 2p photoionization are in good agreement.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-01

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

  13. Magnetic resonance appearance of posterosuperior labral peel back during humeral abduction and external rotation.

    Science.gov (United States)

    Borrero, Camilo G; Casagranda, Bethany U; Towers, Jeffrey D; Bradley, James P

    2010-01-01

    To describe the magnetic resonance appearance of posterosuperior labral peel back and determine the reliability of MR in the abducted and externally rotated (ABER) position for the prospective diagnosis of arthroscopically proven cases of posterosuperior labral peel back. After approval by the institutional review board (IRB) of the University of Pittsburgh Medical Center, USA, databases of patients who underwent arthroscopy over a 2-year period for one of three clinical diagnoses [suspected type 2 superior labrum anterior to posterior (SLAP) tears, posterior instability, or multidirectional instability] were reviewed after anonymization by an honest broker. Sixty-three cases were selected by the following inclusion criteria: operative report documenting labral peel back in the ABER position, age position (n=34). Inclusion criteria for the control group differed from those for the case group insofar as the operative note documented the absence of posterosuperior labral peel back (n=29). Cases and controls were randomized in one list and evaluated independently by two fellowship-trained musculoskeletal radiologists unaware of the surgical results and using a three-point grading system (0 = posterosuperior labrum normally positioned lateral/craniad to glenoid articular plane in ABER; 1 = posterosuperior labral tissue flush with the glenoid articular plane in ABER; 2 = posterosuperior labral tissue identified medial/caudal to glenoid articular plane in ABER). Only one image in ABER showing abnormal posterosuperior labral position was required for a grade of 1 or 2 to be assigned. Sensitivity, specificity, and positive and negative predictive value were calculated as well as the level of agreement between readers (kappa). Both readers assigned a grade of 2 to 25 of 34 patients with surgically proven labral peel back. Of the patients with surgically proven SLAP tears with peel back in ABER, reader A assigned a grade of 1 to seven patients and a grade of 0 to two

  14. Sensitivity and Specificity of Magnetic Resonance Cholangiopancreatography versus Endoscopic Ultrasonography against Endoscopic Retrograde Cholangiopancreatography in Diagnosing Choledocholithiasis: The Indonesian Experience

    Directory of Open Access Journals (Sweden)

    Dadang Makmun

    2017-09-01

    Full Text Available Background/Aims Biliary stone disease is one of the most common conditions leading to hospitalization. In addition to endoscopic retrograde cholangiopancreatography (ERCP, endoscopic ultrasonography (EUS and magnetic resonance cholangiopancreatography (MRCP are required in diagnosing choledocholithiasis. This study aimed to compare the sensitivity and specificity of EUS and MRCP against ERCP in diagnosing choledocholithiasis. Methods This retrospective study was conducted after prospective collection of data involving 62 suspected choledocholithiasis patients who underwent ERCP from June 2013 to August 2014. Patients were divided into two groups. The first group (31 patients underwent EUS and the second group (31 patients underwent MRCP. Then, ERCP was performed in both groups. Sensitivity, specificity, and diagnostic accuracy of EUS and MRCP were determined by comparing them to ERCP, which is the gold standard. Results The male to female ratio was 3:2. The mean ages were 47.25 years in the first group and 52.9 years in the second group. Sensitivity, specificity, accuracy, positive predictive value, and negative predictive value for EUS were 96%, 57%, 87%, 88%, and 80% respectively, and for MRCP were 81%, 40%, 68%, 74%, and 50%, respectively. Conclusions EUS is a better diagnostic tool than MRCP for diagnosing choledocholithiasis.

  15. The research status and development trend of stochastic resonance

    Science.gov (United States)

    Xu, Lei; Peng, Yueping; Liu, Man

    2017-12-01

    The synergistic reaction under specific conditions of the nonlinear system, weak driving signal and moderate noise can make noise to be advantageous in a certain extent, so as to achieve the purpose of signal enhancement, this seemingly anomalous phenomenon is defined as stochastic resonance. In this paper, the weak signal detection under strong noise background is the main line. The principle of white noise to counteract external noise is expounded, and the present research situation and development trend of stochastic resonance are reviewed in that paper, it also pointed out the direction of further research of stochastic resonance technology.

  16. Genetics of traffic assignment models for strategic transport planning

    NARCIS (Netherlands)

    Bliemer, M.C.J.; Raadsen, M.P.H.; Brederode, L.J.N.; Bell, M.G.H.; Wismans, Luc Johannes Josephus; Smith, M.J.

    2016-01-01

    This paper presents a review and classification of traffic assignment models for strategic transport planning purposes by using concepts analogous to genetics in biology. Traffic assignment models share the same theoretical framework (DNA), but differ in capability (genes). We argue that all traffic

  17. ZUT, Resonance Integrals in Resolved Region at Various Temperature, Escape Probability Calculation

    International Nuclear Information System (INIS)

    Kuncir, G.F.

    1984-01-01

    1 - Nature of physical problem solved: ZUT computes resonance integrals from resonance parameters for a wide variety of temperatures, compositions, and geometries for the resolved resonances. 2 - Method of solution: The form used permits specification of escape probability as a function of the lump dimension and the mean free path. The absorber term may be treated by the integral method, the narrow resonance or the infinite mass approximation. Moderator terms may be represented either by the full integral method (IM) or the asymptotic (NR) form

  18. Interaction between resonances through autoionization continua near the 4s-threshold in KrII

    International Nuclear Information System (INIS)

    Demekhin, Ph V; Petrov, I D; Lagutin, B M; Sukhorukov, V L; Vollweiler, F; Klumpp, S; Ehresmann, A; Schartner, K-H; Schmoranzer, H

    2005-01-01

    The interaction between resonances through autoionization continua and the interaction between autoionization continua were investigated theoretically and experimentally for the photoionization process of the 4p- and 4s-shells and for the population of 4p 4 ( 3 P)5s 4 P J , 4p 4 ( 3 P)5s 2 P J and 4p 4 ( 3 P)4d 4 D J satellites of KrII. Cross sections for the satellite production and the angular distribution parameter of the fluorescence radiation were measured by photon-induced fluorescence spectroscopy after excitationx with linearly polarized monochromatized synchrotron radiation at exciting-photon energies between 28.45 eV and 29.95 eV with an exciting-photon energy resolution of 10 meV (FWHM). Measured cross sections are in good agreement with the computed ones. A refined assignment of resonances in the proximity of the 4s 1 4p 6 5p resonance was performed. It was concluded that there is a strong influence of the core rearrangement, of the interaction between resonances through the autoionization continua and of the interaction between autoionization continua, on the investigated processes on the basis of the observed good overall agreement between the computed and measured quantities

  19. Designing Internet research assignments: building a framework for instructor collaboration

    Directory of Open Access Journals (Sweden)

    David Ward

    2000-01-01

    Full Text Available Internet knowledge is increasing steadily among instructors in the academic world. As courses incorporate more instructional technology, traditional undergraduate research assignments are adapting to reflect the changing world of information and information access. New library assignments reflect this shift as well, with term papers and research projects asking students to use Web sites as an information resource, in addition to the standard literature of periodicals and monographs. But the many pitfalls the library profession has learned in its own metamorphosis during the past decade are often repeated in these newer course assignments. The authors in this paper present a framework for librarians to interact with instructors to incorporate Internet resources into traditional term paper and research assignments. They suggest a framework for creating sample assignments librarians can take to campus instructional units, to show the teaching community at large what the library profession has learned from first-hand experience.

