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Sample records for n-15 resonance assignment

  1. H-1, C-13, and N-15 resonance assignment of photoactive yellow protein

    NARCIS (Netherlands)

    Pool, Trijntje J.; Oktaviani, Nur Alia; Kamikubo, Hironari; Kataoka, Mikio; Mulder, Frans A. A.

    Photoactive yellow protein (PYP) is involved in the negative phototactic response towards blue light of the bacterium Halorhodospira halophila. Here, we report nearly complete backbone and side chain H-1, C-13 and N-15 resonance assignments at pH 5.8 and 20 A degrees C of PYP in its electronic

  2. 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....

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

    International Nuclear Information System (INIS)

    Langmead, Christopher James; Donald, Bruce Randall

    2004-01-01

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

  4. CISA: combined NMR resonance connectivity information determination and sequential assignment.

    Science.gov (United States)

    Wan, Xiang; Lin, Guohui

    2007-01-01

    A nearly complete sequential resonance assignment is a key factor leading to successful protein structure determination via NMR spectroscopy. Assuming the availability of a set of NMR spectral peak lists, most of the existing assignment algorithms first use the differences between chemical shift values for common nuclei across multiple spectra to provide the evidence that some pairs of peaks should be assigned to sequentially adjacent amino acid residues in the target protein. They then use these connectivities as constraints to produce a sequential assignment. At various levels of success, these algorithms typically generate a large number of potential connectivity constraints, and it grows exponentially as the quality of spectral data decreases. A key observation used in our sequential assignment program, CISA, is that chemical shift residual signature information can be used to improve the connectivity determination, and thus to dramatically decrease the number of predicted connectivity constraints. Fewer connectivity constraints lead to less ambiguities in the sequential assignment. Extensive simulation studies on several large test datasets demonstrated that CISA is efficient and effective, compared to three most recently proposed sequential resonance assignment programs RANDOM, PACES, and MARS.

  5. Backbone resonance assignments of the PRYSPRY domain of TRIM25.

    Science.gov (United States)

    Kong, Chen; Penumutchu, Srinivasa R; Hung, Kuo-Wei; Huang, Huiying; Lin, Tianwei; Yu, Chin

    2015-10-01

    TRIM25 is a member of the tripartite motif (TRIM) family and has been implicated in the regulation of innate immune signaling via the RIG-I (retinoic acid-inducible gene-I) pathway for antiviral defense. As the essential first step towards the structural and functional characterization of the TRIM25/RIG-I interaction, the backbone resonance of the PRYSPRY domain of TRIM25 is assigned here based on triple-resonance experiments using uniformly [(2)H, (13)C, (15)N]-labeled protein.

  6. Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

    Science.gov (United States)

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2011-01-01

    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0

  7. Intraresidue HNCA and COHNCA Experiments for Protein Backbone Resonance Assignment

    Science.gov (United States)

    Brutscher, Bernhard

    2002-05-01

    Two novel experiments, intra-HNCA and intra-COHNCA, are presented for sequential backbone resonance assignment of 13C, 15N labeled proteins. The advantage with respect to conventional pulse schemes is the suppression of the sequential 15N→13Cα coherence transfer pathway, which can be separately obtained from a HNCOCA correlation experiment. This results in a two-fold reduction of the number of detected correlation peaks. Spectral simplification is especially important for efficient automated assignment protocols as required in the context of high-throughput protein studies by NMR. The performance of the new experiments is demonstrated on an 18-kDa protein fragment of the E. coli sulfite reductase and compared to conventional techniques in terms of sensitivity and resolution.

  8. H-1, C-13 and N-15 resonance assignments of human DCL-1 (CD302) extracellular domain

    Czech Academy of Sciences Publication Activity Database

    Pospíšilová, Eliška; Kavan, Daniel; Novák, Petr; Chmelík, Josef

    2016-01-01

    Roč. 10, č. 1 (2016), s. 189-192 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LO1509; GA MŠk(CZ) EE2.3.20.0055; GA MŠk(CZ) EE2.3.30.0003; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : DCL-1 (CD302) * C-type lectin like receptor * Protein NMR Subject RIV: EE - Microbiology, Virology Impact factor: 0.459, year: 2016

  9. 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 ...

  10. 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.

  11. Proton nuclear magnetic resonance studies on the variant-3 neurotoxin from Centruroides sculpturatus Ewing: Sequential assignment of resonances

    International Nuclear Information System (INIS)

    Nettesheim, D.G.; Klevit, R.E.; Drobny, G.; Watt, D.D.; Krishna, N.R.

    1989-01-01

    The authors report the sequential assignment of resonances to specific residues in the proton nuclear magnetic resonance spectrum of the variant-3 neurotoxin from the scorpion Centruroides sculpturatus Ewing (range southwestern U.S.A.). A combination of two-dimensional NMR experiments such as 2D-COSY, 2D-NOESY, and single- and double-RELAY coherence transfer spectroscopy has been employed on samples of the protein dissolved in D 2 O and in H 2 O for assignment purposes. These studies provide a basis for the determination of the solution-phase conformation of this protein and for undertaking detailed structure-function studies of these neurotoxins that modulate the flow of sodium current by binding to the sodium channels of excitable membranes

  12. 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

  13. (1)H, (13)C and (15)N resonance assignments of human FK506 binding protein 25.

    Science.gov (United States)

    Prakash, Ajit; Shin, Joon; Yoon, Ho Sup

    2015-04-01

    Human FKBP25, a nuclear protein, is a member of FK506 binding protein family (FKBP) and binds to immunosuppressive drugs such as FK506 and rapamycin. Human FKBP25 interacts with several nuclear proteins and regulates nuclear events. To understand the molecular basis of such interactions, we have performed NMR studies. Here, we report (1)H, (15)N and (13)C resonance assignments of the full-length human FKBP25 protein.

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

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

    Science.gov (United States)

    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.

  16. Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach.

    Science.gov (United States)

    Lemak, Alexander; Steren, Carlos A; Arrowsmith, Cheryl H; Llinás, Miguel

    2008-05-01

    ABACUS [Grishaev et al. (2005) Proteins 61:36-43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic search. Here, we report further development of the two main algorithms that increase the flexibility and robustness of the method. Performance of the BACUS [Grishaev and Llinás (2004) J Biomol NMR 28:1-101] algorithm was significantly improved through use of sequential connectivities available from through-bond correlated 3D-NMR experiments, and a new set of likelihood probabilities derived from a database of 56 ultra high resolution X-ray structures. A Multicanonical Monte Carlo procedure, Fragment Monte Carlo (FMC), was developed for sequence-specific assignment of spin-systems. It relies on an enhanced assignment sampling and provides the uncertainty of assignments in a quantitative manner. The efficiency of the protocol was validated on data from four proteins of between 68-116 residues, yielding 100% accuracy in sequence specific assignment of backbone and side chain resonances.

  17. Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics

    Science.gov (United States)

    Basire, Marie; Mouhat, Félix; Fraux, Guillaume; Bordage, Amélie; Hazemann, Jean-Louis; Louvel, Marion; Spezia, Riccardo; Bonella, Sara; Vuilleumier, Rodolphe

    2017-04-01

    Vibrational spectroscopy is a fundamental tool to investigate local atomic arrangements and the effect of the environment, provided that the spectral features can be correctly assigned. This can be challenging in experiments and simulations when double peaks are present because they can have different origins. Fermi dyads are a common class of such doublets, stemming from the resonance of the fundamental excitation of a mode with the overtone of another. We present a new, efficient approach to unambiguously characterize Fermi resonances in density functional theory (DFT) based simulations of condensed phase systems. With it, the spectral features can be assigned and the two resonating modes identified. We also show how data from DFT simulations employing classical nuclear dynamics can be post-processed and combined with a perturbative quantum treatment at a finite temperature to include analytically thermal quantum nuclear effects. The inclusion of these effects is crucial to correct some of the qualitative failures of the Newtonian dynamics simulations at a low temperature such as, in particular, the behavior of the frequency splitting of the Fermi dyad. We show, by comparing with experimental data for the paradigmatic case of supercritical CO2, that these thermal quantum effects can be substantial even at ambient conditions and that our scheme provides an accurate and computationally convenient approach to account for them.

  18. Editorial, n. 15, 2003

    Directory of Open Access Journals (Sweden)

    Editor Encontros Bibli

    2003-01-01

    Informação da UFSC, que já está em seu oitavo ano, por sua Comissão Editorial, compartilhada com a presença de colegas do Brasil e exterior, manifesta sua alegria por esta conquista e exulta pela coincidência neste ano das Comemorações dos trinta anos do Curso de Biblioteconomia da UFSC e o início do Mestrado em Ciência da Informação desta instituição. Nesta edição do primeiro semestre do ano de 2003, Encontros Bibli tem a satisfação de trazer quatro artigos, dois oriundos da produção de pesquisadores da Escola de Ciência da Informação da Universidade Federal de Minas Gerais e dois oriundos da produção de pesquisa realizada por pesquisadores do Departamento de Ciência da Informação da UFSC. Aos leitores desejamos que estas contribuições ensejem questões que contribuam com a produção de reflexões e interrogações geradoras de novas investigações as quais naturalmente virão a contribuir para o progresso do conhecimento nacional em Ciência da Informação. Um grande abraço a todos e a todas! Prof. Francisco das Chagas de Souza Editor Departamento de Ciência da Informação Universidade Federal de Santa Catarina Brasil Disponibilizado na WWW em 20/05/2003. Enc. Bibli: R. Eletr. Bibliotecon. Ci. Inf., Florianópolis, n.15, 1º sem. 2003. 1

  19. 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

  20. NMR resonance assignments of a hypoallergenic isoform of the major birch pollen allergen Bet v 1.

    Science.gov (United States)

    Ahammer, Linda; Grutsch, Sarina; Wallner, Michael; Ferreira, Fatima; Tollinger, Martin

    2017-10-01

    In Northern America and Europe a great number of people are suffering from birch pollen allergy and pollen related food allergies. The trigger for these immunological reactions is the 17.5 kDa major birch pollen allergen Bet v 1, which belongs to the family of PR-10 (pathogenesis-related) proteins. In nature, Bet v 1 occurs as a mixture of various isoforms that possess different immunological properties despite their high sequence identities. Bet v 1.0102 (Bet v 1d), which is investigated here, is a hypoallergenic isoform of Bet v 1 and a potential candidate for allergen-specific immunotherapy. We assigned the backbone and side chain 1 H, 13 C and 15 N resonances of this protein and predicted its secondary structure. The NMR-chemical shift data indicate that Bet v 1.0102 is composed of three α-helices and a seven stranded β-sheet, in agreement with the known structure of the hyperallergenic isoform Bet v 1.0101 (Bet v 1a). Our resonance assignments create the foundation for detailed characterization of the dynamic properties of Bet v 1 isoforms by NMR relaxation measurements.

  1. Automated probabilistic method for assigning backbone resonances of (13C,15N)-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Lukin, Jonathan A. [Carnegie Mellon University, Department of Biological Sciences (United States); Gove, Andrew P.; Talukdar, Sarosh N. [Carnegie Mellon University, Robotics Institute (United States); Ho Chien [Carnegie Mellon University, Department of Biological Sciences (United States)

    1997-02-15

    We present a computer algorithm for the automated assignment of polypeptide backbone and 13C{beta} resonances of a protein of known primary sequence. Input to the algorithm consists of cross peaks from several 3D NMR experiments: HNCA, HN(CA)CO, HN(CA)HA,HNCACB, COCAH, HCA(CO)N, HNCO, HN(CO)CA, HN(COCA)HA, and CBCA(CO)NH. Data from these experiments performed on glutamine-binding protein are analyzed statistically using Bayes' theorem to yield objective probability scoring functions for matching chemical shifts. Such scoring is used in the first stage of the algorithm to combine cross peaks from the first five experiments to form intraresidue segments of chemical shifts{l_brace}Ni,HiN,Ci{alpha},Ci{beta},C'i{r_brace}, while the latter five are combined into interresidue segments {l_brace}Ci{alpha},Ci{beta},C'i,Ni+1,HNi+1{r_brace}. Given a tentative assignment of segments,the second stage of the procedure calculates probability scores based on the likelihood of matching the chemical shifts of each segment with (i) overlapping segments; and (ii) chemical shift distributions of the underlying amino acid type (and secondary structure, if known). This joint probability is maximized by rearranging segments using a simulated annealing program,optimized for efficiency. The automated assignment program was tested using CBCANH and CBCA(CO)NH cross peaks of the two previously assigned proteins, calmodulin and CheA.The agreement between the results of our method and the published assignments was excellent. Our algorithm was also applied to the observed cross peaks of glutamine-binding protein of Escherichia coli, yielding an assignment in excellent agreement with that obtained by time-consuming, manual methods. The chemical shift assignment procedure described here should be most useful for NMR studies of large proteins, which are now feasible with the use of pulsed-field gradients and random partial deuteration of samples.

  2. Resonance assignments of a VapC family toxin from Clostridium thermocellum.

    Science.gov (United States)

    Wang, Chen; Xuan, Jinsong; Cui, Qiu; Feng, Yingang

    2016-10-01

    Toxin-antitoxin (TA) systems widely exist in bacterial plasmids, phages, and chromosomes and play important roles in growth persistence and host-pathogen interaction. Virulence associated protein BC (VapBC) family TAs are the most abundant TAs in bacteria and many pathogens contain a large number of vapBC loci in the genome which have been extensively studied. Clostridium thermocellum, a cellulolytic anaerobic gram-positive bacterium with promising applications in biofuel production, also contains a VapBC TA in the genome. Despite the structures of several VapBC family TAs have been determined, the toxin and anti-toxin components of C. thermocellum VapBC have very low sequence identity to the proteins in PDB. Therefore, the structure and functional mechanism of this TA is largely unknown. Here we reported the NMR resonance assignments of the VapC toxin from C. thermocellum as a basis for further structural and functional studies.

  3. Resonance assignments of cohesin and dockerin domains from Clostridium acetobutylicum ATCC824.

    Science.gov (United States)

    Cui, Zhenling; Li, Yifei; Xiao, Yan; Feng, Yingang; Cui, Qiu; Cui, Qui

    2013-04-01

    Cohesin and dockerin domains are critical assembling components of cellulosome, a large extracellular multienzyme complex which is used by anaerobic cellulolytic bacteria to efficiently degrade lignocellulose. According to sequence homology, cohesins can be divided into three major groups, whereas cohesins from Clostridium acetobutylicum are beyond these groups and emanate from a branching point between the type I and type III cohesins. Cohesins and dockerins from C. acetobutylicum show low sequence homology to those from other cellulolytic bacteria, and their interactions are specific in corresponding species. Therefore the interactions between cohesins and dockerins from C. acetobutylicum are meaningful to the studies of both cellulosome assembling mechanism and the construction of designer cellulosome. Here we report the NMR resonance assignments of one cohesin from cellulosome scaffoldin cipA and one dockerin from a cellulosomal glycoside hydrolase (family 9) of C. acetobutylicum for further structural determination and functional studies.

  4. 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.

  5. Resonance assignments and secondary structure of a phytocystatin from Sesamum indicum.

    Science.gov (United States)

    Hu, Yu-Jun; Irene, Deli; Lo, Chi-Jen; Cai, Yong-Liang; Tzen, T-C; Lin, Ta-Hsien; Chyan, Chia-Lin

    2015-10-01

    A cDNA encoding a cysteine protease inhibitor, cystatin was cloned from sesame (Sesamum indicum L.) seed. This clone was constructed into an expression vector and expressed in E. coli and purified to homogeneous. The recombinant sesame cystatin (SiCYS) showed effectively inhibitory activity toward C1 cysteine proteases. In order to unravel its inhibitory action from structural point of view, multidimensional heteronuclear NMR techniques were used to characterize the structure of SiCYS. The full (1)H, (15)N, and (13)C resonances of SiCYS were assigned. The secondary structure of SiCYS was identified by using the assigned chemical shifts of (1)H(α), (13)C(α), (13)C(β), and (13)CO through the consensus chemical shift index (CSI). The results of CSI analysis of SiCYS suggest eight β-strands (residues 33-46, 51-61, 63-75, 80-87, 150-155, 157-169, 172-183, and 192-195) and two α-helices (residues 16-30, and 120-135).

  6. Resonance assignments of Ca²⁺-bound human S100A11.

    Science.gov (United States)

    Hung, Kuo-Wei; Chang, Yuan-Ming; Yu, Chin

    2013-10-01

    The S100 family belongs to the EF-hand calcium-binding proteins regulating a wide range of important cellular processes via protein-protein interactions. Most S100 proteins adopt a conformation of non-covalent homodimer for their functions. Calcium binding to the EF-hand motifs of S100 proteins is essential for triggering the structural changes, promoting exposure of hydrophobic regions necessary for target protein interactions. S100A11 is a protein found in diverse tissues and possesses multiple functions upon binding to different target proteins. RAGE is a multiligand receptor binding to S100A11 and the interactions at molecular level have not been reported. However, the three-dimensional structure of human S100A11 containing 105 amino acids is still not available for further interaction studies. To determine the solution structure, for the first time we report the (1)H, (15)N and (13)C resonance assignments and protein secondary structure prediction of human S100A11 dimer in complex with calcium using a variety of triple resonance NMR experiments and the chemical shift index (CSI) method, respectively.