  20. Characterization of hepatic lesions (≤30 mm) with liver-specific contrast agents: A comparison between ultrasound and magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Masanori, E-mail: machat1215@yahoo.co.jp [Department of Medicine and Clinical Oncology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Maruyama, Hitoshi, E-mail: maru-cib@umin.ac.jp [Department of Medicine and Clinical Oncology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Shimada, Taro, E-mail: bobtaro51@yahoo.co.jp [Department of Medicine and Clinical Oncology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Kamezaki, Hidehiro, E-mail: ugn29814@yahoo.co.jp [Department of Medicine and Clinical Oncology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Sekimoto, Tadashi, E-mail: tad_sekimoto@yahoo.co.jp [Department of Medicine and Clinical Oncology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Kanai, Fumihiko, E-mail: kanaif@faculty.chiba-u.jp [Department of Medicine and Clinical Oncology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan); Yokosuka, Osamu, E-mail: yokosukao@faculty.chiba-u.jp [Department of Medicine and Clinical Oncology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 (Japan)

    2013-01-15

    Purpose: Imaging-based differentiation of hepatic lesions (≤30 mm) between well-differentiated hepatocellular carcinomas (w-HCC) and regenerative nodules (RN) presents difficulties. The aim was to compare the diagnostic abilities to differentiate w-HCC from RN using contrast-enhanced ultrasound and magnetic resonance imaging (MRI) both with liver-specific contrast agents. Materials and methods: This prospective study included 67 pathologically proven hepatic lesions (17.5 ± 5.4 mm, 54 w-HCCs, 13 RNs) in 56 patients with chronic hepatitis/cirrhosis (male 40, female 16; 29–79y). Hepatic-arterial/liver-specific phase enhancements were assessed quantitatively by ultrasound with perflubutane microbubble agent and MRI with gadolinium-ethoxybenzyl-diethylenetriamine with respect to the histological findings. Results: Sensitivity, specificity and accuracy of hepatic-arterial phase hyper-enhancement for w-HCC were 59.3%, 100% and 67.2% by ultrasound and 46.3%, 100% and 56.7% by MRI without significant difference. Meanwhile, those of liver-specific-phase hypo-enhancement for w-HCC were 44.4%, 100% and 55.2% by ultrasound and 87.0% (p < 0.0001), 46.2% (p = 0.0052) and 79.1% (p = 0.0032) by MRI. Diagnostic accuracies for w-HCC by area under the receiver operating characteristic curves were higher in the hepatic-arterial phase in ultrasound (0.8316) than MRI (0.6659, p = 0.0101) and similar in the liver-specific phase in ultrasound (0.7225) and MRI (0.7347, p = 0.8814). Conclusions: Hypervascularity is a significant feature which distinguishes w-HCC from RN, and ultrasound exerts a beneficial impact better than MRI for such characterization. However, both imaging have comparable abilities in the characterization of non-hypervascular lesions, compensating mutually for the poor sensitivity of ultrasound and the poor specificity of MRI in the liver-specific phase.

  1. Immediate analysis of the oil content of seeds by carbon-13 nuclear magnetic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Leal, K Z; Costa, V E.U.; Seidl, P R; Campos, M P.A.; Colnago, L A [Instituto Militar de Engenharia, Rio de Janeiro (Brazil). Secao de Quimica

    1981-11-01

    The carbon 13 nuclear magnetic resonance (CMR) spectra of a series of Brazilian oilseeds was registered. The main constituents of the oils are identified and signals for each carbon atom are assigned. Chemical shifts are estimated for the free fatty acids and compared to those observed from the seeds, with good results. Besides being non-destructive, the RMC method proves to be fast and is useful in the determination of the principal components of the oil fraction of different types of seeds.

  2. Persistence, resistance, resonance

    Science.gov (United States)

    Tsadka, Maayan

    Sound cannot travel in a vacuum, physically or socially. The ways in which sound operates are a result of acoustic properties, and the ways by which it is considered to be music are a result of social constructions. Therefore, music is always political, regardless of its content: the way it is performed and composed; the choice of instrumentation, notation, tuning; the medium of its distribution; its inherent hierarchy and power dynamics, and more. My compositional praxis makes me less interested in defining a relationship between music and politics than I am in erasing---or at least blurring---the borders between them. In this paper I discuss the aesthetics of resonance and echo in their metaphorical, physical, social, and musical manifestations. Also discussed is a political aesthetic of resonance, manifested through protest chants. I transcribe and analyze common protest chants from around the world, categorizing and unifying them as universal crowd-mobilizing rhythms. These ideas are explored musically in three pieces. Sumud: Rhetoric of Resistance in Three Movements, for two pianos and two percussion players, is a musical interpretation of the political/social concept of sumud, an Arabic word that literally means "steadfastness" and represents Palestinian non-violent resistance. The piece is based on common protest rhythms and uses the acoustic properties inherent to the instruments. The second piece, Three Piano Studies, extends some of the musical ideas and techniques used in Sumud, and explores the acoustic properties and resonance of the piano. The final set of pieces is part of my Critical Mess Music Project. These are site-specific musical works that attempt to blur the boundaries between audience, performers and composer, in part by including people without traditional musical training in the process of music making. These pieces use the natural structure and resonance of an environment, in this case, locations on the UCSC campus, and offer an active

  3. Postgraduate diploma collaborative assignment: Implications for ...

    African Journals Online (AJOL)

    Postgraduate diploma collaborative assignment: Implications for ESL students ... and collaborative teaching/learning model involving the major course convenors. ... The quality of the work and mood of all concerned improved tremendously.

  4. A linear program for assessing the assignment and scheduling of radioactive wastes for disposal to sea

    International Nuclear Information System (INIS)

    Hutchinson, W.

    1983-04-01

    The report takes the form of a user guide to a computer program using linear programming techniques to aid the assignment and scheduling of radioactive wastes for disposal to sea. The program is aimed at the identification of 'optimum' amounts of each waste stream for disposal to sea without violating specific constraints values and/or fairness parameters. (author)

  5. Effect of endorsed body weight on specific absorption rate during magnetic resonance imaging

    International Nuclear Information System (INIS)

    Singh, Harish K.; Gupta, R.K.; Gujral, R.B.; Shukla, A.K.

    2001-01-01

    As a routine safety of the patients undergoing magnetic resonance imaging (MRI), the limits of radiofrequency (RF) specific absorption rate (SAR) are set by the manufacturers of all MRI systems because RF causes thermo genesis of the RF exposed tissue. It has been mandatory practice to endorse body weight and age of the patients required by the MRI systems for the SAR check. The problems arise on those patients who are critically ill, and consequently body weight could not be measured. In such cases, approximate body weight has to be endorsed. In case of underweight and overweight patients, sometimes SAR check does not permit to run the MRI pulse sequences. Also, in such cases, body weight remains the parameter which is being changed to get the MRI done. The purpose of this study is to assess the change of SAR with endorsed body weight. The change of SAR was recorded with the endorsed weight using phantoms and most commonly used T1 and T2 weighted pulse sequence on clinical MRI system. At true endorsed weight, using respective coils and the head and spine coil phantoms, the body averaged and localised SAR were found to be within limits while this was not the case with body coil phantom. Unrealistic endorsed weights are permissible for the adult age cases in all coils while using the routine T1 and T2 weighted pulse sequences. This finding is absolutely new in the field and certainly, will be of great applicability to develop a uniform and standard system of SAR checks in the patient interest. (author)

  6. Design of high power solid-state pulsed laser resonators

    International Nuclear Information System (INIS)

    Narro, R.; Ponce, L.; Arronte, M.

    2009-01-01

    Methods and configurations for the design of high power solid-state pulsed laser resonators, operating in free running, are presented. For fundamental mode high power resonators, a method is proposed for the design of a resonator with joined stability zones. In the case of multimode resonators, two configurations are introduced for maximizing the laser overall efficiency due to the compensation of the astigmatism induced by the excitation. The first configuration consists in a triangular ring resonator. The results for this configuration are discussed theoretically, showing that it is possible to compensate the astigmatism of the thermal lens virtually in a 100%; however this is only possible for a specific pumping power. The second configuration proposes a dual-active medium resonator, rotated 90 degree one from the other around the optical axis, where each active medium acts as an astigmatic lens of the same dioptric power. The reliability of this configuration is corroborated experimentally using a Nd:YAG dual-active medium resonator. It is found that in the pumping power range where the astigmatism compensation is possible, the overall efficiency is constant, even when increasing the excitation power with the consequent increase of the thermal lens dioptric power. (Author)

  7. Tracing the geographic origin of traded leopard body parts in the indian subcontinent with DNA-based assignment tests.

    Science.gov (United States)

    Mondol, Samrat; Sridhar, Vanjulavalli; Yadav, Prasanjeet; Gubbi, Sanjay; Ramakrishnan, Uma

    2015-04-01

    Illicit trade in wildlife products is rapidly decimating many species across the globe. Such trade is often underestimated for wide-ranging species until it is too late for the survival of their remaining populations. Policing this trade could be vastly improved if one could reliably determine geographic origins of illegal wildlife products and identify areas where greater enforcement is needed. Using DNA-based assignment tests (i.e., samples are assigned to geographic locations), we addressed these factors for leopards (Panthera pardus) on the Indian subcontinent. We created geography-specific allele frequencies from a genetic reference database of 173 leopards across India to infer geographic origins of DNA samples from 40 seized leopard skins. Sensitivity analyses of samples of known geographic origins and assignments of seized skins demonstrated robust assignments for Indian leopards. We found that confiscated pelts seized in small numbers were not necessarily from local leopards. The geographic footprint of large seizures appeared to be bigger than the cumulative footprint of several smaller seizures, indicating widespread leopard poaching across the subcontinent. Our seized samples had male-biased sex ratios, especially the large seizures. From multiple seized sample assignments, we identified central India as a poaching hotspot for leopards. The techniques we applied can be used to identify origins of seized illegal wildlife products and trade routes at the subcontinent scale and beyond. © 2014 Society for Conservation Biology.

  8. Resonating Statements: Discursive acts in IT projects

    DEFF Research Database (Denmark)

    Hjelholt, Morten; Jensen, Tina Blegind

    2015-01-01

    IT projects are often complex arrangements of technological components, social actions, and organizational transformation that are difficult to manage in practice. This paper takes an analytical discourse perspective to explore the process of legitimizing IT projects. We introduce the concept...... of resonating statements to highlight how central actors navigate in various discourses over time. Particularly, the statements and actions of an IT project manager are portrayed to show how individuals can legitimize actions by connecting statements to historically produced discourses. The case study...... of an IT project in a Danish local government spans a two-year time period and demonstrates a double-loop legitimization process. First, resonating statements are produced to localize a national IT initiative to support the specificity of a local government discourse. Second, the resonating statements are used...

  9. Parentage assignment of progeny in mixed milt fertilization of ...

    African Journals Online (AJOL)

    Administrator

    2011-06-13

    Jun 13, 2011 ... individuals. Overall, 98.8% of progeny were assigned to their parents using Family Assignment. Program (FAP). Selection of hyper-variable microsatellites in Caspian brown trout to identify unique alleles was effective for unambiguous parentage determination and estimation of genetic diversity in this study.

  10. Element-specific ferromagnetic resonance in epitaxial Heusler spin valve systems

    Energy Technology Data Exchange (ETDEWEB)

    Klaer, P; Jorge, E Arbelo; Jourdan, M; Elmers, H J [Institut fuer Physik, Johannes Gutenberg-Universitaet Mainz, D-55128 Mainz (Germany); Hoffmann, F; Woltersdorf, G; Back, C H, E-mail: elmers@uni-mainz.de [Institut fuer Experimentelle und Angewandte Physik, Universitaet Regensburg, D-93040 Regensburg (Germany)

    2011-10-26

    Time-resolved x-ray magnetic circular dichroism was used to investigate epitaxial MgO(100)/Co{sub 2}Cr{sub 0.6}Fe{sub 0.4}Al and MgO(100)/Co{sub 2}Cr{sub 0.6}Fe{sub 0.4}Al/Cr/CoFe films. The precessional motion of the individual sublattice magnetization, excited by continuous microwave excitation in the range 2-10 GHz, was detected by tuning the x-ray photon energy to the L{sub 3} absorption edges of Cr, Fe and Co. The relative phase angle of the sublattice magnetization's response is smaller than the detection limit of 2{sup 0}. A weakly antiferromagnetically coupled CoFe layer causes an increase in the ferromagnetic resonance linewidth consisting of a constant offset and a component linearly increasing with frequency that we partly attribute to non-local damping due to spin pumping.

  11. Integrating Academic Journal Review Assignments into a Graduate Business Leadership Course

    Science.gov (United States)

    Schultz, Jennifer L.; Agrimonti, Lisa M.; Higbee, Jeanne L.

    2016-01-01

    Graduate course assignments that are pragmatic, challenging, scaffold prior learning, and support academic career aspirations can be difficult to create and even more problematic to assess for even the most experienced faculty. This paper presents a class assignment that incorporated a real-world journal reviewing assignment into an elective…

  12. 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough.

    Science.gov (United States)

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

    2011-10-01

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

  13. 20 CFR 422.104 - Who can be assigned a social security number.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Who can be assigned a social security number... General Procedures § 422.104 Who can be assigned a social security number. (a) Persons eligible for SSN assignment. We can assign you a social security number if you meet the evidence requirements in § 422.107 and...

  14. 32 CFR 644.396 - Assignment of personnel to administer.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 4 2010-07-01 2010-07-01 true Assignment of personnel to administer. 644.396... PROPERTY REAL ESTATE HANDBOOK Disposal Predisposal Action § 644.396 Assignment of personnel to administer... responsible representative to each installation, or group of installations, to act under his staff supervision...