  7. Backbone resonance assignments of the human p73 DNA binding domain.

    Science.gov (United States)

    Cino, Elio A; Soares, Iaci N; Freitas, Mônica S; Silva, Jerson L

    2016-04-01

    p53, p63, p73 family of proteins are transcription factors with crucial roles in regulating cellular processes such apoptosis, proliferation, differentiation, and DNA damage response. The three family members have both overlapping and unique biological functions. Sequence and structural homology are greatest in the DNA binding domains (DBD), which is the site of the majority of p53 mutations. Structurally unstable p53 DBD mutants can associate with themselves or p63 and p73 DBDs, impeding tumor suppressor functions. Evidence suggests that these proteins associate to form amyloid-like oligomers and fibrils through an aggregation-prone sequence within the DBDs. Despite having high sequence and structure similarities, p63 and p73 DBDs appear to have considerably lower tendencies to be incorporated into p53 aggregates, relative to p53. The backbone resonance assignments of p73 DBD reported here complement those previously reported for p53 and p63, allowing comparisons and providing molecular insights into their biological functions and roles in aggregation and tumor development.

  8. Assignment of Proton Resonances and Conformational Characterization of Oligodeoxyribonucleic Acid d(CCGTACGG) in Solution.

    Science.gov (United States)

    Wang, Ping; Shi, Gen-Bin; Song, Guo-Qiang; Chen, Kai-Xian; Ji, Ru-Yun

    1996-01-01

    Lycobetaine prepared from lycorine is a new anticancer agent. The experimental and quantum pharmacological studies revealed that lycobetaine can interact with DNA by intercalation, preferentially into GO base pairs. In order to provide detailed interaction model of lycobetaine-DNA, a self-complementary octanucleotide d(CCGTACGG) was designed and synthesized by using new HELP (high efficiency Liquid phase) According to its nature, the sample was prepared to the desired final concentration by adding salt and buffer solutions. Two-dimensional (1)H-(1)H COSY and NOESY spectra in 99.8% D(2)O and 95% H(2)O were recorded for the duplex, and the NMR techniques of presaturation and WATERGATE were applied to water suppression. Protons of every spin system were identified by their scalar couplings, then through their special couplings all protons in the molecule were assigned except the poorly resolved H5' and H5' ' resonances. The chemical shifts of exchangeable protons and NOE intensities of nonexchangeable protons indicate qualitatively that the d(CCGTACGG) helix is right-handed B-DNA in aqueous solution.

  9. Secondary structure and (1)H, (13)C, (15)N resonance assignments of the endosomal sorting protein sorting nexin 3

    OpenAIRE

    Overduin Michael; Rajesh Sandya; Gruenberg Jean; Lenoir Marc

    2015-01-01

    Sorting nexin 3 (SNX3) belongs to a sub family of sorting nexins that primarily contain a single Phox homology domain capable of binding phosphoinositides and membranes. We report the complete (1)H (13)C and (15)N resonance assignments of the full length human SNX3 protein and identification of its secondary structure elements revealing a canonical fold and unstructured termini.

  10. Secondary structure and (1)H, (13)C, (15)N resonance assignments of the endosomal sorting protein sorting nexin 3.

    Science.gov (United States)

    Overduin, Michael; Rajesh, Sandya; Gruenberg, Jean; Lenoir, Marc

    2015-10-01

    Sorting nexin 3 (SNX3) belongs to a sub-family of sorting nexins that primarily contain a single Phox homology domain capable of binding phosphoinositides and membranes. We report the complete (1)H, (13)C and (15)N resonance assignments of the full-length human SNX3 protein and identification of its secondary structure elements, revealing a canonical fold and unstructured termini.

  11. FLAMEnGO 2.0: an enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances.

    Science.gov (United States)

    Chao, Fa-An; Kim, Jonggul; Xia, Youlin; Milligan, Michael; Rowe, Nancy; Veglia, Gianluigi

    2014-08-01

    We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires either the protein X-ray structure or an NMR structural ensemble including data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) as well as the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at www.chem.umn.edu/groups/veglia/forms/flamengo2-form.html. Copyright © 2014 Elsevier Inc. All rights reserved.

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

    International Nuclear Information System (INIS)

    Schloerb, Christian; Ackermann, Katrin; Richter, Christian; Wirmer, Julia; Schwalbe, Harald

    2005-01-01

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

  13. {sup 13}C-direct detected NMR experiments for the sequential J-based resonance assignment of RNA oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Richter, Christian [Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany); Kovacs, Helena [Bruker BioSpin AG (Switzerland); Buck, Janina; Wacker, Anna [Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany); Fuertig, Boris [Max F. Perutz Laboratories (Austria); Bermel, Wolfgang [Bruker BioSpin GmbH (Germany); Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.d [Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany)

    2010-08-15

    We present here a set of {sup 13}C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose {sup 13}C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4' nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1',H1' ribose signals. The experiments were applied to two RNA hairpin structures. The current set of {sup 13}C-direct detected experiments allows direct and unambiguous assignment of the majority of the hetero nuclei and the identification of the individual ribose moieties following their sequential assignment. Thus, {sup 13}C-direct detected NMR methods constitute useful complements to the conventional {sup 1}H-detected approach for the resonance assignment of oligonucleotides that is often hindered by the limited chemical shift dispersion. The developed methods can also be applied to large deuterated RNAs.

  14. Assignment of glial brain tumors in humans by in vivo 1H-magnetic resonance spectroscopy and multidimensional metabolic classification.

    Science.gov (United States)

    Roser, W; Hagberg, G; Mader, I; Dellas, S; Seelig, J; Radue, E W; Steinbrich, W

    1997-09-01

    This study presents a simple approach for the noninvasive assignment of glial brain tumors according to malignancy by single-voxel proton magnetic resonance spectroscopy at short echo times (TE Based on peak area ratios, a five-dimensional data set was obtained for each investigated subject. This vector was then projected along metabolic coordinates in a two-dimensional metabolic space. These coordinates had been determined in a previous study (Hagberg G et al., 1995, Magn Reson Med 34: 242-252). Tumor assignment was done without any knowledge of histology by comparing the location of the new cases to the features of the previous study. All 11 investigated glioblastomas multiforme, as well as 4 of 5 astrocytomas grade II, could easily be assigned to the groups of high- and low-grade tumors, respectively. Classification was more difficult in the case of a cystic astrocytoma grade II and one astrocytoma grade III. Two spectra measured in normal-appearing matter of glioblastoma patients were not classified as healthy. Using single-voxel proton magnetic resonance spectroscopy at short echo times with the knowledge of a base study, a straightforward, fast, and noninvasive differential diagnosis of glial brain tumors is possible.

  15. 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.

  16. Assignment of resonances in dissociative recombination of HD{sup +} ions: High-resolution measurements compared with accurate computations

    Energy Technology Data Exchange (ETDEWEB)

    Waffeu Tamo, F. O. [Laboratoire Ondes et Milieux Complexes FRE-3102 CNRS and Universite du Havre, 25, rue Philippe Lebon, BP 540, F-76058 Le Havre (France); Centre for Atomic, Molecular Physics and Quantum Optics (CEPAMOQ), University of Douala, P.O. Box 8580, Douala (Cameroon); Laboratoire d' Etude du Rayonnement et de la Matiere en Astrophysique, Observatoire de Paris, F-91295 Meudon Cedex (France); Buhr, H.; Schwalm, D. [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, D-69117 Heidelberg (Germany); Department of Particle Physics, Weizmann Institute of Science, P.O. Box 26, 76100 Rehovot (Israel); Motapon, O. [LPF, UFD Physique et Sciences de l' Ingenieur, University of Douala, P.O. Box 24157, Douala (Cameroon); Altevogt, S.; Andrianarijaona, V. M.; Grieser, M.; Lammich, L.; Lestinsky, M.; Motsch, M.; Novotny, S.; Orlov, D. A.; Pedersen, H. B.; Sprenger, F.; Weigel, U.; Wolf, A. [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, D-69117 Heidelberg (Germany); Nevo, I. [Department of Particle Physics, Weizmann Institute of Science, P.O. Box 26, 76100 Rehovot (Israel); Urbain, X. [Institute of Condensed Matter and Nanosciences, Universite catholique de Louvain, chemin du cyclotron 2, B-1348 Louvain-la Neuve (Belgium); Schneider, I. F. [Laboratoire Ondes et Milieux Complexes FRE-3102 CNRS and Universite du Havre, 25, rue Philippe Lebon, BP 540, F-76058 Le Havre (France)

    2011-08-15

    The collision-energy resolved rate coefficient for dissociative recombination of HD{sup +} ions in the vibrational ground state is measured using the photocathode electron target at the heavy-ion storage ring TSR. Rydberg resonances associated with rovibrational excitation of the HD{sup +} core are scanned as a function of the electron collision energy with an instrumental broadening below 1 meV in the low-energy limit. The measurement is compared to calculations using multichannel quantum defect theory, accounting for rotational structure and interactions and considering the six lowest rotational energy levels as initial ionic states. Using thermal-equilibrium-level populations at 300 K to approximate the experimental conditions, close correspondence between calculated and measured structures is found up to the first vibrational excitation threshold of the cations near 0.24 eV. Detailed assignments, including naturally broadened and overlapping Rydberg resonances, are performed for all structures up to 0.024 eV. Resonances from purely rotational excitation of the ion core are found to have similar strengths as those involving vibrational excitation. A dominant low-energy resonance is assigned to contributions from excited rotational states only. The results indicate strong modifications in the energy dependence of the dissociative recombination rate coefficient through the rotational excitation of the parent ions, and underline the need for studies with rotationally cold species to obtain results reflecting low-temperature ionized media.

  17. 1H, 15N and 13C backbone resonance assignments of pentaerythritol tetranitrate reductase from Enterobacter cloacae PB2.

    Science.gov (United States)

    Iorgu, Andreea I; Baxter, Nicola J; Cliff, Matthew J; Waltho, Jonathan P; Hay, Sam; Scrutton, Nigel S

    2018-04-01

    Pentaerythritol tetranitrate reductase (PETNR) is a flavoenzyme possessing a broad substrate specificity and is a member of the Old Yellow Enzyme family of oxidoreductases. As well as having high potential as an industrial biocatalyst, PETNR is an excellent model system for studying hydrogen transfer reactions. Mechanistic studies performed with PETNR using stopped-flow methods have shown that tunneling contributes towards hydride transfer from the NAD(P)H coenzyme to the flavin mononucleotide (FMN) cofactor and fast protein dynamics have been inferred to facilitate this catalytic step. Herein, we report the near-complete 1 H, 15 N and 13 C backbone resonance assignments of PETNR in a stoichiometric complex with the FMN cofactor in its native oxidized form, which were obtained using heteronuclear multidimensional NMR spectroscopy. A total of 97% of all backbone resonances were assigned, with 333 out of a possible 344 residues assigned in the 1 H- 15 N TROSY spectrum. This is the first report of an NMR structural study of a flavoenzyme from the Old Yellow Enzyme family and it lays the foundation for future investigations of functional dynamics in hydride transfer catalytic mechanism.

  18. 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

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

    Czech Academy of Sciences Publication Activity Database

    Zawadzka-Kazimierczuk, A.; Kozminski, W.; Šanderová, Hana; Krásný, Libor

    2012-01-01

    Roč. 52, č. 4 (2012), s. 329-337 ISSN 0925-2738 R&D Projects: GA ČR GA204/09/0583 Institutional research plan: CEZ:AV0Z50200510 Keywords : Intrinsically disordered proteins * Non-uniform sampling * Backbone assignment Subject RIV: EE - Microbiology, Virology Impact factor: 2.845, year: 2012

  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. (1)H, (15)N and (13)C resonance assignments of translationally-controlled tumor protein from photosynthetic microalga Nannochloropsis oceanica.

    Science.gov (United States)

    Yao, Xingzhe; Xiao, Yan; Cui, Qiu; Feng, Yingang

    2015-10-01

    Translationally-controlled tumor protein (TCTP) is a eukaryote-conserved protein with crucial roles in cellular growth. It has also been proposed that plant TCTP has functions specific to plant, while no structure of TCTP from photosynthetic organism has been reported. Nannochloropsis is a photosynthetic microalga with high yield of lipid and high-value polyunsaturated fatty acid, which is promising for biodiesel production. Study of growth-related proteins may provide new clue for improving the yield of lipid. TCTP from Nannochloropsis oceanica shares low sequence identity with structure-known TCTPs. Here we reported the NMR resonance assignments of TCTP from N. oceanica for further structural and functional studies.

  2. 1H, 13C and 15N resonance assignments of the Calmodulin-Munc13-1 peptide complex

    OpenAIRE

    Rodr?guez-Casta?eda, Fernando; Coudevylle, Nicolas; Becker, Stefan; Brose, Nils; Carlomagno, Teresa; Griesinger, Christian

    2009-01-01

    Ca2+-Calmodulin binding to the variable N-terminal region of the diacylglycerol/phorbol ester-binding UNC13/Munc13 family of proteins modulates the short-term synaptic plasticity characteristics in neurons. Here, we report the sequential backbone and side chain resonance assignment of the Ca2+-Calmodulin/Munc13-1458?492 peptide complex at pH 6.8 and 35?C (BMRB No. 15470). Electronic supplementary material The online version of this article (doi:10.1007/s12104-009-9204-2) contains supplementar...

  3. Resonance assignments for the substrate binding domain of Hsp70 chaperone Ssa1 from Saccharomyces cerevisiae.

    Science.gov (United States)

    Hu, Wanhui; Wu, Huiwen; Zhang, Hong; Gong, Weibin; Perrett, Sarah

    2015-10-01

    Hsp70 chaperone proteins play crucial roles in the cell. Extensive structural and functional studies have been performed for bacterial and mammalian Hsp70s. Ssa1 from Saccharomyces cerevisiae is a member of the Hsp70 family. In vivo and biochemical studies on Ssa1 have revealed that it regulates prion propagation and the cell cycle. However, no structural data has been obtained for Ssa1 up to now. Here we report the almost complete (96 %) (1)H, (13)C, (15)N backbone and side chain NMR assignment of the 18.8 kDa Ssa1 substrate binding domain. The construct includes residues 382-554, which corresponds to the entire substrate binding domain and two following α-helices in homologous structures. The secondary structure predicted from the assigned chemical shifts is consistent with that of homologous Hsp70 substrate binding domains.

  4. Backbone resonance assignments of human cytosolic dNT-1 nucleotidase

    Czech Academy of Sciences Publication Activity Database

    Hnízda, Aleš; Skleničková, Radka; Pachl, Petr; Fábry, Milan; Tošner, Z.; Brynda, Jiří; Veverka, Václav

    2014-01-01

    Roč. 8, č. 2 (2014), s. 425-428 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LK11205; GA ČR GA203/09/0820 Institutional support: RVO:61388963 ; RVO:68378050 Keywords : 5 '-nucleotidase * haloacid dehalogenase superfamily * backbone assignments * NMR * perdeuterated protein * dimer * pyrimidine nucleotides Subject RIV: CE - Biochemistry; EB - Genetics ; Molecular Biology (UMG-J) Impact factor: 0.760, year: 2014

  5. 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

  6. 1H, 13C, and 15N resonance assignments for human regenerating family Iα protein.

    Science.gov (United States)

    Ho, Meng-Ru; Chen, Chinpan

    2012-10-01

    Human regenerating (Reg) genes belong to the C-type lectin superfamily and express secretory proteins in various tissues. Reg Iα, also named lithostathine, has multiple roles in numerous biological events such as cytokines, anti-apoptotic factors and the calcium carbonate crystals inhibitor. Under physiological pH, Reg Iα becomes largely insoluble after a self-proteolysis process, and the N-terminally truncated form readily polymerizes into fibrils, which leads to neurodegenerative diseases. Reg Iα may form protofibril via lateral hydrophobic interactions with a native-like conformation. The structural basis from the native to fibril form, as well as the carbohydrate binding sites on Reg Iα, remain unknown. Here we present the NMR backbone and side-chain assignments of Reg Iα for use in further NMR investigations.

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

    Science.gov (United States)

    Bumba, Ladislav; Sviridova, Ekaterina; Kutá Smatanová, Ivana; Řezáčová, Pavlína; Veverka, Václav

    2014-04-01

    The iron-regulated FrpD protein is a unique lipoprotein embedded into the outer membrane of the Gram-negative bacterium Neisseria meningitidis. The biological function of FrpD remains unknown but might consist in anchoring to the bacterial cell surface the Type I-secreted FrpC protein, which belongs to a Repeat in ToXins (RTX) protein family and binds FrpD with very high affinity (K(d) = 0.2 nM). Here, we report the backbone (1)H, (13)C, and (15)N chemical shift assignments for the FrpD(43-271) protein that allow us to characterize the intimate interaction between FrpD and the N-terminal domain of FrpC.

  8. 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.

  9. 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

  10. 1H, 13C and 15N resonance assignments of a C-terminal domain of human CHD1.

    Science.gov (United States)

    Mohanty, Biswaranjan; Silva, Ana P G; Mackay, Joel P; Ryan, Daniel P

    2016-04-01

    Chromatin remodelling proteins are an essential family of eukaryotic proteins. They harness the energy from ATP hydrolysis and apply it to alter chromatin structure in order to regulate all aspects of genome biology. Chromodomain helicase DNA-binding protein 1 (CHD1) is one such remodelling protein that has specialised nucleosome organising abilities and is conserved across eukaryotes. CHD1 possesses a pair of tandem chromodomains that directly precede the core catalytic Snf2 helicase-like domain, and a C-terminal SANT-SLIDE DNA-binding domain. We have identified an additional conserved domain in the C-terminal region of CHD1. Here, we report the backbone and side chain resonance assignments for this domain from human CHD1 at pH 6.5 and 25 °C (BMRB No. 25638).

  11. Sequence-specific backbone (1)H, (13)C, and (15)N resonance assignments of human ribonuclease 4.

    Science.gov (United States)

    Gagné, Donald; Doucet, Nicolas

    2015-04-01

    Human ribonuclease 4 (RNase 4) is the most evolutionarily conserved member of the 8 canonical human pancreatic-like RNases, showing more than 90% identity with bovine and porcine homologues. The enzyme displays ribonucleolytic activity with a strong preference for uracil-containing RNA substrates, a feature only shared with human eosinophil derived-neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3). It is also the shortest member of the human family, with a significantly truncated C-terminal tail. Its unique active-site pocket and high degree of conservation among vertebrates suggest that the enzyme plays a crucial biological function. Here, we report on the (1)H, (13)C and (15)N backbone resonance assignments of RNase 4, providing means to characterize its molecular function at the atomic level by NMR.

  12. 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.

  13. 1H, 13C, and 15N backbone and side chain resonance assignments of thermophilic Geobacillus kaustophilus cyclophilin-A

    Energy Technology Data Exchange (ETDEWEB)

    Holliday, Michael; Zhang, Fengli; Isern, Nancy G.; Armstrong, Geoffrey S.; Eisenmesser, Elan Z.

    2014-04-01

    Cyclophilins catalyze the reversible peptidyl-prolyl isomerization of their substrates and are present across all kingdoms of life from humans to bacteria. Although numerous biological roles have now been discovered for cyclophilins, their function was initially ascribed to their chaperone-like activity in protein folding where they catalyze the often rate-limiting step of proline isomerization. This chaperone-like activity may be especially important under extreme conditions where cyclophilins are often over expressed, such as in tumors for human cyclophilins {Lee, 2010 #1167}, but also in organisms that thrive under extreme conditions, such as theromophilic bacteria. Moreover, the reversible nature of the peptidyl-prolyl isomerization reaction catalyzed by cyclophilins has allowed these enzymes to serve as model systems for probing the role of conformational changes during catalytic turnover {Eisenmesser, 2002 #20;Eisenmesser, 2005 #203}. Thus, we present here the resonance assignments of a thermophilic cyclophilin from Geobacillus kaustophilus derived from deep-sea sediment {Takami, 2004 #1384}. This thermophilic cyclophilin may now be studied at a variety of temperatures to provide insight into the comparative structure, dynamics, and catalytic mechanism of cyclophilins.

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

    Science.gov (United States)

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

    2012-10-01

    Guanine-nucleotide binding proteins (G proteins) act 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 GDP-bound form of the G protein α subunit (Gα(GDP)) and 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. G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Each family transduces the signaling from different GPCRs to the specific effectors. Here, we established the backbone resonance assignments of human Gα(i3), a member of the i/o family, with a molecular weight of 41 K in complex with a GTP analogue, GTPγS.

  15. 1H, 13C and 15N resonance assignments of the new lysostaphin family endopeptidase catalytic domain from Staphylococcus aureus.

    Science.gov (United States)

    Raulinaitis, Vytas; Tossavainen, Helena; Aitio, Olli; Seppala, Raili; Permi, Perttu

    2017-04-01

    Lysostaphin family endopeptidases, produced by Staphylococcus genus, are zinc-dependent enzymes that cleave pentaglycine bridges of cell wall peptidoglycan. They act as autolysins to maintain cell wall metabolism or as toxins and weapons against competing strains. Consequently, these enzymes are compelling targets for new drugs as well as are potential antimicrobial agents themselves against Staphylococcus pathogens, which depend on cell wall to retain their immunity against antibiotics. The rapid spread of methicillin and vancomycin-resistant Staphylococcus aureus strains draws demand for new therapeutic approaches. S. aureus gene sa0205 was found to be implicated in resistance to vancomycin and synthesis of the bacteria cell wall. The gene encodes for a catalytic domain of a lysostaphin-type endopeptidase. We aim to obtain the structure of the Sa0205 catalytic domain, the first solution structure of the catalytic domain of the lysostaphin family enzymes. In addition, we are to investigate the apparent binding of the second zinc ion, which has not been previously reported for the enzyme group. Herein, we present the backbone and side chain resonance assignments of Sa0205 endopeptidase catalytic domain in its one and two zinc-bound forms.

  16. 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

  17. Resonance assignment and secondary structure determination and stability of the recombinant human uteroglobin with heteronuclear multidimensional NMR

    Energy Technology Data Exchange (ETDEWEB)

    Carlomagno, Teresa [University of Naples ' Federico II' , Department of Chemistry (Italy); Mantile, Giuditta [Section on Developmental Genetics, Heritable Disorders Branch (United States); Bazzo, Renzo [IRBM P. Angeletti, Spa. (Italy); Miele, Lucio [Section on Developmental Genetics, Heritable Disorders Branch (United States); Paolillo, Livio [University of Naples ' Federico II' , Department of Chemistry (Italy); Mukherjee, Anil B. [Section on Developmental Genetics, Heritable Disorders Branch (United States); Barbato, Gaetano [IRBM P. Angeletti, Spa. (Italy)

    1997-01-15

    Human uteroglobin (h-UG) or Clara cell 10kDa (cc10kDa) is a steroid-dependent, 17 kDahomodimeric, secretory protein with potent anti-inflammatory/immunomodulatory properties. However, the exact physiological role still remains to be determined. It has been hypothesised that its activity is exerted through the binding of a specific target represented by a small molecule (still unknown), and that the binding is regulated by the formation/disruption of two cysteine bonds. The binding properties of the reduced UG have been proved in vitro for several different molecules, but no in vivo data are available to date. However, binding has been observed between reduced rabbit UG and a protein of an apparent molecular mass of 90 kDa and, more recently, we found an h-UG-binding protein (putative receptor), of an apparent molecular mass of 190 kDa, on the surface of several cell types. The recognition involves oxidised h-UG. These findings pose the problem of the relevance of the oxidation state in the recognition process. To determine the solution structure of the oxidised h-UG, we produced wild-type as well as uniformly 15N- and 15N/13C-labelled samples of the recombinant protein. The assignments of the 1H, 15N and 13C resonances are presented,based on a series of homonuclear 2D and 3D and heteronuclear 2D and 3D double and triple resonance NMR experiments. Our results indicate that h-UG is an extremely stable protein under a wide range of temperatures and pH conditions. The secondary structure in solution is in general agreement with previously reported crystal structures of rabbit UG, suggesting that cc10kDa and h-UG are indeed the same protein. Small local differences found in the N-and C-terminal helices seem to support the hypothesis that flexibility involves these residues;moreover, it possibly accounts for the residual binding properties observed when the protein is in the oxidised state.

  18. 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 %.

  19. 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.

  20. N-15-labelled pyrazines of triterpenic acids

    Czech Academy of Sciences Publication Activity Database

    Vlk, M.; Mičolová, P.; Urban, M.; Kvasnica, Miroslav; Šaman, David; Šarek, J.

    2016-01-01

    Roč. 308, č. 2 (2016), s. 733-739 ISSN 0236-5731 R&D Projects: GA ČR GJ15-08202Y; GA MŠk(CZ) LO1304; GA MŠk(CZ) LO1204 Grant - others:GA MŠk(CZ) LK21310; GA TA ČR(CZ) TA03010027; CTU(CZ) SGS15/094/OHK4/1T/14 Institutional support: RVO:61389030 ; RVO:61388963 Keywords : N-15 * Triterpenic acid * Isotopic labelling Subject RIV: CC - Organic Chemistry Impact factor: 1.282, year: 2016

  1. GFT projection NMR based resonance assignment of membrane proteins: application to subunit C of E. coli F(1)F (0) ATP synthase in LPPG micelles.

    Science.gov (United States)

    Zhang, Qi; Atreya, Hanudatta S; Kamen, Douglas E; Girvin, Mark E; Szyperski, Thomas

    2008-03-01

    G-matrix FT projection NMR spectroscopy was employed for resonance assignment of the 79-residue subunit c of the Escherichia coli F(1)F(0) ATP synthase embedded in micelles formed by lyso palmitoyl phosphatidyl glycerol (LPPG). Five GFT NMR experiments, that is, (3,2)D HNNCO, L-(4,3)D HNNC (alphabeta) C (alpha), L-(4,3)D HNN(CO)C (alphabeta) C (alpha), (4,2)D HACA(CO)NHN and (4,3)D HCCH, were acquired along with simultaneous 3D (15)N, (13)C(aliphatic), (13)C(aromatic)-resolved [(1)H,(1)H]-NOESY with a total measurement time of approximately 43 h. Data analysis resulted in sequence specific assignments for all routinely measured backbone and (13)C(beta) shifts, and for 97% of the side chain shifts. Moreover, the use of two G(2)FT NMR experiments, that is, (5,3)D HN{N,CO}{C (alphabeta) C (alpha)} and (5,3)D {C (alphabeta) C (alpha)}{CON}HN, was explored to break the very high chemical shift degeneracy typically encountered for membrane proteins. It is shown that the 4D and 5D spectral information obtained rapidly from GFT and G(2)FT NMR experiments enables one to efficiently obtain (nearly) complete resonance assignments of membrane proteins.

  2. 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

  3. 1H, 13C, and 15N resonance assignments of the N-terminal domain of human TIG3.

    Science.gov (United States)

    Wang, Lei; Yu, Wenyu; Ren, Xiaobai; Lin, Jian; Jin, Changwen; Xia, Bin

    2012-10-01

    Human TIG3 protein is a member of H-REV107 protein family which belongs to the type II tumor suppressor family. TIG3 can induce apoptosis in cancer cells, and it also possesses Ca(2+)-independent phospholipase A(1/2) activity. The NMR assignments of the N-terminal domain of TIG3 are essential for its solution structure determination.

  4. 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.

  5. Experimental nuclear magnetic resonance spectral assignments, 1H/13C GIAO calculations, molecular structure and molecular resonance states of 4-Methyl-1H-Indazole-5-Boronic acid

    Science.gov (United States)

    Dikmen, Gökhan

    2018-03-01

    Some molecules such as 4-Methyl-1H-Indazole-5-Boronic Acid (4M1HI5BA) have different resonance states under different temperatures. Henceforth, it is difficult to characterize these type of molecules. Since, in general one or more hydrogen atoms move through the molecule and molecular symmetry changes. The possible 3 different resonance forms and molecular structure of 4-Methyl-1H-Indazole-5-Boronic Acid (4M1HI5BA) molecule have been studied experimentally using nuclear magnetic resonance (NMR) spectroscopy. 13C cross-polarization magic-angle spinning, 11B, 1H, 13C, COSY, HMBC, NOESY, T1 relaxation time NMR spectra of 4M1HI5BA molecule have been reported. Moreover, 1H NMR spectra were obtained in different solvents and under variable temperatures. Results from experimental datas showed that title molecule has three different resonance states and these resonance states change with different temperature. In addition, 1H and 13C chemical shift values were calculated by GIAO method and computed values were compared with experimentally obtained values. There are good agreement between experimental and theoretical chemical shift values.

  6. Multinuclear magnetic resonance studies of the 2Feter dot 2S sup * ferredoxin from Anabaena species strain PCC 7120. 1. Sequence-specific hydrogen-1 resonance assignments and secondary structure in solution of the oxidized form

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Byung-Ha; Markley, J.L. (Univ. of Wisconsin, Madison (USA))

    1990-04-24

    Complete sequence-specific assignments were determined for the diamagnetic {sup 1}H resonances from Anabaena 7120 ferredoxin. A novel assignment procedure was followed whose first step was the identification of the {sup 13}C spin systems of the amino acids by a {sup 13}C({sup 13}C) double quantum correlation experiment. Then, the {sup 1}H spin systems of the amino acids were identified from the {sup 13}C spin systems by means of direct and relayed {sup 1}H({sup 13}C) single-bond correlations. The sequential resonance assignments were based mainly on conventional interresidue {sup 1}H{sup {alpha}}{sub i}-{sup 1}H{sup N}{sub i+1} NOE connectivities. Resonances from 18 residues were not resolved in two-dimensional {sup 1}H NMR spectra. When these residues were mapped onto the X-ray crystal structure of the homologous ferredoxin from Spirulina platensis, it was found that they correspond to amino acids close to the paramagnetic 2Fe{center dot}2S cluster. Cross peaks in two-dimensional homonuclear {sup 1}H NMR spectra were not observed for any protons closer than about 7.8 {angstrom} to both iron atoms. Secondary structural features identified in solution include two antiparallel {beta}-sheets, one parallel {beta}-sheet, and one {alpha}-helix.

  7. 1H, 13C and 15N resonance assignments of the GTPase-activating (GAP) and Ral binding domains (GBD) of RLIP76 (RalBP1).

    Science.gov (United States)

    Rajasekar, Karthik V; Campbell, Louise J; Nietlispach, Daniel; Owen, Darerca; Mott, Helen R

    2012-10-01

    RLIP76 (also known as RalBP1) is an effector for Ral small G proteins. RLIP76 is a multifunctional, multi-domain protein that includes a GTPase activating domain for the Rho family (RhoGAP domain) and a GTPase binding domain (GBD) for the Ral small G proteins. The juxtaposition of these two domains (GAP and GBD) may be a strategy employed to co-ordinate regulation of Rho family and Ral-controlled signalling pathways at a crossover node. Here we present the (1)H, (15)N and (13)C NMR backbone and sidechain resonance assignments of the GAP and GBD di-domain (31 kDa).

  8. ¹H, ¹³C and ¹⁵N resonance assignments of the pyrin domain from human PYNOD.

    Science.gov (United States)

    Su, Ming-Yuan; Chang, Chung-I; Chang, Chi-Fon

    2013-10-01

    PYNOD is a novel protein belonging to a large family of proteins containing the nucleotide-binding and oligomerization domain (NOD) involved in inflammation and apoptosis. Human PYNOD inhibits inflammatory response mediated by caspase-1 and apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC). Here we report the (1)H, (13)C and (15)N resonance assignments and secondary structure identification of the pyrin domain (PYD) of human PYNOD as the first step towards elucidating the structural basis of the anti-inflammatory activity of PYNOD.

  9. Sequence-specific 1H, 15N and 13C resonance assignments of Art v 1: a proline-rich allergen of Artemisia vulgaris pollen.

    Science.gov (United States)

    Razzera, Guilherme; Gadermaier, Gabriele; Almeida, Marcius S; Ferreira, Fatima; Almeida, Fabio C L; Valente, Ana Paula

    2009-06-01

    Art v 1 is the major allergen of Artemisia vulgaris. The IgE raised against Art v 1 not only can cross-react with other proteins from the Asteraceae family members but also with components of various forms of food. Art v 1 is an important target for immunotherapy strategies, including vaccination with hypoallergenic derivatives or chimeras. We report the (1)H, (13)C, and (15)N resonance assignments of the recombinant Art v 1 and identification of secondary structures based on (13)C chemical shifts.

  10. 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.

  11. 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.

  12. Backbone and side-chain 1H, 15N, and 13C resonance assignments of a novel Staphylococcal inhibitor of myeloperoxidase.

    Science.gov (United States)

    Ploscariu, Nicoleta T; Herrera, Alvaro I; Jayanthi, Srinivas; Suresh Kumar, Thallapuranam K; Geisbrecht, Brian V; Prakash, Om

    2017-10-01

    The bacterium Staphylococcus aureus produces an array of anti-inflammatory molecules that prevent the innate immune system from recognizing it as a pathogen and clearing it from the host. In the acute phase of inflammation, our immune system relies on neutrophils to clear invading bacteria. Recently, novel classes of secreted proteins from S. aureus, including the Extracellular Adherence Protein (EAP) family (Stapels et al., Proc Natl Acad Sci USA 111:13187-13192, 2014) and the Staphylococcal Peroxidase Inhibitor (SPIN), (unpublished work) have been identified as highly selective inhibitors acting on Neutrophil Serine Proteases (NSPs) and myeloperoxidase (MPO) respectively. SPIN is a protein found only in Staphylococci, with no sequence homology to any known proteins. Solution NMR structural studies of SPIN are therefore expected to provide a deeper understanding of its interaction with MPO. In this study, we report the backbone and side-chain 1 H, 15 N, and 13 C resonance assignments of SPIN. Furthermore, using the chemical shifts of these resonances, we predicted the secondary structure of SPIN in solution via the TALOS-N server. The assignment data has been deposited in the BMRB data bank under Accession No. 27069.

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

    Energy Technology Data Exchange (ETDEWEB)

    McCoy, Mark A.; Dellwo, Martin J.; Schneider, Diane M.; Banks, Tracey M.; Falvo, Joseph [Sterling Winthrop Pharmaceuticals Research Division (United States); Vavra, Karen J.; Mathiowetz, Alan M. [Eastman Kodak Company (United States); Qoronfleh, M. Walid; Ciccarelli, Richard; Cook, Ewell R. [Sterling Winthrop Pharmaceuticals Research Division (United States); Pulvino, Tricia A. [Eastman Kodak Company (United States); Wahl, Robert C.; Wang Hsin [Sterling Winthrop Pharmaceuticals Research Division (United States)

    1997-01-15

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

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

    International Nuclear Information System (INIS)

    McCoy, Mark A.; Dellwo, Martin J.; Schneider, Diane M.; Banks, Tracey M.; Falvo, Joseph; Vavra, Karen J.; Mathiowetz, Alan M.; Qoronfleh, M. Walid; Ciccarelli, Richard; Cook, Ewell R.; Pulvino, Tricia A.; Wahl, Robert C.; Wang Hsin

    1997-01-01

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

  15. ¹H, ¹³C and ¹⁵N resonance assignments of the complement control protein modules of the complement component C7.