  15. A Poster Assignment Connects Information Literacy and Writing Skills

    Science.gov (United States)

    Waters, Natalie

    2015-01-01

    This paper describes the implementation of a poster assignment in a writing and information literacy course required for undergraduate Life Sciences and Environmental Biology majors with the Faculty of Agricultural and Environmental Sciences at McGill University. The assignment was introduced in response to weaknesses identified through course…

  16. Generating Unstable Resonances for Extraction Schemes Based on Transverse Splitting

    CERN Document Server

    Giovannozzi, M; Turchetti, G

    2009-01-01

    A few years ago, a novel multi-turn extraction scheme was proposed, based on particle trapping inside stable resonances. Numerical simulations and experimental tests have confirmed the feasibility of such a scheme for low order resonances. While the third-order resonance is generically unstable and those higher than fourth-order are generically stable, the fourth-order resonance can be either stable or unstable depending on the specifics of the system under consideration. By means of the Normal Form a general approach to control the stability of the fourth-order resonance has been derived. This approach is based on the control of the amplitude detuning and the general form for a lattice with an arbitrary number of sextupole and octupole families is derived in this paper. Numerical simulations have confirmed the analytical results and have shown that, when crossing the unstable fourth-order resonance, the region around the centre of the phase space is depleted and particles are trapped in only the four stable ...

  17. 42 CFR 421.114 - Assignment and reassignment of providers by CMS.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Assignment and reassignment of providers by CMS. 421.114 Section 421.114 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH... Assignment and reassignment of providers by CMS. CMS may assign or reassign any provider to any intermediary...

  18. 28 CFR 0.153 - Selection and assignment of employees for training.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Selection and assignment of employees for... Selection and assignment of employees for training. The Director of the Federal Bureau of Investigation, the....S.C. 4109, with respect to the selection and assignment of employees for training by, in, or through...

  19. 26 CFR 1.401(a)-13 - Assignment or alienation of benefits.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 5 2010-04-01 2010-04-01 false Assignment or alienation of benefits. 1.401(a...)-13 Assignment or alienation of benefits. (a) Scope of the regulations. This section applies only to..., provided for employer contributions. (b) No assignment or alienation—(1) General rule. Under section 401(a...

  20. Control of Resonances and Optical Properties of Plasmonic-Patch Metamaterials

    Science.gov (United States)

    2012-08-01

    nanostructures made of plasmonic materials like gold and silver can resonantly interact with radiation over a range of wavelengths from micro...specific metal nanostructures, such as nanorods, hemispheres, nanocrescent arrays, nanorings , dimers, nanoprisms, nanocrystals, nanoparticles in a periodic...known that nanostructures made of plasmonic materials like gold and silver can resonantly interact with radiation over a range of wavelengths from micro

  1. 1H, 13C, and 15N resonance assignment of the N-terminal domainof Mason-Pfizer monkey virus capsid protein, CA 1-140

    Czech Academy of Sciences Publication Activity Database

    Macek, Pavel; Žídek, L.; Rumlová, Michaela; Pichová, Iva; Sklenář, V.

    2008-01-01

    Roč. 2, č. 1 (2008), s. 43-45 ISSN 1874-2718 R&D Projects: GA MŠk LC545; GA MŠk(CZ) LC06030; GA MŠk 1M0508 Institutional research plan: CEZ:AV0Z50200510; CEZ:AV0Z40550506 Keywords : nmr * assignment * capsid protein Subject RIV: EE - Microbiology, Virology Impact factor: 0.015, year: 2008

  2. Silicon photonic resonator for label-free bio-sensing application

    Science.gov (United States)

    Udomsom, Suruk; Mankong, Ukrit; Theera-Umpon, Nipon; Ittipratheep, Nattapol; Umezawa, Toshimasa; Matsumoto, Atsushi; Yamamoto, Naokatsu

    2018-03-01

    In medical diagnostics there is an increasing demand for biosensors that can specifically detect biological analytes in a fluid. Especially label-free sensing, consistings of a transducer with biorecognition molecules immobilized on its surface without relying on fluorescent dye. In this paper we study the design and fabrication of a silicon nanowire photonic ring resonator and its feasibility as a biosensor. We have simulated and fabricated racetrack ring resonators which have a few tenths of micrometer gap, up to 0.5 μm between the input / output waveguides and the resonators. It is found that the devices can be designed with large Q factors. Sensitivity to biomaterial detection has been simulated for antibody (goat anti-mouse IgG) - antigen (mouse IgG) using 3-dimensional Finite Difference Time Domain technique. The simulated results show that the ring resonator has a response 15 nm resonance shift per refractive index unit. Antibody coating method is also discussed in this paper which can be applied to other antibody-antigen types.

  3. Redefining the Practice of Peer Review Through Intelligent Automation Part 2: Data-Driven Peer Review Selection and Assignment.

    Science.gov (United States)

    Reiner, Bruce I

    2017-12-01

    In conventional radiology peer review practice, a small number of exams (routinely 5% of the total volume) is randomly selected, which may significantly underestimate the true error rate within a given radiology practice. An alternative and preferable approach would be to create a data-driven model which mathematically quantifies a peer review risk score for each individual exam and uses this data to identify high risk exams and readers, and selectively target these exams for peer review. An analogous model can also be created to assist in the assignment of these peer review cases in keeping with specific priorities of the service provider. An additional option to enhance the peer review process would be to assign the peer review cases in a truly blinded fashion. In addition to eliminating traditional peer review bias, this approach has the potential to better define exam-specific standard of care, particularly when multiple readers participate in the peer review process.

  4. DNATCO: assignment of DNA conformers at dnatco.org.

    Science.gov (United States)

    Černý, Jiří; Božíková, Paulína; Schneider, Bohdan

    2016-07-08

    The web service DNATCO (dnatco.org) classifies local conformations of DNA molecules beyond their traditional sorting to A, B and Z DNA forms. DNATCO provides an interface to robust algorithms assigning conformation classes called NTC: to dinucleotides extracted from DNA-containing structures uploaded in PDB format version 3.1 or above. The assigned dinucleotide NTC: classes are further grouped into DNA structural alphabet NTA: , to the best of our knowledge the first DNA structural alphabet. The results are presented at two levels: in the form of user friendly visualization and analysis of the assignment, and in the form of a downloadable, more detailed table for further analysis offline. The website is free and open to all users and there is no login requirement. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Effective Homework Assignments. Research Brief

    Science.gov (United States)

    Cooper, Harris

    2008-01-01

    Perhaps more than any question other than "How much time should students spend doing homework?" parents and educators want to know, "What kinds of homework assignments are most effective?" Clearly, the answers to this question vary according to many factors, especially the developmental level of students and the topic area. Generally, answers are…

  6. Effects of mutation on the downfield proton nuclear magnetic resonance spectrum of the 5S RNA of Escherichia coli

    International Nuclear Information System (INIS)

    Gewirth, D.T.; Moore, P.B.

    1987-01-01

    The imino proton spectra of several mutants of the 5S RNA of Escherichia coli are compared with that of the wild type. Three of the variants discussed are point mutations, and the fourth is a deletion mutant lacking bases 11-69 of the parent sequence, all obtained by site-directed mutagenesis techniques. The spectroscopic effects of mutation are limited in all cases, and the differences between normal and mutant spectra can be used to make or confirm the assignments of resonances. Several new assignments in the 5S spectrum are reported. Spectroscopic differences due to sequence differences permit the products of single genes within the 5S gene family to be distinguished and their fates followed by NMR

  7. Dynamic traffic assignment : genetic algorithms approach

    Science.gov (United States)

    1997-01-01

    Real-time route guidance is a promising approach to alleviating congestion on the nations highways. A dynamic traffic assignment model is central to the development of guidance strategies. The artificial intelligence technique of genetic algorithm...