    Science.gov (United States)

    Clark, Carla; Thai, Chuong-Thu; Phelan, Marie M; Bella, Juraj; Uhrín, Dušan; Ogata, Ronald T; Barlow, Paul N; Bramham, Janice

    2013-10-01

    Human C7 is one of four homologous complement proteins that self-assemble on the nascent activation-specific fragment, C5b, thus forming the cytolytic membrane attack complex (MAC). In addition to the conserved modular core of the MAC/perforin protein family, C7 has four C-terminal domains comprising a pair of complement control protein modules (CCPs) preceding two Factor-I like modules (FIMs). It is proposed that the C7-CCPs might serve as a molecular arm for delivery of C7-FIMs to their binding site on C5b. Here we present the NMR chemical shift assignments for the C7-CCPs produced as a 14-kDa recombinant protein. Based upon triple-resonance experiments, 98 and 94 % of the backbone and side-chain ((1)H, (13)C and (15)N) assignments, respectively, have been completed. The chemical shifts and assignments have been deposited in the BioMagResBank database under accession number 18530.

  16. 1H, 13C and 15N resonance assignments of the arsenate reductase from Synechocystis sp. strain PCC 6803.

    Science.gov (United States)

    Yu, Caifang; Xia, Bin; Jin, Changwen

    2011-04-01

    Arsenate reductases (ArsC) are a group of enzymes that play essential roles in biological arsenic detoxification pathways by catalyzing the intracellular reduction of arsenate to arsenite, which is subsequently extruded from the cells by specific transport systems. The ArsC protein from cyanobacterium Synechocystis sp. strain PCC 6803 (SynArsC) is related to the thioredoxin-dependent ArsC family, but uses the glutathione/glutaredoxin system for arsenate reduction. Therefore, it is classified to a novel thioredoxin/glutaredoxin hybrid arsenate reductase family. Herein we report the chemical shift assignments of (1)H, (13)C and (15)N atoms for the reduced form of SynArsC, which provides a starting point for further structural analysis and elucidation of its enzymatic mechanism.

  17. 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.

  18. 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

  19. Sequence-specific 1H, 13C, and 15N resonance assignments of Diva (Boo), an apoptosis regulator of the Bcl-2 family.

    Science.gov (United States)

    Sborgi, Lorenzo; de Alba, Eva

    2010-04-01

    Diva, also known as Boo, is a member of the Bcl-2 family that regulates apoptosis by interacting with other Bcl-2 proteins and with the key component of the apoptosome Apaf-1. The function of Diva is puzzling as it apparently can both promote and inhibit apoptosis depending on the cellular context. The structural characterization of Diva will likely help to understand this dual behavior in programmed cell death. To this aim we report here the NMR resonance assignments of residues 1-160 of mouse Diva (lacking the predicted transmembrane domain, which spans residues 161-191). These data are used to obtain information on Diva's secondary structure and provide the basis for further structural studies.

  20. ¹H, ¹³C and ¹⁵N resonance assignments of an N-terminal domain of CHD4.

    Science.gov (United States)

    Silva, Ana P G; Kwan, Ann H; Mackay, Joel P

    2014-04-01

    Chromatin-remodeling proteins have a pivotal role in normal cell function and development, catalyzing conformational changes in DNA that ultimately result in changes in gene expression patterns. Chromodomain helicase DNA-binding protein 4 (CHD4), the defining subunit of the nucleosome remodeling and deacetylase (NuRD) complex, is a nucleosome-remodeling protein of the SNF2/ISWI2 family, members of which contain two chromo domains and an ATP-dependent helicase module. CHD3, CHD4 and CHD5 also contain two contiguous PHD domains and have an extended N-terminal region that has not previously been characterized. We have identified a stable domain in the N-terminal region of CHD4 and report here the backbone and side chain resonance assignments for this domain at pH 7.5 and 25 °C (BMRB No. 18906).

  1. ¹H, ¹³C, and ¹⁵N resonance assignments of mouse lipocalin-type prostaglandin D synthase/substrate analog complex.

    Science.gov (United States)

    Shimamoto, Shigeru; Maruo, Hiroko; Yoshida, Takuya; Ohkubo, Tadayasu

    2014-04-01

    Lipocalin-type Prostaglandin D synthase (L-PGDS) acts as the PGD2-synthesizing enzyme in the brain of various mammalian species. It belongs to the lipocalin superfamily and is the first member of this family to be recognized as an enzyme. Although the solution and crystal structure of L-PGDS has been determined to understand the molecular mechanism of catalytic reaction, the structural analysis of L-PGDS in complex with its substrate remains to be performed. Here, we present the nearly complete assignment of the backbone and side chain resonances of L-PGDS/substrate analog (U-46619) complex. This study lays the essential basis for further understanding the substrate recognition mechanism of L-PGDS.

  2. 3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample

    Energy Technology Data Exchange (ETDEWEB)

    Krejcirikova, Anna; Tugarinov, Vitali, E-mail: vitali@umd.edu [University of Maryland, Department of Chemistry and Biochemistry (United States)

    2012-10-15

    The feasibility of practically complete backbone and ILV methyl chemical shift assignments from a single [U-{sup 2}H,{sup 15}N,{sup 13}C; Ile{delta}1-{l_brace}{sup 13}CH{sub 3}{r_brace}; Leu,Val-{l_brace}{sup 13}CH{sub 3}/{sup 12}CD{sub 3}{r_brace}]-labeled protein sample of the truncated form of ligand-free Bst-Tyrosyl tRNA Synthetase (Bst-{Delta}YRS), a 319-residue predominantly helical homodimer, is established. Protonation of ILV residues at methyl positions does not appreciably detract from the quality of TROSY triple resonance data. The assignments are performed at 40 Degree-Sign C to improve the sensitivity of the measurements and alleviate the overlap of {sup 1}H-{sup 15}N correlations in the abundant {alpha}-helical segments of the protein. A number of auxiliary approaches are used to assist in the assignment process: (1) selection of {sup 1}H-{sup 15}N amide correlations of certain residue types (Ala, Thr/Ser) that simplifies 2D {sup 1}H-{sup 15}N TROSY spectra, (2) straightforward identification of ILV residue types from the methyl-detected 'out-and-back' HMCM(CG)CBCA experiment, and (3) strong sequential HN-HN NOE connectivities in the helical regions. The two subunits of Bst-YRS were predicted earlier to exist in two different conformations in the absence of ligands. In agreement with our earlier findings (Godoy-Ruiz in J Am Chem Soc 133:19578-195781, 2011), no evidence of dimer asymmetry has been observed in either amide- or methyl-detected experiments.

  3. {sup 1}H and {sup 15}N resonance assignment, secondary structure and dynamic behaviour of the C-terminal domain of human papillomavirus oncoprotein E6

    Energy Technology Data Exchange (ETDEWEB)

    Nomine, Yves; Charbonnier, Sebastian [Laboratoire d' Immunotechnologie, CNRS UMR 7100, Ecole Superieure de Biotechnologie de Strasbourg (France); Miguet, Laurent; Potier, Noelle; Dorsselaer, Alain Van [Laboratoire de Spectrometrie de Masse Bio-Organique, CNRS UMR 7509, Faculte de Chimie (France); Atkinson, R. Andrew [Laboratoire de RMN, CNRS UMR 7104, Ecole Superieure de Biotechnologie de Strasbourg (France); Trave, Gilles [Laboratoire d' Immunotechnologie, CNRS UMR 7100, Ecole Superieure de Biotechnologie de Strasbourg (France)], E-mail: trave@esbs.u-strasbg.fr; Kieffer, Bruno [Laboratoire de RMN, CNRS UMR 7104, Ecole Superieure de Biotechnologie de Strasbourg (France)], E-mail: kieffer@esbs.u-strasbg.fr

    2005-02-15

    E6 is a viral oncoprotein implicated in cervical cancers, produced by human papillomaviruses (HPVs). E6 contains two putative zinc-binding domains of about 75 residues each. The difficulty in producing recombinant E6 has long hindered the obtention of structural data. Recently, we described the expression and purification of E6-C 4C/4S, a stable, folded mutant of the C-terminal domain of HPV16 E6. Here, we have produced {sup 15}N-labelled samples of E6-C 4C/4S for structural studies by NMR. We have assigned most {sup 1}H and {sup 15}N resonances and identified the elements of secondary structure of the domain. The domain displays an original {alpha}/{beta} topology with roughly equal proportions of {alpha}-helix and {beta}-sheet. The PDZ-binding region of E6, located at the extreme C-terminus of the domain, is in a random conformation. Mass spectrometry demonstrated the presence of one zinc ion per protein molecule. Kinetics of replacement of zinc by cadmium followed by {sup 1}H,{sup 15}N-HSQC experiments revealed specific frequency changes for the zinc-binding cysteines and their immediate neighbours. NMR spectra were affected by severe line-broadening effects which seriously hindered the assignment work. Investigation of these effects by {sup 15}N relaxation experiments showed that they are due to heterogeneous dynamic behaviour with {mu}s-ms time scale motions occurring in localised regions of the monomeric domain.

  4. Sequence-specific 1H, 15N, and 13C resonance assignments of the autophagy-related protein LC3C.

    Science.gov (United States)

    Krichel, Carsten; Weiergräber, Oliver H; Pavlidou, Marina; Mohrlüder, Jeannine; Schwarten, Melanie; Willbold, Dieter; Neudecker, Philipp

    2016-04-01

    Autophagy is a versatile catabolic pathway for lysosomal degradation of cytoplasmic material. While the phenomenological and molecular characteristics of autophagic non-selective (bulk) decomposition have been investigated for decades, the focus of interest is increasingly shifting towards the selective mechanisms of autophagy. Both, selective as well as bulk autophagy critically depend on ubiquitin-like modifiers belonging to the Atg8 (autophagy-related 8) protein family. During evolution, Atg8 has diversified into eight different human genes. While all human homologues participate in the formation of autophagosomal membrane compartments, microtubule-associated protein light chain 3C (LC3C) additionally plays a unique role in selective autophagic clearance of intracellular pathogens (xenophagy), which relies on specific protein-protein recognition events mediated by conserved motifs. The sequence-specific (1)H, (15)N, and (13)C resonance assignments presented here form the stepping stone to investigate the high-resolution structure and dynamics of LC3C and to delineate LC3C's complex network of molecular interactions with the autophagic machinery by NMR spectroscopy.

  5. (1)H, (15)N and (13)C resonance assignments of the conserved region in the middle domain of S. pombe Sin1 protein.

    Science.gov (United States)

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

    2015-04-01

    SAPK-interacting protein 1 (Sin1) is an important component of the target of rapamycin (TOR) complex 2 (TORC2). TOR is a serine/threonine-specific protein kinase and forms functionally distinct protein complexes referred to as TORC1 and TORC2. TORC2, conserved from yeast to humans, phosphorylates AGC-family protein kinases and has many cellular functions including the regulation of actin cytoskeleton. The Sin1 subunit of TORC2 is required for the binding of TORC2 to substrates, and the conserved region in the middle (CRIM) domain of Sin1 is important in the substrate recognition of TORC2. Here, we report on the (1)H, (13)C and (15)N resonance assignments of fission yeast Schizosaccharomyces pombe Sin1 (amino acids 247-400) (Sin1CRIM), which possesses the CRIM domain. These data contribute toward the structure determination of Sin1CRIM and an understanding of the interactions of Sin1CRIM with substrates of TORC2.

  6. NMR resonance assignments for the N-terminal domain of the δ subunit of the E. coli γ clamp loader complex.

    Science.gov (United States)

    Alyami, Esmael M; Rizzo, Alessandro A; Beuning, Penny J; Korzhnev, Dmitry M

    2017-10-01

    The β-clamp protein and the γ clamp loader complex are essential components of bacterial DNA replication machinery. The β-clamp is a ring-shaped homodimer that encircles DNA and increases the efficiency of replication by providing a binding platform for DNA polymerases and other replication-related proteins. The β-clamp is loaded onto DNA by the five-subunit γ clamp loader complex in a multi-step ATP-dependent process. The initial steps of this process involve the cooperative binding of the β-clamp by the five subunits of ATP-bound clamp loader, which induces or traps an open conformation of the clamp. Remarkably, the δ subunit of the E. coli clamp loader, or even its 140 residue N-terminal domain (called mini-δ), alone can shift conformational equilibrium of the β-clamp towards the open state. Here we report nearly complete backbone and side-chain 1 H, 13 C and 15 N NMR resonance assignments of mini-δ that will facilitate NMR studies of the mechanisms of β-clamp opening and its loading on DNA by the clamp loader.

  7. Novel DNA packaging recognition in the unusual bacteriophage N15

    International Nuclear Information System (INIS)

    Feiss, Michael; Geyer, Henriette; Klingberg, Franco; Moreno, Norma; Forystek, Amanda; Maluf, Nasib Karl; Sippy, Jean

    2015-01-01

    Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cos N15 ) is closely related to cos λ , but whereas the cosB N15 subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosB λ . A bioinformatic study of N15-like phages indicates that cosB N15 also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15 plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15

  8. Novel DNA packaging recognition in the unusual bacteriophage N15

    Energy Technology Data Exchange (ETDEWEB)

    Feiss, Michael [Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242 (United States); Geyer, Henriette, E-mail: henriettegeyer@gmail.com [Division of Viral Infections, Robert Koch Institute, Berlin (Germany); Division of Viral Infections, Robert Koch Institute, Berlin (Germany); Klingberg, Franco, E-mail: franco.klingberg@thermofisher.com [Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Moreno, Norma, E-mail: nmoreno@islander.tamucc.edu [Texas A& M University – Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, United States. (United States); Texas A& M University – Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, United States. (United States); Forystek, Amanda, E-mail: eamanda-forystek@uiowa.edu [Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Room # 2911 JPP, Dept. of Psychiatry, The University of Iowa, 200 Hawkins Drive, Iowa City, Iowa, 52242 (United States); Maluf, Nasib Karl, E-mail: fKarl.Maluf@ap-lab.com [Flow Cytometry, Imaging & Microscopy, Thermo Fisher Scientific, Frankfurter Strasse 129B 64293 Darmstadt (Germany); Alliance Protein Laboratories, Inc. 6042 Cornerstone Court West, Suite ASan Diego, CA 92121, USA. (United States); Sippy, Jean [Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242 (United States)

    2015-08-15

    Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cos{sup N15}) is closely related to cos{sup λ}, but whereas the cosB{sup N15} subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosB{sup λ}. A bioinformatic study of N15-like phages indicates that cosB{sup N15} also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15 plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15.

  9. Pentacyclic triterpenoids of Mentha villosa: structural identification and {sup 1}H and {sup 13}C resonance assignments; Triterpenoides pentaciclicos de Mentha villosa: identificacao estrutural e atribuicao dos deslocamentos quimicos dos atomos de hidrogenio e carbono

    Energy Technology Data Exchange (ETDEWEB)

    Monte, Francisco J. Queiroz; Oliveira, Eliete F. de [Ceara Univ., Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica; Braz Filho, Raimundo [Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ (Brazil). Setor de Quimica de Produtos Naturais

    2001-08-01

    The structures of seven oleanene and ursene triterpenoids (1-7) isolated from aerial parts of Mentha villosa were identified. In addition, the complete {sup 1} H and {sup 13} C resonance assignments of these triterpenoids were accomplished using 1D and 2D NMR spectroscopic experiments. (author)

  10. 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

  11. 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.

  12. 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.

  13. Accredited Standards Committee N15 Developments And Future Directions

    International Nuclear Information System (INIS)

    Mathews, Caroline E.; May, Melanie; Preston, Lynne

    2009-01-01

    Accredited Standards Committee (ASC) N15, Methods of Nuclear Material Control, is sponsored by the Institute of Nuclear Materials Management (INMM) to develop standards for protection, control and accounting of special nuclear materials in all phases of the nuclear fuel cycle, including analytical procedures where necessary and special to this purpose, except that physical protection of special nuclear material within a nuclear power plant is not included. Voluntary consensus standards complement federal regulations and technical standards and fulfill an important role for the nuclear regulatory agencies. This paper describes the N15 standards development process, with INMM as the Standards Developing Organization (SDO) and the N15 Committee responsible for implementation. Key components of the N15 standards development process include ANSI accreditation; compliance with the ANSI Essential Requirements (ER), coordination with other SDOs, communication with stakeholders, maintenance of balance between interest categories, and ANSI periodic audits. Recent and future ASC N15 activities are discussed, with a particular focus on new directions in anticipation of renewed growth in nuclear power.

  14. Resonance

    DEFF Research Database (Denmark)

    Petersen, Nils Holger

    2014-01-01

    A chapter in a book about terminology within the field of medievalism: the chapter discusses the resonance of medieval music and ritual in modern (classical) music culture and liturgical practice.......A chapter in a book about terminology within the field of medievalism: the chapter discusses the resonance of medieval music and ritual in modern (classical) music culture and liturgical practice....

  15. Two-dimensional sup 1 H nuclear magnetic resonance study of AaH IT, an anti-insect toxin from the scorpion Androctonus australis Hector. Sequential resonance assignments and folding of the polypeptide chain

    Energy Technology Data Exchange (ETDEWEB)

    Darbon, H. (Laboratoire de Biochimie, Marseille (France)); Weber, C.; Braun, W. (Institut fur Molekularbiologie und Biophysik, Zuerich (Switzerland))

    1991-02-19

    Sequence-specific nuclear magnetic resonance assignments for the polypeptide backbone and for most of the amino acid side-chain protons, as well as the general folding of AaH IT, are described. AaH IT is a neurotoxin purified from the venom of the scorpion Androctonus australis Hector and is specifically active on the insect nervous system. The secondary structure and the hydrogen-bonding patterns in the regular secondary structure elements are deduced from nuclear Overhauser effects and the sequence locations of the slowly exchanging amide protons. The backbone folding is determined by distance geometry calculations with the DISMAN program. The regular secondary structure includes two and a half turns of {alpha}-helix running from residues 21 to 30 and a three-stranded antiparallel {beta}-sheet including peptides 3-5, 34-38, and 41-46. Two tight turns are present, one connecting the end of the {alpha}-helix to an external strand of the {beta}-sheet, i.e., turn 31-34, and another connecting this same strand to the central one, i.e., turn 38-41. The differences in the specificity of these related proteins, which are able to discriminate between mammalian and insect voltage-dependent sodium channels of excitable tissues, are most probably brought about by the position of the C-terminal peptide with regard to a hydrophobic surface common to all scorpion toxins examined thus far. Thus, the interaction of a given scorpion toxin with its receptor might well be governed by the presence of this solvent-exposed hydrophobic surface, whereas adjacent areas modulate the specificity of the interaction.

  16. NMR backbone resonance assignments of the N, P domains of CopA, a copper-transporting ATPase, in the apo and ligand bound states.

    Science.gov (United States)

    Meng, Dan; Bruschweiler-Li, Lei; Zhang, Fengli; Brüschweiler, Rafael

    2015-04-01

    Copper-transporting ATPase, a member of P-type ATPase family, plays a key role in the homeostasis of cellular copper levels. Here, the backbone assignments of the directly connected N and P domains (292 residues, 31 kDa) of Cu-transporting ATPase in the ligand free and the AMPPCP-bound states are reported in solution. The NMR assignments pave the way for binding and dynamics studies of this enzyme to better understand its function.

  17. Resonances

    DEFF Research Database (Denmark)

    an impetus or drive to that account: change, innovation, rupture, or discontinuity. Resonances: Historical Essays on Continuity and Change explores the historiographical question of the modes of interrelation between these motifs in historical narratives. The essays in the collection attempt to realize...... theoretical consciousness through historical narrative ‘in practice’, by discussing selected historical topics from Western cultural history, within the disciplines of history, literature, visual arts, musicology, archaeology, philosophy, and theology. The title Resonances indicates the overall perspective...... of the book: how connotations of past meanings may resonate through time, in new contexts, assuming new meanings without surrendering the old....

  18. (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.

  19. RESONANCE

    Indian Academy of Sciences (India)

    maceutical, paper, food, dyes, petrochemi- cals, pigments, etc., to identify molecules, to monitor reaction products and so on. One of the most spectacular contributions of NMR has been in the development of magnetic resonance imaging (MRI), a method that has today revolutionized diagnosis and treatment of diseases in ...

  20. ¹H, ¹³C, and ¹⁵N backbone resonance assignments of the 37 kDa voltage-gated Ca²⁺ channel β4 subunit core SH3-GK domains.

    Science.gov (United States)

    Xu, Xingfu; Horne, William A

    2014-04-01

    The β subunit of the voltage-gated Ca(2+) channel (α1, α2δ, and β subunits) is a member of the MAGUK family of proteins and plays an essential role in regulating Ca(2+) channel trafficking and gating. It also serves as a central interaction partner for various Ca(2+) channel regulatory proteins. We report here the nearly complete (1)H, (13)C, and (15)N backbone resonance assignments of the 37 kDa core SH3-GK domains of the β4 subunit. This is the first report of solution assignments for β subunits, and as such will lay the foundation for future investigations of interaction site mapping, functional dynamics, and protein complex structure determination.

  1. 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.

  2. ¹H, ¹³C and ¹⁵N resonance assignments of the apo and holo states of flavodoxin YqcA from Escherichia coli.

    Science.gov (United States)

    Ye, Qian; Hu, Yunfei; Jin, Changwen

    2014-10-01

    Flavodoxins are a family of FMN binding proteins widely distributed in prokaryotes. They involve in various electron transfer reactions using the non-covalently bound FMN cofactor as the redox center. The Escherichia coli yqcA gene was identified to encode a short-chain favodoxin based on sequence information. However, the structure of YqcA protein is unknown and its exact biological function in cell is yet to be investigated. Herein, we report the resonance assignments of (1)H, (13)C and (15)N atoms of E. coli YqcA in both the apo and holo states.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-08-15

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

  4. 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

  5. A Study of Secondary and Tertiary Solution Structure of Yeast tRNAAsp by Nuclear Magnetic Resonance. Assignment of G·U Ring NH and Hydrogen-Bonded Base Pair Proton Resonances

    NARCIS (Netherlands)

    Robillard, George T.; Hilbers, C.W.; Reid, Brian R.; Gangloff, Jean; Dirheimer, Guy; Shulman, R.G.

    1976-01-01

    The 270-MHz spectra of yeast tRNAAsp in H2O solutions containing Mg2+ show clearly resolved resonances in the region from -15 to -9.5 ppm. Resonances between -15 and -11.5 ppm from the hydrogen-bonded protons of the acceptor stem and anticodon arm decrease in intensity with increasing temperature

  6. Final report on improved N15 analyser NOI-6e

    International Nuclear Information System (INIS)

    Meier, G.; Hollenthoner, S.

    1985-05-01

    This report gives a general view of the computerized NOI-6e nitrogen analyzer. The construction of the new prototype is described. The new version of the N15 analyzer together with the microcomputer program which has been developed improves the convenience of operation and also has high reliability. Many practical test measurements have been made. The most important result is the remarkable reduction of the standard deviation σsub(x): a standard deviation of less than 0.5% is achieved. We have not found such a low standard deviation in descriptions of similar analyzers which use emission spectroscopy

  7. 1H, 13C, and 15N resonance assignments of an enzymatically active domain from the catalytic component (CDTa, residues 216-420) of a binary toxin from Clostridium difficile.

    Science.gov (United States)

    Roth, Braden M; Godoy-Ruiz, Raquel; Varney, Kristen M; Rustandi, Richard R; Weber, David J

    2016-04-01

    Clostridium difficile is a bacterial pathogen and is the most commonly reported source of nosocomial infection in industrialized nations. Symptoms of C. difficile infection (CDI) include antibiotic-associated diarrhea, pseudomembranous colitis, sepsis and death. Over the last decade, rates and severity of hospital infections in North America and Europe have increased dramatically and correlate with the emergence of a hypervirulent strain of C. difficile characterized by the presence of a binary toxin, CDT (C. difficile toxin). The binary toxin consists of an enzymatic component (CDTa) and a cellular binding component (CDTb) that together form the active binary toxin complex. CDTa harbors a pair of structurally similar but functionally distinct domains, an N-terminal domain (residues 1-215; (1-215)CDTa) that interacts with CDTb and a C-terminal domain (residues 216-420; (216-420)CDTa) that harbors the intact ADP-ribosyltransferase (ART) active site. Reported here are the (1)H, (13)C, and (15)N backbone resonance assignments of the 23 kDa, 205 amino acid C-terminal enzymatic domain of CDTa, termed (216-420)CDTa. These NMR resonance assignments for (216-420)CDTa represent the first for a family of ART binary toxins and provide the framework for detailed characterization of the solution-state protein structure determination, dynamic studies of this domain, as well as NMR-based drug discovery efforts.

  8. 1H, 15N and 13C resonance assignments of light organ-associated fatty acid-binding protein of Taiwanese fireflies.

    Science.gov (United States)

    Tseng, Kai-Li; Lee, Yi-Zong; Chen, Yun-Ru; Lyu, Ping-Chiang

    2016-04-01

    Fatty acid-binding proteins (FABPs) are a family of proteins that modulate the transfer of various fatty acids in the cytosol and constitute a significant portion in many energy-consuming cells. The ligand binding properties and specific functions of a particular type of FABP seem to be diverse and depend on the respective binding cavity as well as the cell type from which this protein is derived. Previously, a novel FABP (lcFABP; lc: Luciola cerata) was identified in the light organ of Taiwanese fireflies. The lcFABP was proved to possess fatty acids binding capabilities, especially for fatty acids of length C14-C18. However, the structural details are unknown, and the structure-function relationship has remained to be further investigated. In this study, we finished the (1)H, (15)N and (13)C chemical shift assignments of (15)N/(13)C-enriched lcFABP by solution NMR spectroscopy. In addition, the secondary structure distribution was revealed based on the backbone N, H, Cα, Hα, C and side chain Cβ assignments. These results can provide the basis for further structural exploration of lcFABP.

  9. 1H, 15N, 13C Resonance Assignments of the Reduced and Active Form of Human Protein Tyrosine Phosphatase, PRL-1

    Science.gov (United States)

    Skinner, Andria L.; Laurence, Jennifer S.

    2009-01-01

    Phosphatase of regenerating liver-1 (PRL-1) is a novel target for potentially treating cancer metastases. Although its specific biochemical role in these processes has yet to be delineated, considerable evidence suggests the phosphatase activity of PRL-1 is required for promoting cancer and metastasis. PRL-1 belongs to the protein tyrosine phosphatase (PTPase) family and functions using the CX5R consensus active site motif. Like other PTPases, PRL-1 is inhibited by oxidation at its active site Cys, however, disulfide bond formation occurs unusually readily in wild-type PRL-1. Chemical shift assignments are available for oxidized wild type, but numerous, substantial changes are observed in the spectra upon reduction. Because the reduced form is active, we sought to identify a stable mutant that would resist oxidation and be useful for facilitating drug screening and development using NMR-based assays. We present here NMR assignments for a full-length, reduced and active form of PRL-1, PRL-1-C170S-C171S, that is well suited for this purpose. PMID:19636948

  10. GFT projection NMR based resonance assignment of membrane proteins: application to subunit c of E. coli F{sub 1}F{sub 0} ATP synthase in LPPG micelles

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Qi [State University of New York at Buffalo, Department of Chemistry (United States); Atreya, Hanudatta S. [NMR Research Centre, Indian Institute of Science (India); Kamen, Douglas E.; Girvin, Mark E. [Albert Einstein College of Medicine, Biochemistry Department (United States); Szyperski, Thomas [State University of New York at Buffalo, Department of Chemistry (United States)], E-mail: szypersk@chem.buffalo.edu

    2008-03-15

    G-matrix FT projection NMR spectroscopy was employed for resonance assignment of the 79-residue subunit c of the Escherichia coli F{sub 1}F{sub 0} ATP synthase embedded in micelles formed by lyso palmitoyl phosphatidyl glycerol (LPPG). Five GFT NMR experiments, that is, (3,2)D HNNCO, L-(4,3)D HNNC{sup {alpha}}{sup {beta}}C{sup {alpha}}, L-(4,3)D HNN(CO)C{sup {alpha}}{sup {beta}}C{sup {alpha}}, (4,2)D HACA(CO)NHN and (4,3)D HCCH, were acquired along with simultaneous 3D {sup 15}N, {sup 13}C{sup aliphatic}, {sup 13}C{sup aromatic}-resolved [{sup 1}H,{sup 1}H]-NOESY with a total measurement time of {approx}43 h. Data analysis resulted in sequence specific assignments for all routinely measured backbone and {sup 13}C{sup {beta}} shifts, and for 97% of the side chain shifts. Moreover, the use of two G{sup 2}FT NMR experiments, that is, (5,3)D HN{l_brace}N,CO{r_brace}{l_brace}C{sup {alpha}}{sup {beta}}C{sup {alpha}}{r_brace} and (5,3)D {l_brace}C{sup {alpha}}{sup {beta}}C{sup {alpha}}{r_brace}{l_brace}CON{r_brace}HN, was explored to break the very high chemical shift degeneracy typically encountered for membrane proteins. It is shown that the 4D and 5D spectral information obtained rapidly from GFT and G{sup 2}FT NMR experiments enables one to efficiently obtain (nearly) complete resonance assignments of membrane proteins.

  11. Backbone NMR resonance assignments of the nucleotide binding domain of the ABC multidrug transporter LmrA from Lactococcus lactis in its ADP-bound state.

    Science.gov (United States)

    Hellmich, Ute A; Duchardt-Ferner, Elke; Glaubitz, Clemens; Wöhnert, Jens

    2012-04-01

    LmrA from Lactococcus lactis is a multidrug transporter and a member of the ATP binding cassette (ABC) transporter family. ABC transporters consist of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). The NBD contains the highly conserved signature motifs of this transporter superfamily. In the case of LmrA, the TMD and the NBD are expressed as a single polypeptide. LmrA catalyzes the extrusion of hydrophobic compounds including antibiotics from the cell membrane at the expense of ATP hydrolysis. ATP binds to the NBD, where binding and hydrolysis induce conformational changes that lead to the extrusion of the substrate via the TMD. Here, we report the (1)H, (13)C and (15)N backbone chemical shift assignments of the isolated 263 amino acid containing NBD of LmrA in its ADP bound state.

  12. HNCA-TOCSY-CANH experiments with alternate 13C-12C labeling: a set of 3D experiment with unique supra-sequential information for mainchain resonance assignment

    International Nuclear Information System (INIS)

    Takeuchi, Koh; Gal, Maayan; Takahashi, Hideo; Shimada, Ichio; Wagner, Gerhard

    2011-01-01

    Described here is a set of three-dimensional (3D) NMR experiments that rely on CACA-TOCSY magnetization transfer via the weak 3 J(C α C α ) coupling. These pulse sequences, which resemble recently described 13 C detected CACA-TOCSY (Takeuchi et al. 2010) experiments, are recorded in 1 H 2 O, and use 1 H excitation and detection. These experiments require alternate 13 C- 12 C labeling together with perdeuteration, which allows utilizing the small 3 J(C α C α ) scalar coupling that is otherwise masked by the stronger 1 J CC couplings in uniformly 13 C labeled samples. These new experiments provide a unique assignment ladder-mark that yields bidirectional supra-sequential information and can readily straddle proline residues. Unlike the conventional HNCA experiment, which contains only sequential information to the 13 (C α ) of the preceding residue, the 3D hnCA-TOCSY-caNH experiment can yield sequential correlations to alpha carbons in positions i−1, i + 1 and i−2. Furthermore, the 3D hNca-TOCSY-caNH and Hnca-TOCSY-caNH experiments, which share the same magnetization pathway but use a different chemical shift encoding, directly couple the 15 N- 1 H spin pair of residue i to adjacent amide protons and nitrogens at positions i−2, i−1, i + 1 and i + 2, respectively. These new experimental features make protein backbone assignments more robust by reducing the degeneracy problem associated with the conventional 3D NMR experiments.

  13. CACA-TOCSY with alternate 13C–12C labeling: a 13Cα direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification

    Science.gov (United States)

    Takeuchi, Koh; Frueh, Dominique P.; Sun, Zhen-Yu J.; Hiller, Sebastian

    2010-01-01

    We present a 13C direct detection CACA-TOCSY experiment for samples with alternate 13C–12C labeling. It provides inter-residue correlations between 13Cα resonances of residue i and adjacent Cαs at positions i − 1 and i + 1. Furthermore, longer mixing times yield correlations to Cα nuclei separated by more than one residue. The experiment also provides Cα-to-sidechain correlations, some amino acid type identifications and estimates for ψ dihedral angles. The power of the experiment derives from the alternate 13C–12C labeling with [1,3-13C] glycerol or [2-13C] glycerol, which allows utilizing the small scalar 3JCC couplings that are masked by strong 1JCC couplings in uniformly 13C labeled samples. PMID:20383561

  14. CACA-TOCSY with alternate 13C-12C labeling: a 13Cα direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification

    International Nuclear Information System (INIS)

    Takeuchi, Koh; Frueh, Dominique P.; Sun, Zhen-Yu J.; Hiller, Sebastian; Wagner, Gerhard

    2010-01-01

    We present a 13 C direct detection CACA-TOCSY experiment for samples with alternate 13 C- 12 C labeling. It provides inter-residue correlations between 13 C α resonances of residue i and adjacent C α s at positions i - 1 and i + 1. Furthermore, longer mixing times yield correlations to C α nuclei separated by more than one residue. The experiment also provides C α -to-sidechain correlations, some amino acid type identifications and estimates for ψ dihedral angles. The power of the experiment derives from the alternate 13 C- 12 C labeling with [1,3- 13 C] glycerol or [2- 13 C] glycerol, which allows utilizing the small scalar 3 J CC couplings that are masked by strong 1 J CC couplings in uniformly 13 C labeled samples.

  15. CACA-TOCSY with alternate 13C-12C labeling: a 13Calpha direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification.

    Science.gov (United States)

    Takeuchi, Koh; Frueh, Dominique P; Sun, Zhen-Yu J; Hiller, Sebastian; Wagner, Gerhard

    2010-05-01

    We present a (13)C direct detection CACA-TOCSY experiment for samples with alternate (13)C-(12)C labeling. It provides inter-residue correlations between (13)C(alpha) resonances of residue i and adjacent C(alpha)s at positions i - 1 and i + 1. Furthermore, longer mixing times yield correlations to C(alpha) nuclei separated by more than one residue. The experiment also provides C(alpha)-to-sidechain correlations, some amino acid type identifications and estimates for psi dihedral angles. The power of the experiment derives from the alternate (13)C-(12)C labeling with [1,3-(13)C] glycerol or [2-(13)C] glycerol, which allows utilizing the small scalar (3)J(CC) couplings that are masked by strong (1)J(CC) couplings in uniformly (13)C labeled samples.