  8. On some special cases of the restricted assignment problem

    NARCIS (Netherlands)

    Wang, C. (Chao); R.A. Sitters (René)

    2016-01-01

    textabstractWe consider some special cases of the restricted assignment problem. In this scheduling problem on parallel machines, any job j can only be assigned to one of the machines in its given subset Mj of machines. We give an LP-formulation for the problem with two job sizes and show that it

  9. 13 CFR 500.210 - Assignment or transfer of loans.

    Science.gov (United States)

    2010-01-01

    ... has the effect of distributing the risks of the credit among other Lenders if: (i) Neither the loan... be modified, assigned, conveyed, sold or otherwise transferred by the Lender, in whole or in part... assignment or transfer of less than 100 percent of a Lender's interest in the Loan Documents and Guarantee...

  10. Efficient primary and parametric resonance excitation of bistable resonators

    KAUST Repository

    Ramini, Abdallah

    2016-09-12

    We experimentally demonstrate an efficient approach to excite primary and parametric (up to the 4th) resonance of Microelectromechanical system MEMS arch resonators with large vibrational amplitudes. A single crystal silicon in-plane arch microbeam is fabricated such that it can be excited axially from one of its ends by a parallel-plate electrode. Its micro/nano scale vibrations are transduced using a high speed camera. Through the parallel-plate electrode, a time varying electrostatic force is applied, which is converted into a time varying axial force that modulates dynamically the stiffness of the arch resonator. Due to the initial curvature of the structure, not only parametric excitation is induced, but also primary resonance. Experimental investigation is conducted comparing the response of the arch near primary resonance using the axial excitation to that of a classical parallel-plate actuation where the arch itself forms an electrode. The results show that the axial excitation can be more efficient and requires less power for primary resonance excitation. Moreover, unlike the classical method where the structure is vulnerable to the dynamic pull-in instability, the axial excitation technique can provide large amplitude motion while protecting the structure from pull-in. In addition to primary resonance, parametrical resonances are demonstrated at twice, one-half, and two-thirds the primary resonance frequency. The ability to actuate primary and/or parametric resonances can serve various applications, such as for resonator based logic and memory devices. (C) 2016 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license

  11. Transluminal color-coded three-dimensional magnetic resonance angiography for visualization of signal Intensity distribution pattern within an unruptured cerebral aneurysm: preliminarily assessment with anterior communicating artery aneurysms

    International Nuclear Information System (INIS)

    Satoh, T.; Ekino, C.; Ohsako, C.

    2004-01-01

    The natural history of unruptured cerebral aneurysm is not known; also unknown is the potential growth and rupture in any individual aneurysm. The authors have developed transluminal color-coded three-dimensional magnetic resonance angiography (MRA) obtained by a time-of-flight sequence to investigate the interaction between the intra-aneurysmal signal intensity distribution patterns and configuration of unruptured cerebral aneurysms. Transluminal color-coded images were reconstructed from volume data of source magnetic resonance angiography by using a parallel volume-rendering algorithm with transluminal imaging technique. By selecting a numerical threshold range from a signal intensity opacity chart of the three-dimensional volume-rendering dataset several areas of signal intensity were depicted, assigned different colors, and visualized transparently through the walls of parent arteries and an aneurysm. Patterns of signal intensity distribution were analyzed with three operated cases of an unruptured anterior communicating artery aneurysm and compared with the actual configurations observed at microneurosurgery. A little difference in marginal features of an aneurysm was observed; however, transluminal color-coded images visualized the complex signal intensity distribution within an aneurysm in conjunction with aneurysmal geometry. Transluminal color-coded three-dimensional magnetic resonance angiography can thus provide numerical analysis of the interaction between spatial signal intensity distribution patterns and aneurysmal configurations and may offer an alternative and practical method to investigate the patient-specific natural history of individual unruptured cerebral aneurysms. (orig.)

  12. Immediate analysis of the oil content of seeds by carbon-13 nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Leal, K.Z.; Costa, V.E.U.; Seidl, P.R.; Campos, M.P.A.; Colnago, L.A.

    1981-01-01

    The carbon 13 nuclear magnetic resonance (CMR) spectra of a series of Brazilian oilseeds was registered. The main constituents of the oils are identified and signals for each carbon atom are assigned. Chemical shifts are estimated for the free fatty acids and compared to those observed from the seeds, with good results. Besides being non-destructive, the RMC method proves to be fast and is useful in the determination of the principal components of the oil fraction of different types of seeds. (Author) [pt

  13. Resonance structure of 32S+n from measurements of neutron total and capture cross sections

    International Nuclear Information System (INIS)

    Halperin, J.; Johnson, C.H.; Winters, R.R.; Macklin, R.L.

    1980-01-01

    Neutron total and capture cross sections of 32 S have been measured up to 1100 keV neutron energy [E/sub exc/( 33 S) =9700 keV]. Spin and parity assignments have been made for 28 of the 64 resonances found in this region. Values of total radiation widths, reduced neutron widths, level spacings, and neutron strength functions have been evaluated for s/sub 1/2/, p/sub 1/2/, p/sub 3/2/, and d/sub 5/2/ levels. Single particle contributions using the valency model account for a significant portion of the total radiation width only for the p/sub 1/2/-wave resonances. A significant number of resonances can be identified with reported levels excited in 32 S(d,p) and 29 Si(α,n) reactions. A calculation of the Maxwellian average cross section appropriate to stellar interiors indicates an average capture cross section at 30 keV, sigma-bar approx. = 4.2(2) mb, a result that is relatively insensitive to the assumed stellar temperature. Direct (potential) capture and the s-wave resonance capture contributions to the thermal capture cross section do not fully account for the reported thermal cross section (530 +- 40 mb) and a bound state is invoked to account for the discrepancy

  14. Interference effect as resonance killer of newly observed charmoniumlike states Y(4320) and Y(4390)

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Dian-Yong [Southeast University, School of Physics, Nanjing (China); Liu, Xiang [Lanzhou University, School of Physical Science and Technology, Lanzhou (China); Lanzhou University, Research Center for Hadron and CSR Physics, Institute of Modern Physics of CAS, Lanzhou (China); Matsuki, Takayuki [Tokyo Kasei University, Tokyo (Japan); Nishina Center, RIKEN, Wako, Theoretical Research Division, Saitama (Japan)

    2018-02-15

    In this letter, we decode the newly observed charmoniumlike states, Y(4320) and Y(4390), by introducing interference effect between ψ(4160) and ψ(4415), which plays a role of resonance killer for Y(4320) and Y(4390). It means that two newly reported charmoniumlike states are not genuine resonances, according to which we can naturally explain why two well-established charmonia ψ(4160) and ψ(4415) are missing in the cross sections of e{sup +}e{sup -} → π{sup +}π{sup -}J/ψ and π{sup +}π{sup -}h{sub c} simultaneously. To well describe the detailed data of these cross sections around √(s) = 4.2 GeV, our study further illustrates that a charmoniumlike structure Y(4220) must be introduced. As a charmonium, Y(4220) should dominantly decay into its open-charm channel e{sup +}e{sup -} → D{sup 0}π{sup +}D{sup *-}, which provides an extra support to ψ(4S) assignment to Y(4220). In fact, this interference effect introduced to explain Y(4320) and Y(4390) gives a typical example of non-resonant explanations to the observed XYZ states, which should be paid more attention especially before identifying the observed XYZ states as genuine resonances. (orig.)