  16. 1H, 13C and 15N resonance assignments and secondary structure analysis of CmPI-II, a serine protease inhibitor isolated from marine snail Cenchritis muricatus.

    Science.gov (United States)

    Cabrera-Muñoz, Aymara; Rojas, Laritza; Alonso-del-Rivero Antigua, Maday; Pires, José Ricardo

    2016-04-01

    A protease inhibitor (CmPI-II) (UNIPROT: IPK2_CENMR) from the marine mollusc Cenchritis muricatus, has been isolated and characterized. It is the first member of a new group (group 3) of non-classical Kazal-type inhibitors. CmPI-II is a tight-binding inhibitor of serine proteases: trypsin, human neutrophil elastase (HNE), subtilisin A and pancreatic elastase. This specificity is exceptional in the members of Kazal-type inhibitor family. Several models of three-dimensional structure of CmPI-II have been constructed by homology with other inhibitors of the family but its structure has not yet been solved experimentally. Here we report the (1)H, (15)N and (13)C chemical shift assignments of CmPI-II as basis for NMR structure determination and interaction studies. Secondary structure analyses deduced from the NMR chemical shift data have identified three β-strands β1: residues 14-19, β2: 23-35 and β3: 43-45 and one helix α1: 28-37 arranged in the sequential order β1-β2-α1-β3. These secondary structure elements suggest that CmPI-II adopts the typical scaffold of a Kazal-type inhibitor.

  17. 1H, 13C and 15N resonance assignments and second structure information of Fag s 1: Fagales allergen from Fagus sylvatica.

    Science.gov (United States)

    Moraes, A H; Asam, C; Batista, A; Almeida, F C L; Wallner, M; Ferreira, F; Valente, A P

    2016-04-01

    Fagales allergens belonging to the Bet v 1 family account responsible for the majority of spring pollinosis in the temperate climate zones in the Northern hemisphere. Among them, Fag s 1 from beech pollen is an important trigger of Fagales pollen associated allergic reactions. The protein shares high similarity with birch pollen Bet v 1, the best-characterized member of this allergen family. Of note, recent work on Bet v 1 and its homologues found in Fagales pollen demonstrated that not all allergenic members of this family have the capacity to induce allergic sensitization. Fag s 1 was shown to bind pre-existing IgE antibodies most likely primarily directed against other members of this multi-allergen family. Therefore, it is especially interesting to compare the structures of Bet v 1-like pollen allergens, which have the potential to induce allergic sensitization with allergens that are mainly cross-reactive. This in the end will help to identify allergy eliciting molecular pattern on Bet v 1-like allergens. In this work, we report the (1)H, (15)N and (13)C NMR assignment of beech pollen Fag s 1 as well as the secondary structure information based on backbone chemical shifts.

  18. ¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of a family 36 carbohydrate binding module of xylanase from Paenibacillus campinasensis.

    Science.gov (United States)

    Wang, Yu-Sheng; Ko, Chun-Han; Chang, Hao-Ting; Yang, Kai-Jay; Chen, Yu-Jen; Huang, Shing-Jong; Fang, Pei-Ju; Chang, Chi-Fon; Tzou, Der-Lii M

    2014-10-01

    Paenibacillus campinasensis BL11 isolated from black liquor secretes multiple glycoside hydrolases (GHs) against all kinds of polysaccharides. GH consists of a catalytic module and non-catalytic carbohydrate-binding modules (CBMs), in which CBMs append to the catalytic module, mediating specific interactions with insoluble carbohydrates to promote the hydrolysis efficiency of the cognate enzyme. Endo-β-1,4-xylanase (XylX) is one of the GHs reveals high enzymatic activity in a wide range of pH and thermal endurance, suitable for bioconversion and bio-refinement applications. In this work, we report the resonance assignments of a family 36 CBM (characterized as CBM36) derived from XylX. Our investigations will facilitate molecular structure determination and molecular dynamics analysis of CBMs.

  19. ¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of the N-terminal ubiquitin-binding domains of the human deubiquitinase Usp28.

    Science.gov (United States)

    Wen, Yi; Cui, Rong; Zhang, Huaqun; Zhang, Naixia

    2014-10-01

    Deubiquitinases (DUBs) reversibly remove ubiquitin tags from polypeptides and play crucial regulatory roles in multiple cellular processes. Ubiquitin-specific protease 28 (Usp28), a member of the DUB family, exerts its deubiquitination function on key protein molecules in a couple of cancer-associated pathways, likely acting as an oncogenic factor in vivo. The N-terminal ubiquitin-binding domains (UBDs) of Usp28 are potentially required for the full catalytic capacity of Usp28 toward ubiquitin chains. Here we report the expression, purification and (1)H, (13)C and (15)N backbone and side-chain resonance assignments of the N-terminal UBDs of Usp28. The BMRB accession number is 19077.

  20. Backbone and sterospecific methyl side chain resonance assignments of the homodimeric zinc sensor AdcR (32 kDa) in the apo- and Zn(II)-bound states.

    Science.gov (United States)

    Guerra, Alfredo J; Giedroc, David P

    2014-04-01

    Streptococcus pneumoniae adhesin competence repressor (AdcR) is a Zn(II)-dependent 32 kDa homodimer that controls the transcription of a zinc-specific ABC uptake system (AdcABC), three pneumococcal histidine triad proteins (PhtA, PhtD and PhtE), and an AdcA homolog AdcAII. AdcR is the first metal-dependent member of the MarR family of prokaryotic transcriptional repressors. Two-dimensional NMR studies reveal large changes in the spectrum upon Zn(II) binding. Near complete backbone and stereospecific methyl group resonance assignments for apo- and Zn(II)-AdcR are presented here.

  1. ¹H, ¹³C and ¹⁵N resonance assignments and second structure information of Gad m 1: a β-parvalbumin allergen from Atlantic cod (Gadus morhua).

    Science.gov (United States)

    Moraes, A H; Ackerbauer, D; Kostadinova, M; Bublin, M; Ferreira, F; Almeida, F C L; Breiteneder, H; Valente, A P

    2013-10-01

    Gad m 1 is the major allergen from Atlantic cod. It belongs to β-parvalbumin protein family and is characterized by the presence of two calcium-binding sites so called EF-hand motifs. β-Parvalbumins such as Gad m 1 are the most important fish allergens and their high cross-reactivity is the cause of the observed polysensitization to various fish species in allergic patients. Despite extensive efforts, the complete elucidation of β-parvalbumin-IgE complexes has not been achieved yet. Allergen structural studies are essential for the development of novel immunotherapy strategies, including vaccination with hypoallergenic derivatives and chimeric molecules. Here, we report for the first time the NMR study of a β-parvalbumin: Gad m 1. This report includes: (1)H, (13)C and (15)N resonance assignments of Gad m 1 as well as the second structure information based on the (13)C chemical shifts.

  2. ¹H, ¹³C, and ¹⁵N backbone resonance assignments of the L124D mutant of StAR-related lipid transfer domain protein 4 (StARD4).

    Science.gov (United States)

    Dikiy, Igor; Ramlall, Trudy F; Eliezer, David

    2013-10-01

    Protein-mediated cholesterol trafficking is central to maintaining cholesterol homeostasis in cells. START (Steroidogenic acute regulatory protein-related lipid transfer) domains constitute a sterol and lipid binding motif and the START domain protein StARD4 typifies a small family of mammalian sterol transport proteins. StARD4 consists of a single START domain and has been reported to act as a general cholesterol transporter in cells. However, the structural basis of cholesterol uptake and transport is not well understood and no cholesterol-bound START domain structures have been reported. We have undertaken the study of cholesterol binding and transport by StARD4 using solution state NMR spectroscopy. To this end, we report nearly complete (1)H, (15)N, and (13)C backbone resonance assignments of an inactive but well behaved mutant (L124D) of StARD4.

  3. 1H, 13C, and 15N backbone resonance assignments of the L124D mutant of StAR-related lipid transfer domain protein 4 (StARD4)

    Science.gov (United States)

    Dikiy, Igor; Ramlall, Trudy F.; Eliezer, David

    2012-01-01

    Protein-mediated cholesterol trafficking is central to maintaining cholesterol homeostasis in cells. START (Steroidogenic acute regulatory protein-related lipid transfer) domains constitute a sterol and lipid binding motif and the START domain protein StARD4 typifies a small family of mammalian sterol transport proteins. StARD4 consists of a single START domain and has been reported to act as a general cholesterol transporter in cells. However, the structural basis of cholesterol uptake and transport is not well understood and no cholesterol-bound START domain structures have been reported. We have undertaken the study of cholesterol binding and transport by StARD4 using solution state NMR spectroscopy. To this end, we report nearly complete 1H, 15N, and 13C backbone resonance assignments of an inactive but well behaved mutant (L124D) of StARD4. PMID:22918595

  4. 1HN, 13C, and 15N Resonance Assignments of the CDTb-Interacting Domain (CDTaBID) from the Clostridium difficile Binary Toxin Catalytic Component (CDTa, residues 1–221)

    Science.gov (United States)

    Roth, Braden M.; Varney, Kristen M.; Rustandi, Richard R.; Weber, David J.

    2016-01-01

    Once considered a relatively harmless bacterium, Clostridium difficile has become a major concern for healthcare facilities, now the most commonly reported hospital-acquired pathogen. C. difficile infection (CDI) is usually contracted when the normal gut microbiome is compromised by antibiotic therapy, allowing the opportunistic pathogen to grow and produce its toxins. The severity of infection ranges from watery diarrhea and abdominal cramping to pseudomembranous colitis, sepsis, or death. The past decade has seen a marked increase in the frequency and severity of CDI among industrialized nations owing directly to the emergence of a highly virulent C. difficile strain, NAP1. Along with the large Clostridial toxins expressed by non-epidemic strains, C. difficile NAP1 produces a binary toxin, CDT (C. difficile transferase). As the name suggests, CDT is a two-component toxin comprised of an ADP-ribosyltransferase (ART) component (CDTa) and a cell-binding/translocation component (CDTb) that function to destabilize the host cytoskeleton by covalent modification of actin monomers. Central to the mechanism of binary toxin-induced pathogenicity is the formation of CDTa/CDTb complexes at the cell surface. From the perspective of CDTa, this interaction is mediated by the N-terminal domain (residues 1–215) and is spatially and functionally independent of ART activity, which is located in the C-terminal domain (residues 216–420). Here we report the 1HN, 13C, and 15N backbone resonance assignments of a 212 amino acid, ~23 kDa N-terminal CDTb-interacting domain (CDTaBID) construct by heteronuclear NMR spectroscopy. These NMR assignments represent the first component coordination domain for a family of Clostridium or Bacillus species harboring ART activity. Our assignments lay the foundation for detailed solution state characterization of structure-function relationships, toxin complex formation, and NMR-based drug discovery efforts. PMID:27351891

  5. 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.

  6. The utility of N-15 nuclear magnetic resonance spectroscopy for the study of natural products

    International Nuclear Information System (INIS)

    Randall, E.W.

    1978-01-01

    The utility of 15 N NMR spectroscopy for the study of natural products and the difficulties which must be overcome arte discussed. The widespread use of pulse Fourier techniques, decouplings, larger magnetic fields and large tube sizes allows a large number of 15 N studies of natural products, the more recent and important of these being peptides, nucleosides and nucleotides. Sites of protonation, tautomerism, sites of nitrosation and proton exchange behaviour for some of these natrual products have been studied. (A.G.)

  7. 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.

  8. ¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of the N-terminal ubiquitin-binding domains of USP25.

    Science.gov (United States)

    Shi, Li; Wen, Yi; Zhang, Naixia

    2014-10-01

    Ubiquitin Specific Protease 25 (USP25), a member of the deubiquitinase family, is involved in several disease-related signal pathways including myogenesis, immunity and protein degradation. It specially catalyzes the hydrolysis of the K48-linked and K63-linked polyubiquitin chains. USP25 contains one ubiquitin-associated domain and two ubiquitin-interacting motifs (UIMs) in its N-terminal region, which interact with ubiquitin and play a role in substrate recognition. Besides, it has been shown that the catalysis activity of USP25 is either impaired by sumoylation or enhanced by ubiquitination within its UIM. To elucidate the structural basis of the cross-regulation of USP25 function by non-covalent binding and covalent modifications of ubiquitin and SUMO2/3, a systematic structural biology study of USP25 is required. Here, we report the (1)H, (13)C and (15)N backbone and side-chain resonance assignments of the N-terminal ubiquitin binding domains (UBDs) of USP25 with BMRB accession number of 19111, which is the first step of the systematic structural biology study of the enzyme.

  9. 1H, 13C, 15N backbone and side chain NMR resonance assignments of the N-terminal NEAr Iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of Staphylococcus aureus

    Science.gov (United States)

    Fonner, Brittany A.; Tripet, Brian P.; Lui, Mengyao; Zhu, Hui; Lei, Benfang; Copié, Valérie

    2013-01-01

    Staphylococcus aureus is an opportunistic pathogen that causes skin and severe infections in mammals. Critical to S. aureus growth is its ability to scavenge iron from host cells. To this effect, S. aureus has evolved a sophisticated pathway to acquire heme from hemoglobin (Hb) as a preferred iron source. The pathway is comprised of nine iron-regulated surface determinant (Isd) proteins involved in heme capture, transport, and degradation. A key protein of the heme acquisition pathway is the surface-anchored hemoglobin receptor protein IsdB, which is comprised of two NEAr transporter (NEAT) domains that act in concert to bind Hb and extract heme for subsequent transfer to downstream acquisition pathway proteins. Despite significant advances in the structural knowledge of other Isd proteins, the structural mechanisms and molecular basis of the IsdB-mediated heme acquisition process are not well understood. In order to provide more insights into the mode of function of IsdB, we have initiated NMR structural studies of the first NEAT domain of IsdB (IsdBN1). Herein, we report the near complete 1H, 13C and 15N resonance assignments of backbone and side chain atoms, and the secondary structural topology of the 148-residue IsdB NEAT 1 domain. The NMR results are consistent with the presence of eight β-strands and one α-helix characteristic of an immunoglobulin-like fold observed in other NEAT domain family proteins. This work provides a solid framework to obtain atomic-level insights toward understanding how IsdB mediates IsdB-Hb protein-protein interactions critical for heme capture and transfer. PMID:23686822

  10. Structural NMR assignment

    International Nuclear Information System (INIS)

    Procter, J.B.; Torda, A.E.

    1999-01-01

    Full text: General automated NMR assignment approaches are aimed at full heteronuclear assignment, which is needed for structure determination. Usually, full assignment requires at least as much spectral information as is used for structure generation. For large proteins, obtaining sufficient spectral information may require a number of sample preparations and many spectra, resulting in a significant overhead for the use of NMR in biochemical investigation. For a protein of biochemical interest one may already have an x-ray crystal structure, but spectral assignment is still needed to use NMR as a structural probe for ligand binding studies. In this situation it may be possible to use much less spectral information to make an assignment based purely on the correspondence of structural data to the measurements contained in a few simple spectra. We introduce a framework to accomplish this 'structural assignment', and give some observations on the practical requirements for a structural assignment to succeed

  11. Metabolism of nonessential N-15-labeled amino acids and the measurement of human whole-body protein synthesis rates

    Science.gov (United States)

    Stein, T. P.; Settle, R. G.; Albina, J. A.; Melnick, G.; Dempsey, D. T.

    1991-01-01

    Eight N-15-labeled nonessential amino acids plus (N-15)H4Cl were administered over a 10-h period to four healthy adult males using a primed-constant dosage regimen. The amount of N-15 excreted in the urine and the urinary ammonia, hippuric acid, and plasma alanine N-15 enrichments were measured. There was a high degree of consistency across subjects in the ordering of the nine compounds based on the fraction of N-15 excreted.

  12. Faculty Assignment Classification System.

    Science.gov (United States)

    Whatcom Community Coll., Ferndale, WA.

    This document outlines the point-based faculty assignment classification system in effect at Whatcom Community College (Washington). The purpose of the point system is to provide an equitable and flexible means of compensating faculty members based on a system of assigning quantitative values to tasks. Teaching, which includes classroom…

  13. Application of C30B15N15 heterofullerene in the isoniazid drug delivery: DFT studies

    Science.gov (United States)

    Hazrati, Mehrnoosh Khodam; Bagheri, Zargham; Bodaghi, Ali

    2017-05-01

    Using density functional theory, we have investigated the potential application of a C30B15N15 heterofullerene in anti-cancer isoniazid drug delivery. It was found that isoniazid prefers to attach via its -NH2 group to a boron atom of the C30B15N15 with releasing a large energy of about 21.91 kcal/mol. Our partial density of states analysis demonstrates that the boron atoms significantly contribute in generation of virtual orbitals of C30B15N15 fullerene, indicating that these atoms will be suitable for nucleophilic attack rather than carbon atoms. In addition to the large released energy, the electronic properties C30B15N15 are significantly sensitive to the isoniazid attachment which can recognize the drug trajectory by affecting the fluorescence emission properties. Unlike, different nanostructures whose structures need to be manipulated to be suitable for drug delivery, the C30B15N15 fullerene can be used in the pristine form. We proposed a drug release mechanism in cancer tissues, representing that in the low pH of the cancer cells the drug and C30B15N15 fullerene are considerably protonated, thereby separating the drug from the surface of the fullerene. The reaction mechanism of the drug with the fullerene is changed from covalence in natural environment to hydrogen bonding in acidic cancer cells.

  14. 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....

  15. 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)

  16. The use of N15 for studying the mechanism of transformation in the soil and plant

    International Nuclear Information System (INIS)

    Alchater, M.S.

    1995-01-01

    This research pertains to the study of the mechanism of transformation of added N 15 in the soil and plant in an attempt to determine the competition between microbial biomass and the plant for the use of N fertilizer in the form of (N 15 H 4)2 So 4. Additional amounts of barley straw were added as a source of energy. The study led to determining the real utilization coefficient of the canopy and the root system which amounted to 79% of N 15 added alone. Whereas it amounted to the treatments in which barley straw was added to N 15. Furthermore, there was a decrease in the amount of organic N 15 in the form of Gamma-amine as compared with other forms of organic N which also decreased to lesser degree. The results also indicated that the important N in the immobilization of nitrogen, as observed in previous field trials. Nitrogen balance and the contribution of soil N to plant nutrition were also calculated. 2 figs., 5 tabs

  17. 42 CFR 433.146 - Rights assigned; assignment method.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Rights assigned; assignment method. 433.146 Section... Assignment of Rights to Benefits § 433.146 Rights assigned; assignment method. (a) Except as specified in... rights to any medical care support available under an order of a court or an administrative agency, and...

  18. Random Cell Identifiers Assignment

    Directory of Open Access Journals (Sweden)

    Robert Bestak

    2012-01-01

    Full Text Available Despite integration of advanced functions that enable Femto Access Points (FAPs to be deployed in a plug-and-play manner, the femtocell concept still cause several opened issues to be resolved. One of them represents an assignment of Physical Cell Identifiers (PCIs to FAPs. This paper analyses a random based assignment algorithm in LTE systems operating in diverse femtocell scenarios. The performance of the algorithm is evaluated by comparing the number of confusions for various femtocell densities, PCI ranges and knowledge of vicinity. Simulation results show that better knowledge of vicinity can significantly reduce the number of confusions events.

  19. 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

  20. Case Assignment in Agrammatism.

    Science.gov (United States)

    Ruigendijk, Esther; van Zonneveld, Ron; Bastiaanse, Roelien

    1999-01-01

    This study evaluated the omission patterns of case markers in the spontaneous speech of 12 Dutch and German adult speakers with agrammatic aphasia within the framework of Chomsky's case theory. Data supported the hypothesis that, if no case assigner is produced, the noun will receive nominative case by default or the case-marking morpheme will be…

  1. DIFFERENTIATION IN N15 UPTAKE AND THE ORGANIZATION OF AN ARCTIC TUNDRA PLANT COMMUNITY

    Science.gov (United States)

    We used N15 soil-labeling techniques to examine how the dominant species in a N-limited, tussock tundra plant community partitioned soil N, and how such partitioning may contribute to community organization. The five most abundant species were well differentiated with respect to...

  2. 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.

  3. 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

  4. Scaffolding students’ assignments

    DEFF Research Database (Denmark)

    Slot, Marie Falkesgaard

    2013-01-01

    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......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...

  5. Assignment Tracking Android Application

    OpenAIRE

    Akanni, Feranmi Timothy

    2016-01-01

    One of the common ways of checking that knowledge is impacted into students at every level of education is by giving various tasks to students and part of the responsibilities of the teacher is to give assignments to students and check the solution provided by the students. Increase in technology development involves a number of mobile applications that are being developed and released on a daily basis, out of which Android operating application is one of the dominant mobile application. T...

  6. NMR assignment of a KlbA intein precursor from Methanococcus jannaschii.

    Science.gov (United States)

    Johnson, Margaret A; Southworth, Maurice W; Perler, Francine B; Wüthrich, Kurt

    2007-07-01

    The backbone and side chain resonance assignments of a precursor of the KlbA intein from Methanococcus jannaschii have been determined, based on triple-resonance experiments with the uniformly [13C,15N]-labeled protein.

  7. Nitrogen fixation in different chickpea cultivars as affected by iron application N-15 Technique

    International Nuclear Information System (INIS)

    Gadalla, A.M.; Soliman, S.M.; Abdelmonem, M.

    1995-01-01

    With development of new cultivars of winter chickpea, it became important to evaluate the potential of these cultivars to fix nitrogen from air, and the effect of different agronomic factors on this important process. Greenhouse experiment was conducted to screen five cultivars of chickpea for N 2- fixation ability as affected by iron application. These cultivars were Giza 1,2,531 and 88 as compared with L 3 which was developed from the genotype NEC 1055 by irradiation. N 2- fixation was estimated using N-15 technique. Plant materials were collected after 55 days from planing. Plants samples were analysed for total N-15 atom excess. Results show that Giza 88 gave the highest dry matter as well as nitrogen fixation. Nitrogen derived from air (NDFA) ranged from 27 to 50% due to variety difference and iron treatment. 1 fig., 3 tabs

  8. The use of N-15 labelling to study the turnover and utilization of ruminant manure N

    DEFF Research Database (Denmark)

    Sørensen, P.; Jensen, E.S.

    1998-01-01

    An improved understanding of the cycling of animal manure N is a prerequisite for malting better use of this N source. A sheep was fed N-15-Iabelled grass in order to study the fate of N-15-Iabelled ruminant manure N in the plant-soil system. The uniformity of labelling was found to be satisfactory...... when an appropriate feeding strategy was used. The mineralization of labelled faecal N was compared to the mineralization of labelled feed N and indigestible feed N by measuring residual labelled organic N in unplanted topsoil in the field. After18 months, 61% of both faecal N and feed N was recovered...... was low irrespective of the slurry distribution in soil. The results demonstrate that the contact between animal manure and the soil matrix significantly influences the short-term turnover and availability of faecal and ammonium N in slurry, especially in fine-textured soils....

  9. Constituents of the leaves of Woodfordia fruticosa Kurz. I. Isolation, structure, and proton and carbon-13 nuclear magnetic resonance signal assignments of woodfruticosin (woodfordin C), an inhibitor of deoxyribonucleic acid topoisomerase II.

    Science.gov (United States)

    Kadota, S; Takamori, Y; Nyein, K N; Kikuchi, T; Tanaka, K; Ekimoto, H

    1990-10-01

    Woodfruticosin (woodfordin C), a new cyclic dimeric hydrolyzable tannin having an inhibitory activity toward deoxyribonucleic acid (DNA) topoisomerase II, has been isolated from the leaves of Woodfordia fruticosa Kurz (Lythraceae) along with three known flavonol glycosides and three known flavonol glycoside gallates. The structure of wood fruticosin (woodfordin C) was determined by the use of two-dimensional nuclear magnetic resonance (2-D NMR) spectroscopy including heteronuclear multiple quantum coherence (HMQC) and heteronuclear multiple bond connectivity (HMBC) techniques. Detailed analyses of the proton and carbon-13 NMR (1H- and 13C-NMR) spectra of six known flavonoids were performed.

  10. H-1, C-13, and N-15 NMR assignments of the hypothetical Nudix protein DR0079 from the extremely radiation-resistant bacterium Deinococcus radiodurans.

    Energy Technology Data Exchange (ETDEWEB)

    Buchko, Garry W.; Ni, Shuisong; Holbrook, Stephen R.; Kennedy, Michael A.

    2003-02-05

    Letter to the Editor. Biological context Deinococcus radiodurans is a bacterium that is extremely resistant to the lethal and mutagenic effects of ionizing radiation, ultraviolet radiation, and other physical and chemical DNA-damaging agents (Battista, 1997). It has been suggested that this resistance is due to unusually efficient DNA repair mechanisms (Minton, 1994). Analysis of the complete genome sequence of D. radiodurans reveals a full suite of genes with potential DNA repair activities (White et al, 1999), essentially all of which have functional homologues in other procaryotes. These hypothetical DNA repair genes display a high amount of redundancy and include 21 genes that have sequence homology with the Nudix family of polyphosphate pyrophosphohydrolases (Bessman et al., 1996). Nudix proteins are identified by the consensus sequence GX5EX7REUXEEXGU (where U= I, L, or V and X= any amino acid) that forms part of the catalytic site for diphosphate hydrolysis (Bessman et al., 1996). Consequently, a nucleoside diphosphate linkage is a feature common in Nudix substrates that include NADH, nucleotide sugars, dinucleotide polyphosphates, and (deoxy)ribonucleoside triphosphates (NTPs). The general biochemical function of the Nudix family of proteins is believed to be sanitizing the cell (Bessman et al., 1996). For example, MutT preferably hydrolyzes the promutagenic NTP 7,8-dihydro-8-oxoguanosine triphosphate to nucleotide monophosphate and inorganic phosphate. Despite the identification of over 450 putative Nudix proteins in genomes on the basis of the Nudix consensus sequence (Gabelli et al., 2001), few Nudix protein structures have been determined (Holbrook et al., 2002). To better understand the relevance, function, and mechanism of the Nudix family of proteins, and to better understand the roles played by the hypothetical D. radiodurans Nudix proteins in radiation-resistance, we have crystallized the hypothetical D.

  11. Backbone and side-chain ¹H, ¹⁵N, and ¹³C resonance assignments of the microtubule-binding domain of yeast cytoplasmic dynein in the high and low-affinity states.

    Science.gov (United States)

    Takarada, Osamu; Nishida, Noritaka; Kikkawa, Masahide; Shimada, Ichio

    2014-10-01

    Cytoplasmic dynein is a motor protein that walks toward the minus end of microtubules (MTs) by utilizing the energy of ATP hydrolysis. The heavy chain of cytoplasmic dynein contains the microtubule-binding domain (MTBD). Switching of MTBD between high and low affinity states for MTs is crucial for processive movement of cytoplasmic dynein. Previous biochemical studies demonstrated that the affinity of MTBD is regulated by the AAA+ family ATPase domain, which is separated by 15 nm long coiled-coil helix. In order to elucidate the structural basis of the affinity switching mechanism of MTBD, we designed two MTBD constructs, termed MTBD-High and MTBD-Low, which are locked in high and low affinity state for MTs, respectively, by introducing a disulfide bond between the coiled-coil helix. Here, we established the backbone and side-chain assignments of MTBD-High and MTBD-Low for further structural analyses.

  12. NMR study of non-structural proteins-part III:1H,13C,15N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).

    Science.gov (United States)

    Lykouras, Michail V; Tsika, Aikaterini C; Lichière, Julie; Papageorgiou, Nicolas; Coutard, Bruno; Bentrop, Detlef; Spyroulias, Georgios A

    2018-04-01

    Macro domains are conserved protein domains found in eukaryotic organisms, bacteria, and archaea as well as in certain viruses. They consist of 130-190 amino acids and can bind ADP-ribose. Although the exact role of these domains is not fully understood, the conserved binding affinity for ADP-ribose indicates that this ligand is important for the function of the domain. Such a macro domain is also present in the non-structural protein 3 (nsP3) of Chikungunya Alphavirus (CHIKV) and consists of 160 amino acids. In this study we describe the high yield expression of the macro domain from CHIKV and its preliminary structural analysis via solution NMR spectroscopy. The macro domain seems to be folded in solution and an almost complete backbone assignment was achieved. In addition, the α/β/α sandwich topology with 4 α-helices and 6 β-strands was predicted by TALOS+.

  13. HNCA-TOCSY-CANH experiments with alternate {sup 13}C-{sup 12}C labeling: a set of 3D experiment with unique supra-sequential information for mainchain resonance assignment

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Koh; Gal, Maayan [Harvard Medical School, Department of Biochemistry and Molecular Pharmacology (United States); Takahashi, Hideo; Shimada, Ichio [National Institute of Advanced Industrial Science and Technology, Biomedicinal Information Research Center (Japan); Wagner, Gerhard, E-mail: gerhard_wagner@hms.harvard.edu [Harvard Medical School, Department of Biochemistry and Molecular Pharmacology (United States)

    2011-01-15

    Described here is a set of three-dimensional (3D) NMR experiments that rely on CACA-TOCSY magnetization transfer via the weak {sup 3}J(C{sub {alpha}}C{sub {alpha}}) coupling. These pulse sequences, which resemble recently described {sup 13}C detected CACA-TOCSY (Takeuchi et al. 2010) experiments, are recorded in {sup 1}H{sub 2}O, and use {sup 1}H excitation and detection. These experiments require alternate {sup 13}C-{sup 12}C labeling together with perdeuteration, which allows utilizing the small {sup 3}J(C{sub {alpha}}C{sub {alpha}}) scalar coupling that is otherwise masked by the stronger {sup 1}J{sub CC} couplings in uniformly {sup 13}C labeled samples. These new experiments provide a unique assignment ladder-mark that yields bidirectional supra-sequential information and can readily straddle proline residues. Unlike the conventional HNCA experiment, which contains only sequential information to the {sup 13}(C{sub {alpha}}) of the preceding residue, the 3D hnCA-TOCSY-caNH experiment can yield sequential correlations to alpha carbons in positions i-1, i + 1 and i-2. Furthermore, the 3D hNca-TOCSY-caNH and Hnca-TOCSY-caNH experiments, which share the same magnetization pathway but use a different chemical shift encoding, directly couple the {sup 15}N-{sup 1}H spin pair of residue i to adjacent amide protons and nitrogens at positions i-2, i-1, i + 1 and i + 2, respectively. These new experimental features make protein backbone assignments more robust by reducing the degeneracy problem associated with the conventional 3D NMR experiments.

  14. CACA-TOCSY with alternate {sup 13}C-{sup 12}C labeling: a {sup 13}C{sup {alpha}} direct detection experiment for mainchain resonance assignment, dihedral angle information, and amino acid type identification

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Koh [National Institute of Advanced Industrial Science and Technology (AIST), Biomedicinal Information Research Center (BIRC) (Japan); Frueh, Dominique P.; Sun, Zhen-Yu J.; Hiller, Sebastian; Wagner, Gerhard, E-mail: gerhard_wagner@hms.harvard.ed [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States)

    2010-05-15

    We present a {sup 13}C direct detection CACA-TOCSY experiment for samples with alternate {sup 13}C-{sup 12}C labeling. It provides inter-residue correlations between {sup 13}C{sup {alpha}} resonances of residue i and adjacent C{sup {alpha}s} at positions i - 1 and i + 1. Furthermore, longer mixing times yield correlations to C{sup {alpha}} nuclei separated by more than one residue. The experiment also provides C{sup {alpha}}-to-side chain correlations, some amino acid type identifications and estimates for {psi} dihedral angles. The power of the experiment derives from the alternate {sup 13}C-{sup 12}C labeling with [1,3-{sup 13}C] glycerol or [2-{sup 13}C] glycerol, which allows utilizing the small scalar {sup 3}J{sub CC} couplings that are masked by strong {sup 1}J{sub CC} couplings in uniformly {sup 13}C labeled samples.

  15. 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...

  16. ¹H, ¹³C, and ¹⁵N backbone and side chain resonance assignments of the C-terminal DNA binding and dimerization domain of v-Myc.

    Science.gov (United States)

    Kızılsavaş, Gönül; Saxena, Saurabh; Żerko, Szymon; Koźmiński, Wiktor; Bister, Klaus; Konrat, Robert

    2013-10-01

    The oncogenic transcription factor Myc is one of the most interesting members of the basic-helix-loop-helix-zipper (bHLHZip) protein family. Deregulation of Myc via gene amplification, chromosomal translocation or other mechanisms lead to tumorigenesis including Burkitt lymphoma, multiple myeloma, and many other malignancies. The oncogene myc is a highly potent transforming gene and capable to transform various cell types in vivo and in vitro. Its oncogenic activity initialized by deregulated expression leads to a shift of the equilibrium in the Myc/Max/Mad network towards Myc/Max complexes. The Myc/Max heterodimerization is a prerequisite for transcriptional functionality of Myc. Primarily, we are focusing on the apo-state of the C-terminal domain of v-Myc, the retroviral homolog of human c-Myc. Based on multi-dimensional NMR measurements v-Myc appears to be neither a fully structured nor a completely unstructured protein. The bHLHZip domain of v-Myc does not exist as a random coil but exhibits partially pre-formed α-helical regions in its apo-state. In order to elucidate the structural propensities of Myc in more detail, the backbone and side-chain assignments obtained here for apo-Myc are a crucial prerequisite for further NMR measurements.

  17. Metabolism of Nonessential N15-Labeled Amino Acids and the Measurement of Human Whole-Body Protein Synthesis Rates

    Science.gov (United States)

    Stein, T. P.; Settle, R. G.; Albina, J. A.; Dempsey, D. T.; Melnick, G.

    1991-01-01

    Eight N-15 labeled nonessential amino acids plus (15)NH4Cl were administered over a 10 h period to four healthy adult males using a primed-constant dosage regimen. The amount of N-15 excreted in the urine and the urinary ammonia, hippuric acid, and plasma alanine N-15 enrichments were measured. There was a high degree of consistency across subjects in the ordering of the nine compounds based on the fraction of N-15 excreted (Kendall coefficient of concordance W = 0.83, P is less than 0.01). Protein synthesis rates were calculated from the urinary ammonia plateau enrichment and the cumulative excretion of N-15. Glycine was one of the few amino acids that gave similar values by both methods.