  15. Synchrotron radiation resonance Raman spectroscopy (SR3S)

    International Nuclear Information System (INIS)

    Hester, R.E.

    1979-01-01

    The use of normal Raman spectroscopy and resonance Raman spectroscopy to study the structure of molecular species and the nature of their chemical bonds is discussed. The availability of a fully tunable radiation source (the Synchrotron Radiation Source) extending into the ultraviolet raises the possibility of using synchrotron radiation resonance Raman spectroscopy as a sensitive and specific analytical probe. The pulsed nature of the SRS beam may be exploited for time-resolved resonance Raman spectroscopy and its high degree of polarization could be very helpful in the interpretation of spectra. The possibilities are considered under the headings: intensity requirements and comparison with other sources; some applications (e.g. structure of proteins; study of iron-porphyrin unit; study of chlorophylls). (U.K.)

  16. Cyclotron resonance for electrons over helium in resonator

    CERN Document Server

    Shikin, V B

    2002-01-01

    The problem on the cyclotron resonance (CR) for electrons on the helium film, positioned in the resonator lower part, is solved. It is shown, that it relates to one of the examples of the known problem on the oscillations of the coupled oscillators system. The coupling constant between these oscillators constituting the variable function of the problem parameters. It is minimal in the zero magnetic field and reaches its maximum under the resonance conditions, when the cyclotron frequency coincides with one of the resonator modes. The CR details of the Uhf CR-energy absorption coupled by the electrons + resonator system, are calculated. The applications of the obtained results to the available CR experiments for electrons over helium

  17. Microstrip resonators for electron paramagnetic resonance experiments

    Science.gov (United States)

    Torrezan, A. C.; Mayer Alegre, T. P.; Medeiros-Ribeiro, G.

    2009-07-01

    In this article we evaluate the performance of an electron paramagnetic resonance (EPR) setup using a microstrip resonator (MR). The design and characterization of the resonator are described and parameters of importance to EPR and spin manipulation are examined, including cavity quality factor, filling factor, and microwave magnetic field in the sample region. Simulated microwave electric and magnetic field distributions in the resonator are also presented and compared with qualitative measurements of the field distribution obtained by a perturbation technique. Based on EPR experiments carried out with a standard marker at room temperature and a MR resonating at 8.17 GHz, the minimum detectable number of spins was found to be 5×1010 spins/GHz1/2 despite the low MR unloaded quality factor Q0=60. The functionality of the EPR setup was further evaluated at low temperature, where the spin resonance of Cr dopants present in a GaAs wafer was detected at 2.3 K. The design and characterization of a more versatile MR targeting an improved EPR sensitivity and featuring an integrated biasing circuit for the study of samples that require an electrical contact are also discussed.

  18. Microstrip resonators for electron paramagnetic resonance experiments.

    Science.gov (United States)

    Torrezan, A C; Mayer Alegre, T P; Medeiros-Ribeiro, G

    2009-07-01

    In this article we evaluate the performance of an electron paramagnetic resonance (EPR) setup using a microstrip resonator (MR). The design and characterization of the resonator are described and parameters of importance to EPR and spin manipulation are examined, including cavity quality factor, filling factor, and microwave magnetic field in the sample region. Simulated microwave electric and magnetic field distributions in the resonator are also presented and compared with qualitative measurements of the field distribution obtained by a perturbation technique. Based on EPR experiments carried out with a standard marker at room temperature and a MR resonating at 8.17 GHz, the minimum detectable number of spins was found to be 5 x 10(10) spins/GHz(1/2) despite the low MR unloaded quality factor Q0=60. The functionality of the EPR setup was further evaluated at low temperature, where the spin resonance of Cr dopants present in a GaAs wafer was detected at 2.3 K. The design and characterization of a more versatile MR targeting an improved EPR sensitivity and featuring an integrated biasing circuit for the study of samples that require an electrical contact are also discussed.

  19. A parametric visualization software for the assignment problem

    Directory of Open Access Journals (Sweden)

    Papamanthou Charalampos

    2005-01-01

    Full Text Available In this paper we present a parametric visualization software used to assist the teaching of the Network Primal Simplex Algorithm for the assignment problem (AP. The assignment problem is a special case of the balanced transportation problem. The main functions of the algorithm and design techniques are also presented. Through this process, we aim to underline the importance and necessity of using such educational methods in order to improve the teaching of Computer Algorithms.

  20. The Utility of Writing Assignments in Undergraduate Bioscience

    Science.gov (United States)

    Libarkin, Julie; Ording, Gabriel

    2012-01-01

    We tested the hypothesis that engagement in a few, brief writing assignments in a nonmajors science course can improve student ability to convey critical thought about science. A sample of three papers written by students (n = 30) was coded for presence and accuracy of elements related to scientific writing. Scores for different aspects of scientific writing were significantly correlated, suggesting that students recognized relationships between components of scientific thought. We found that students' ability to write about science topics and state conclusions based on data improved over the course of three writing assignments, while the abilities to state a hypothesis and draw clear connections between human activities and environmental impacts did not improve. Three writing assignments generated significant change in student ability to write scientifically, although our results suggest that three is an insufficient number to generate complete development of scientific writing skills. PMID:22383616

  1. A search asymmetry reversed by figure-ground assignment.

    Science.gov (United States)

    Humphreys, G W; Müller, H

    2000-05-01

    We report evidence demonstrating that a search asymmetry favoring concave over convex targets can be reversed by altering the figure-ground assignment of edges in shapes. Visual search for a concave target among convex distractors is faster than search for a convex target among concave distractors (a search asymmetry). By using shapes with ambiguous local figure-ground relations, we demonstrated that search can be efficient (with search slopes around 10 ms/item) or inefficient (with search slopes around 30-40 ms/item) with the same stimuli, depending on whether edges are assigned to concave or convex "figures." This assignment process can operate in a top-down manner, according to the task set. The results suggest that attention is allocated to spatial regions following the computation of figure-ground relations in parallel across the elements present. This computation can also be modulated by top-down processes.

  2. The breakout of the Hot CNO cycle via ^18Ne resonant states

    Science.gov (United States)

    Almaraz-Calderon, S.; Tan, W.; Aprahamian, A.; Bucher, B.; Gorres, J.; Roberts, A.; Villano, A.; Wiescher, M.; Brune, C.; Heinen, Z.; Massey, T.; Ozkan, N.; Guray, R. T.; Mach, H.

    2010-11-01

    The energy generation rate in the HCNO cycle is limited by the β decay of the waiting point nuclei ^14O and ^15O. However, when the temperatures and densities are high enough (e.g. Novae and X-ray Bursts) it is possible to bypass them by p/α captures resulting in a thermonuclear runaway towards the rp-process. One of the two paths for breakouts from the HCNO cycle is the reaction chain ^14O(α,p)^17F(p,γ)^18Ne(α,p), which proceeds through resonant states on ^18Ne, making their reactions rates very sensitive on the partial and total widths, excitation energies and spins of such resonances. We studied the resonant states in ^18Ne via ^16O(^3He,n) reaction. The neutrons were measured with an array of liquid scintillators using Time-of-Flight and pulse-shape discrimination techniques. The charged particles were detected in coincidence with neutrons by an array of silicon detectors, allowing us to measure α, p, p' and 2p decay branching ratios. Tentative spin assignments were made in comparison with zero range DWBA calculations. This new information will be included in reaction network calculations to evaluate its impact on the nuclear energy generation that occurs in these stellar explosive environments.

  3. Electrical crosstalk in two-port piezoelectric resonators and compensation solutions

    International Nuclear Information System (INIS)

    Qiu, H C; Schwarz, P; Völlm, H; Feili, D; Seidel, H; Wu, X Z

    2013-01-01

    Crosstalk is an impediment to electrically interfaced two-port resonators. The overall output function of two-port piezoelectric resonator is a superposition of the mechanical resonance behavior and electrical crosstalk, the latter coming mainly from the coupling feedthrough capacitance. In this paper, two crosstalk compensation solutions have been developed for an aluminum nitride-based doubly clamped beam resonator. The first solution demonstrates an on-chip self-cancellation technique of the feedthrough capacitance by using a compensation electrode and applying a complementary voltage to it, while the second solution applies an adjustable compensation voltage to the common bottom electrode. A specifically designed compensation-readout circuit is presented. Experimental investigations of the output signal have proved the efficiency of both crosstalk compensation solutions. (paper)

  4. Photocurrent mapping of near-field optical antenna resonances

    KAUST Repository

    Barnard, Edward S.; Pala, Ragip A.; Brongersma, Mark L.

    2011-01-01

    An increasing number of photonics applications make use of nanoscale optical antennas that exhibit a strong, resonant interaction with photons of a specific frequency. The resonant properties of such antennas are conventionally characterized by far-field light-scattering techniques. However, many applications require quantitative knowledge of the near-field behaviour, and existing local field measurement techniques provide only relative, rather than absolute, data. Here, we demonstrate a photodetector platform that uses a silicon-on-insulator substrate to spectrally and spatially map the absolute values of enhanced fields near any type of optical antenna by transducing local electric fields into photocurrent. We are able to quantify the resonant optical and materials properties of nanoscale (∼50nm) and wavelength-scale (∼1μm) metallic antennas as well as high-refractive-index semiconductor antennas. The data agree well with light-scattering measurements, full-field simulations and intuitive resonator models. © 2011 Macmillan Publishers Limited. All rights reserved.

  5. Photocurrent mapping of near-field optical antenna resonances

    KAUST Repository

    Barnard, Edward S.

    2011-08-21

    An increasing number of photonics applications make use of nanoscale optical antennas that exhibit a strong, resonant interaction with photons of a specific frequency. The resonant properties of such antennas are conventionally characterized by far-field light-scattering techniques. However, many applications require quantitative knowledge of the near-field behaviour, and existing local field measurement techniques provide only relative, rather than absolute, data. Here, we demonstrate a photodetector platform that uses a silicon-on-insulator substrate to spectrally and spatially map the absolute values of enhanced fields near any type of optical antenna by transducing local electric fields into photocurrent. We are able to quantify the resonant optical and materials properties of nanoscale (∼50nm) and wavelength-scale (∼1μm) metallic antennas as well as high-refractive-index semiconductor antennas. The data agree well with light-scattering measurements, full-field simulations and intuitive resonator models. © 2011 Macmillan Publishers Limited. All rights reserved.

  6. Interactive Level Design for iOS Assignment Delivery: A Case Study

    Directory of Open Access Journals (Sweden)

    Anson Brown

    2014-02-01

    Full Text Available This paper presents an application of an iOS-based online gaming assignment in a real classroom. The core concept of the project is a gameplay environment involving two players that have full control over creation and modification of levels. This level design mechanism was implemented in an iOS-based game in the area of genetics and based on an existing written assignment. The game includes support for both instructors, who have the ability to create and post assignments and students, who can take the assignments. Two trials of the iOS application consisted of in-class testing of twenty- one students. Students first took the original paper assignment, followed by the iOS version. Start times, end times, and grades were recorded for both versions. A comprehensive study of the grades and times for the iOS version of the assignment versus the paper version was conducted and is presented in this paper. Our Study showed that the iOS version was completed much faster in nearly every case while a strong delivery mechanism is needed to ensure student grades and completion of the assignment will not be affected. These results are not unexpected due to some major difference between the two formats. Future updates and additions will address any currently existing issues.

  7. Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations.

    Directory of Open Access Journals (Sweden)

    Paul Moran

    Full Text Available Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

  8. Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations

    Science.gov (United States)

    Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

    2014-01-01

    Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

  9. Multiphoton resonances

    International Nuclear Information System (INIS)

    Shore, B.W.

    1977-01-01

    The long-time average of level populations in a coherently-excited anharmonic sequence of energy levels (e.g., an anharmonic oscillator) exhibits sharp resonances as a function of laser frequency. For simple linearly-increasing anharmonicity, each resonance is a superposition of various multiphoton resonances (e.g., a superposition of 3, 5, 7, . . . photon resonances), each having its own characteristic width predictable from perturbation theory

  10. Efficient telecom to visible wavelength conversion in doubly resonant gallium phosphide microdisks

    Science.gov (United States)

    Lake, David P.; Mitchell, Matthew; Jayakumar, Harishankar; dos Santos, Laís Fujii; Curic, Davor; Barclay, Paul E.

    2016-01-01

    Resonant second harmonic generation between 1550 nm and 775 nm with normalized outside efficiency > 3.8 × 10 - 4 mW - 1 is demonstrated in a gallium phosphide microdisk supporting high-Q modes at visible ( Q ˜ 10 4 ) and infrared ( Q ˜ 10 5 ) wavelengths. The double resonance condition is satisfied for a specific pump power through intracavity photothermal temperature tuning using ˜ 360 μ W of 1550 nm light input to a fiber taper and coupled to a microdisk resonance. Power dependent efficiency consistent with a simple model for thermal tuning of the double resonance condition is observed.

  11. 14 CFR 1245.109 - Assignment of title to NASA.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Assignment of title to NASA. 1245.109... INTELLECTUAL PROPERTY RIGHTS Patent Waiver Regulations § 1245.109 Assignment of title to NASA. (a) The instrument of waiver set forth in § 1245.115(c) shall be voided by NASA with respect to the domestic title to...

  12. Cue competition affects temporal dynamics of edge-assignment in human visual cortex.

    Science.gov (United States)

    Brooks, Joseph L; Palmer, Stephen E

    2011-03-01

    Edge-assignment determines the perception of relative depth across an edge and the shape of the closer side. Many cues determine edge-assignment, but relatively little is known about the neural mechanisms involved in combining these cues. Here, we manipulated extremal edge and attention cues to bias edge-assignment such that these two cues either cooperated or competed. To index their neural representations, we flickered figure and ground regions at different frequencies and measured the corresponding steady-state visual-evoked potentials (SSVEPs). Figural regions had stronger SSVEP responses than ground regions, independent of whether they were attended or unattended. In addition, competition and cooperation between the two edge-assignment cues significantly affected the temporal dynamics of edge-assignment processes. The figural SSVEP response peaked earlier when the cues causing it cooperated than when they competed, but sustained edge-assignment effects were equivalent for cooperating and competing cues, consistent with a winner-take-all outcome. These results provide physiological evidence that figure-ground organization involves competitive processes that can affect the latency of figural assignment.

  13. Task assignment and coaching

    OpenAIRE

    Dominguez-Martinez, S.

    2009-01-01

    An important task of a manager is to motivate her subordinates. One way in which a manager can give incentives to junior employees is through the assignment of tasks. How a manager allocates tasks in an organization, provides information to the junior employees about his ability. Without coaching from a manager, the junior employee only has information about his past performance. Based on his past performance, a talented junior who has performed a difficult task sometimes decides to leave the...

  14. Recent research directions in Fribourg: nuclear dynamics in resonances revealed by 2-dimensional EEL spectra, electron collisions with ionic liquids and electronic excitation of pyrimidine

    International Nuclear Information System (INIS)

    Allan, M.; Regeta, K.; Gorfinkiel, J.D.; Masin, Z.; Grimme, S.; Bannwarth, C.

    2016-01-01

    The article briefly reviews three subjects recently investigated in Fribourg: 1) electron collisions with surfaces of ionic liquids, 2) two-dimensional (2D) electron energy loss spectra and 3) resonances in absolute cross sections for electronic excitation of unsaturated compounds. Electron energy loss spectra of four ionic liquids revealed a number of excited states, including triplet states. A solution of a dye in an ionic liquid showed an energy-loss band of the solute, but not in all ionic liquids. 2D spectra reveal state-to-state information (given resonance to given final state) and are shown to be an interesting means to gain insight into dynamics of nuclear motion in resonances. Absolute cross sections for pyrimidine are reported as a function of scattering angle and as a function of electron energy. They reveal resonant structure which was reproduced very nicely by R-matrix calculations. The calculation provided an assignment of the resonances which reveals common patterns in compounds containing double bonds. (authors)

  15. Magnetic resonance spectroscopy as a diagnostic modality for carcinoma thyroid

    International Nuclear Information System (INIS)

    Gupta, Nikhil; Kakar, Arun K.; Chowdhury, Veena; Gulati, Praveen; Shankar, L. Ravi; Vindal, Anubhav

    2007-01-01

    Aim: The aim of this study was to observe the findings of magnetic resonance spectroscopy of solitary thyroid nodules and its correlation with histopathology. Materials and methods: In this study, magnetic resonance spectroscopy was carried out on 26 patients having solitary thyroid nodules. Magnetic resonance spectroscopy (MRS) was performed on a 1.5 T super conductive system with gradient strength of 33 mTs. Fine needle aspiration cytology was done after MRS. All 26 patients underwent surgery either because of cytopathologically proven malignancy or because of cosmetic reasons. Findings of magnetic resonance spectroscopy were compared with histopathology of thyroid specimens. Results and conclusion: It was seen that presence or absence of choline peak correlates very well with presence or absence of malignant foci with in the nodule (sensitivity = 100%; specificity = 88.88%). These results indicate that magnetic resonance spectroscopy may prove to be an useful diagnostic modality for carcinoma thyroid

  16. Implementing a cornerstone of culture change: Consistent staff assignment in VHA community living centers.

    Science.gov (United States)

    Lemke, Sonne; Brennan, Penny L; SooHoo, Sonya; Schutte, Kathleen K

    2017-08-01

    In 2011, the Veterans Health Administration (VHA) began implementing consistent staff assignment in its nursing homes (called Community Living Centers or CLCs). Consistent assignment, a cornerstone of culture change, minimizes the number of staff who provide a resident's care. The present research assessed the level and stability of consistent assignment in units within VHA CLCs and identified unit characteristics related to implementation of this staff assignment model. Schedulers in 185 of 335 organizational units that make up VHA CLCs completed a Staffing Practices Survey. For the month prior to the survey, 53% of CLC units had full implementation of consistent assignment. Tracked back over time, 37% of CLC units had stable high consistent assignment, 29% had stable low consistent assignment, and 34% were variable. Units with stable high consistent assignment were most likely to use care teams with stable membership and to obtain staff input for care assignments. Schedulers in these units reported more positive experiences with consistent staff assignment and better unit functioning in terms of staff absences, complaints about workload fairness, and resolution of scheduling problems. Units with stable low and variable consistent assignment were similar in most of these respects; however, units with variable consistent assignment made greater use of stable care teams and were less likely to change assignments at a staff member's request. Overall, consistent assignment implementation was not related to unit size, nursing hours per resident day, or specialty focus. Findings can help guide consistent staff assignment implementation in VHA and community nursing homes. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  17. Diagnostic imaging of psoriatic arthritis. Part II: magnetic resonance imaging and ultrasonography

    Directory of Open Access Journals (Sweden)

    Iwona Sudoł-Szopińska

    2016-06-01

    Full Text Available Plain radiography reveals specific, yet late changes of advanced psoriatic arthritis. Early inflammatory changes are seen both on magnetic resonance imaging and ultrasound within peripheral joints (arthritis, synovitis, tendons sheaths (tenosynovitis, tendovaginitis and entheses (enthesitis, enthesopathy. In addition, magnetic resonance imaging enables the assessment of inflammatory features in the sacroiliac joints (sacroiliitis, and the spine (spondylitis. In this article, we review current opinions on the diagnostics of some selective, and distinctive features of psoriatic arthritis concerning magnetic resonance imaging and ultrasound and present some hypotheses on psoriatic arthritis etiopathogenesis, which have been studied with the use of magnetic resonance imaging. The following elements of the psoriatic arthritis are discussed: enthesitis, extracapsular inflammation, dactylitis, distal interphalangeal joint and nail disease, and the ability of magnetic resonance imaging to differentiate undifferentiated arthritis, the value of whole-body magnetic resonance imaging and dynamic contrast-enhanced magnetic resonance imaging.

  18. The impact of taxation on international assignment decisions: A principal-agent approach

    OpenAIRE

    Martini, Jan Thomas; Niemann, Rainer

    2013-01-01

    In many industries like management consulting, IT consulting, or construction highly qualified employees, i.e., experts or executive managers, have to be assigned to temporary projects. In firms with many employees and various different projects, this assignment decision involves a complex optimization procedure. Obviously, the employees’ productivities in the respective projects are crucial for the employer’s optimal assignment decision, but assignment can also be affected by risk-incent...

  19. Automated Bug Assignment: Ensemble-based Machine Learning in Large Scale Industrial Contexts

    OpenAIRE

    Jonsson, Leif; Borg, Markus; Broman, David; Sandahl, Kristian; Eldh, Sigrid; Runeson, Per

    2016-01-01

    Bug report assignment is an important part of software maintenance. In particular, incorrect assignments of bug reports to development teams can be very expensive in large software development projects. Several studies propose automating bug assignment techniques using machine learning in open source software contexts, but no study exists for large-scale proprietary projects in industry. The goal of this study is to evaluate automated bug assignment techniques that are based on machine learni...

  20. Time domain-nuclear magnetic resonance study of chars from southern hardwoods

    International Nuclear Information System (INIS)

    Elder, Thomas; Labbe, Nicole; Harper, David; Rials, Timothy

    2006-01-01

    Chars from the thermal degradation of silver maple (Acer saccharinum), red maple (Acer rubrum), sugar maple (Acer saccharum), and white oak (Quercus spp.), performed at temperatures from 250 to 350 o C, were examined using time domain-nuclear magnetic resonance spectroscopy. Prior to analysis, the chars were equilibrated under conditions insuring the presence of bound water only and both bound water and free water. Transverse relaxation times were found to be related to the moisture content of the chars, which varied with temperature. At elevated temperatures the number of signals assigned to free water decreased, indicative of an increase in pore size within the chars