  18. 1H, 13C, and 15N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA

    Science.gov (United States)

    Evans, Robert L.; Latham, John A.; Klinman, Judith P.; Wilmot, Carrie M.; Xia, Youlin

    2016-01-01

    The ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is a dehydrogenase cofactor synthesized by, but not exclusively used by, certain prokaryotes. RiPPs represent a rapidly expanding and diverse class of natural products—many of which have therapeutic potential—and the biosynthetic pathways for these are gaining attention. Five gene products from the pqq operon (PqqA, PqqB, PqqC, PqqD, and PqqE) are essential for PQQ biosynthesis. The substrate is the peptide PqqA, which is presented to the radical SAM enzyme PqqE by the small protein PqqD. PqqA is unstructured in solution, and only binds to PqqE when in complex with PqqD. PqqD is a member of a growing family of RiPP chaperone proteins (or domains in some cases) that present their associated peptide substrates to the initial RiPP biosynthesis enzymes. An X-ray crystal dimer structure exists for Xanthomonas campestris PqqD (PDB ID: 3G2B), but PqqD is now known to act as a monomer under physiological conditions. In this study, the PqqD truncation from naturally fused Methylobacterium extorquens (Mex) PqqCD was overexpressed in Escherichia coli and MexPqqA was chemically synthesized. Solution NMR 1H-,15N-HSQC chemical shift studies have identified the PqqD residues involved in binding PqqA, and 1H, 13C, and 15N peak assignments for PqqD alone and for PqqD bound to PqqA are reported herein. PMID:27638737

  19. Interactive Assignments for Online Students

    Directory of Open Access Journals (Sweden)

    Pam Lowry

    2009-04-01

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

  20. Espectro infrarrojo de [zn(mh34](re042 com substituicion isotópica 14n/15n

    Directory of Open Access Journals (Sweden)

    Claudio Téllez

    1983-11-01

    Full Text Available The infrared spectra of [Zn(15NH34] (Re042 and the isotopoc shift 14N/15N (Zn-n for the metal-ligand band, is reportedInforma-se o espectro infravermelho do complexo de Zn(II, [Zn(15NH341(Re04 e o deslocamento isotópico 14N/15N, para a banda metal - ligante v(Zn-N.

  1. 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.

  2. The assessment of nitrogen balance under flooding and saturation circumstances using N-15

    International Nuclear Information System (INIS)

    Abouseeda, M.; Khater, A.; Soliman, S.

    1995-01-01

    The use 15 N- balance techniques has already identified N-loss as a major problem in lowland rice management. Ammonium sulphate labelled with 5% N-15 atom ex. as a basal fertilized through special column in order to study the effect of flooding and saturation condition on the potential loss of nitrogen fertilizer. Rice straw at a rate of 1% was incorporated with the soil in order to study the role of rice straw (as a source of organic matter) on N-loss. Results show that the application of rice straw under flooding condition resulted in an increase of the biomass. It was observed that flooding circumstances may reduce the loss of nitrogen. Since N-recovery under flood and saturation rhizosphere (with plant) conditions were about 75% and 56%, respectively. The effect of rice root (rhizosphere) on nitrification has been observed. Results of flood and non flood rhizossphere show that the nitrogen recovery were about 75% and 86%, respectively. Results show an indirect evidence that the process of rhizosphere nitrification denitrification resulted in a significant amount of N-loss.It is evident that deep placement and flooded condition proved to be an effective means of reducing the potential of N-loss. 1 fig., 3 tabs

  3. Sequence-specific backbone ¹H, ¹³C and ¹⁵N assignments of the catalytic domain of the Escherichia coli protein tyrosine kinase, Wzc.

    Science.gov (United States)

    Temel, Deniz B; Dutta, Kaushik; Ghose, Ranajeet

    2014-04-01

    Protein tyrosine kinases in bacteria are structurally and functionally distinct from their eukaryotic counterparts. The largest family of bacterial tyrosine kinases, the BY-kinase family, is highly conserved in Gram-negative and Gram-positive species, and plays a central role in biofilm and capsule formation. In Escherichia coli the BY-kinase, Wzc, is a critical component of the machinery responsible for the synthesis and export of the exo-polysaccharide colanic acid, a key constituent of biofilms. Here we present the main-chain (1)H(N), (15)N, (13)C' and (13)Cα, side-chain (13)Cβ resonance assignments for a construct that encodes the entire 274-residue cytosolic catalytic domain of Wzc.

  4. Business Etiquette (My Favorite Assignment).

    Science.gov (United States)

    Forbes, Cassie

    1990-01-01

    Describes an assignment for a business communication course in which students give an oral presentation on some aspect of business manners and etiquette, thus increasing their awareness of the impact of social graces on communication in the business setting. (SR)

  5. 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...

  6. Ultra-violet absorption cross sections of isotopically substituted nitrous oxide species: 14N14NO, 15N14NO, 14N15NO and 15N15NO

    Directory of Open Access Journals (Sweden)

    P. von Hessberg

    2004-01-01

    Full Text Available The isotopically substituted nitrous oxide species 14N14NO, 15N14NO, 14N15NO and 15N15NO were investigated by ultra-violet (UV absorption spectroscopy. High precision cross sections were obtained for the wavelength range 181 to 218nm at temperatures of 233 and 283K. These data are used to calculate photolytic isotopic fractionation constants as a function of wavelength. The fractionation constants were used in a three-dimensional chemical transport model in order to simulate the actual fractionation of N2O in the stratosphere, and the results were found to be in good agreement with field studies.

  7. Mechanism of the reactions 14N(d,p)15N and 14N(d,n)15O by Doppler shift line shape method

    International Nuclear Information System (INIS)

    Abdel-Moneim, A.M.

    1976-06-01

    In this investigation the total and the differential absolute cross sections of the 14 N(d,p) 15 N reaction leading to excited states at 7.3, 8.3 and 9.05 MeV levels in 15 N and the 14 N(d,n) 15 O reaction leading to the 6.79 MeV level in 15 O, have been studied over the energy range from 0.5 MeV to 3 MeV. Doppler shift line shape method as well as γ-ray yield measurements have been used. The absolute cross sections are determined relative to the known 14 N(p,p) elastic differential cross sections. A comparison with previously determined values for the same reactions at selected energies shows good agreement in angular distribution as well as in absolute values. The total cross section for the d,p reaction shows a general energy dependence which is typical for direct reactions, but with minor contribution from compound nucleus formation at certain energy ranges. For the 14 N(d,n) 15 N reaction, the method applied is unique, since it allows the differential cross section to be studied all the way down to the threshold energy of deuterons at 2 MeV, with a detectorsystem efficiency which is constant over the entire range of neutron energies. The larger part of the energy range that has been investigated is dominated by a resonance at 2.55 π+ 0.05 MeV deuteron energy and a halfwidth depending on the amount of contribution from the direct reaction of the order of 200-400 keV. (JIW)

  8. 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

  9. Nitrate and ammonium influxes in soybean (Glycine max) roots : Direct comparison of N-13 and N-15 tracing

    NARCIS (Netherlands)

    Clarkson, DT; Gojon, A; Saker, LR; Wiersema, PK; Purves, JV; Tillard, P; Arnold, GM; Paans, AJM; Vaalburg, W; Stulen, [No Value

    We compared influxes and internal transport in soybean plants (Glycine max cv. Kingsoy) of labelled N from external solutions where either ammonium or nitrate was labelled with the stable isotope N-15 and the radioactive isotope N-13. The objective was to see whether mass spectrometric

  10. First Measurement of the 14N/15N Ratio in the Analog of the Sun Progenitor OMC-2 FIR4

    Science.gov (United States)

    Kahane, Claudine; Jaber Al-Edhari, Ali; Ceccarelli, Cecilia; López-Sepulcre, Ana; Fontani, Francesco; Kama, Mihkel

    2018-01-01

    We present a complete census of the 14N/15N isotopic ratio in the most abundant N-bearing molecules toward the cold envelope of the protocluster OMC-2 FIR4, the best known Sun progenitor. To this scope, we analyzed the unbiased spectral survey obtained with the IRAM 30 m telescope at 3, 2, and 1 mm. We detected several lines of CN, HCN, HNC, HC3N, N2H+, and their respective 13C and 15N isotopologues. The lines’ relative fluxes are compatible with LTE conditions, and moderate line opacities have been corrected via a population diagram method or theoretical relative intensity ratios of the hyperfine structures. The five species lead to very similar 14N/15N isotopic ratios, without any systematic difference between amine- and nitrile-bearing species as previously found in other protostellar sources. The weighted average of the 14N/15N isotopic ratio is 270 ± 30. This 14N/15N value is remarkably consistent with the [250–350] range measured for the local galactic ratio but significantly differs from the ratio measured in comets (around 140). High-angular resolution observations are needed to examine whether this discrepancy is maintained at smaller scales. In addition, using the CN, HCN, and HC3N lines, we derived a 12C/13C isotopic ratio of 50 ± 5.

  11. DNA Packaging Specificity of Bacteriophage N15 with an Excursion into the Genetics of a Cohesive End Mismatch.

    Directory of Open Access Journals (Sweden)

    Michael Feiss

    Full Text Available During DNA replication by the λ-like bacteriophages, immature concatemeric DNA is produced by rolling circle replication. The concatemers are processed into mature chromosomes with cohesive ends, and packaged into prohead shells, during virion assembly. Cohesive ends are generated by the viral enzyme terminase, which introduces staggered nicks at cos, an approx. 200 bp-long sequence containing subsites cosQ, cosN and cosB. Interactions of cos subsites of immature concatemeric DNA with terminase orchestrate DNA processing and packaging. To initiate DNA packaging, terminase interacts with cosB and nicks cosN. The cohesive ends of N15 DNA differ from those of λ at 2/12 positions. Genetic experiments show that phages with chromosomes containing mismatched cohesive ends are functional. In at least some infections, the cohesive end mismatch persists through cyclization and replication, so that progeny phages of both allelic types are produced in the infected cell. N15 possesses an asymmetric packaging specificity: N15 DNA is not packaged by phages λ or 21, but surprisingly, N15-specific terminase packages λ DNA. Implications for genetic interactions among λ-like bacteriophages are discussed.

  12. 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…

  13. 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....

  14. 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.

  15. ¹H, ¹³C, ¹⁵N backbone and side chain NMR resonance assignments of the N-terminal NEAr iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of Staphylococcus aureus.

    Science.gov (United States)

    Fonner, Brittany A; Tripet, Brian P; Lui, Mengyao; Zhu, Hui; Lei, Benfang; Copié, Valérie

    2014-04-01

    Staphylococcus aureus is an opportunistic pathogen that causes skin and severe infections in mammals. Critical to S. aureus growth is its ability to scavenge iron from host cells. To this effect, S. aureus has evolved a sophisticated pathway to acquire heme from hemoglobin (Hb) as a preferred iron source. The pathway is comprised of nine iron-regulated surface determinant (Isd) proteins involved in heme capture, transport, and degradation. A key protein of the heme acquisition pathway is the surface-anchored hemoglobin receptor protein IsdB, which is comprised of two NEAr transporter (NEAT) domains that act in concert to bind Hb and extract heme for subsequent transfer to downstream acquisition pathway proteins. Despite significant advances in the structural knowledge of other Isd proteins, the structural mechanisms and molecular basis of the IsdB-mediated heme acquisition process are not well understood. In order to provide more insights into the mode of function of IsdB, we have initiated NMR structural studies of the first NEAT domain of IsdB (IsdB(N1)). Herein, we report the near complete (1)H, (13)C and (15)N resonance assignments of backbone and side chain atoms, and the secondary structural topology of the 148-residue IsdB NEAT 1 domain. The NMR results are consistent with the presence of eight β-strands and one α-helix characteristic of an immunoglobulin-like fold observed in other NEAT domain family proteins. This work provides a solid framework to obtain atomic-level insights toward understanding how IsdB mediates IsdB-Hb protein-protein interactions critical for heme capture and transfer.

  16. Fleet Assignment Using Collective Intelligence

    Science.gov (United States)

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

    2004-01-01

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

  17. Correlation between low-temperature creep and intergranular diffusion of Kh16N15M3B type steel

    International Nuclear Information System (INIS)

    Solonin, M.I.; Kondrat'ev, V.P.; Krasina, T.A.; Voejkov, V.P.; Tarasyuk, V.B.; Fedorov, G.B.; Ryabenko, A.V.

    1990-01-01

    The results are presented for Kh16N15M3B type steel containing different amounts of carbon, molybdenum and niobium that was tested the diffusion mobility of iron-59 species. It is shown that at 400-500 deg C the diffusion of iron-59 is only intergranular. The correlation established between creep and diffusion. It is shwn that the activation energies for creep and intergranular diffusion correlate. 5 refs.; 4 figs.; 3 tabs

  18. Influence of N-15 labelled urea and azotobacter on corn yield and nitrogen budget as affected by organic matter

    International Nuclear Information System (INIS)

    Soliman, S.M.; Abdelmonem, M.A.

    1995-01-01

    As sandy soils of Egypt are poor in their chemical and physical properties, their fertilization with chemical or biological fertilizer is essential. The reported greenhouse experiment was conducted, using sandy soil of Egypt to evaluate the impact of urea fertilizer, applied alone combined with nitrification inhibitors (DCD) or (N-serve) on (corn yield and N-losses) as compared with inoculation with azotobacter under organic matter treatment as soil amendment. Total dry matter was recorded, while N-uptake by corn, and N-recovery due to inoculation with azotobacter was determined using N-15 dilution technique. Data obtained indicated that, application of DCD or N-serve with urea increased corn dry matter weight as well N-15 recovery. Significant increase in N-recovery was obtained due to nitrification inhibitor application and azotobacter inoculation. N-15 losses were reduced due to application of DCD and N-serve from 45% and respectively. Use of bio fertilizers and nitrification inhibitors could play an important role in corn production in sandy soil, as well as decrease the losses of applied N-fertilizers. fig., 3 tabs

  19. 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...... 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...

  20. 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.

  1. More General Optimal Offset Assignment

    Directory of Open Access Journals (Sweden)

    Sven Mallach

    2015-06-01

    Full Text Available This manuscript presents exact approaches to the general offset assignment problem arising in the address code generation phase of compilers for application-specific processors. First, integer programming models for architecture-dependent and theoretically motivated special cases of the problem are established. Then, these models are extended to provide the first widely applicable formulations for the most general problem setting, supporting processors with several address registers and complex addressing capabilities. Existing heuristics are similarly extended and practical applicability of the proposed methods is demonstrated by experimental evaluation using an established and large benchmark set. The experiments allow us to study the impact of exploiting more complex memory addressing capabilities on the address computation costs of real-world programs. We also show how to integrate operand reordering techniques for commutative instructions into existing solution approaches.

  2. The Random Quadratic Assignment Problem

    Science.gov (United States)

    Paul, Gerald; Shao, Jia; Stanley, H. Eugene

    2011-11-01

    The quadratic assignment problem, QAP, is one of the most difficult of all combinatorial optimization problems. Here, we use an abbreviated application of the statistical mechanics replica method to study the asymptotic behavior of instances in which the entries of at least one of the two matrices that specify the problem are chosen from a random distribution P. Surprisingly, the QAP has not been studied before using the replica method despite the fact that the QAP was first proposed over 50 years ago and the replica method was developed over 30 years ago. We find simple forms for C min and C max , the costs of the minimal and maximum solutions respectively. Notable features of our results are the symmetry of the results for C min and C max and their dependence on P only through its mean and standard deviation, independent of the details of P.

  3. Mechanical resonator

    OpenAIRE

    Padowitz, David; Matsiev, L; Kolosov, Oleg

    2004-01-01

    A sensor and methods for making and using the same in which a mechanical resonator is employed, comprising a resonator portion for resonating in a fluid without the substantial generation of acoustic waves; and an electrical connection between the resonator portion for oscillating and a source of an input signal; wherein the portion for resonating, the electrical connection or both includes a base material and a performance-tuning material that is different from the base material.

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

    Science.gov (United States)

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

    2011-01-01

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

  5. 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.

  6. 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

  7. Assigning historic responsibility for extreme weather events

    Science.gov (United States)

    Otto, Friederike E. L.; Skeie, Ragnhild B.; Fuglestvedt, Jan S.; Berntsen, Terje; Allen, Myles R.

    2017-11-01

    Recent scientific advances make it possible to assign extreme events to human-induced climate change and historical emissions. These developments allow losses and damage associated with such events to be assigned country-level responsibility.

  8. 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

  9. Lexical Stress Assignment in Italian Developmental Dyslexia

    Science.gov (United States)

    Paizi, Despina; Zoccolotti, Pierluigi; Burani, Cristina

    2011-01-01

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

  10. Assigning Homework to Couples and Families

    Science.gov (United States)

    Dattilio, Frank M.; Dickson, Jan

    2007-01-01

    Homework assignments, or "out-of-session assignments," have gained popularity among couple and family therapists due to their potential to solidify the work achieved during the course of therapy and to help clients take responsibility for their own change. Homework assignments also serve as a testing ground in therapy to determine what works and…

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2000-06-15

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

  12. Measurement of the 20 and 90 keV Resonances in the O-18(p,alpha)N-15 Reaction via the Trojan Horse Method

    Czech Academy of Sciences Publication Activity Database

    La Cognata, M.; Spitareli, C.; Mukhamedzhanov, A. M.; Irgaziev, B.; Tribble, R. E.; Banu, A.; Cherubini, S.; Coc, A.; Crucilla, V.; Goldberg, V.Z.; Gulino, M.; Kiss, G. G.; Lamia, L.; Mrázek, Jaromír; Pizzone, R. G.; Puglia, S. M. R.; Rapisarda, G. G.; Romano, S.; Sergi, M. L.; Tabacaru, G.; Trache, L.; Trzaska, W.; Tumino, A.

    2008-01-01

    Roč. 101, č. 15 (2008), 152501/1-152501/4 ISSN 0031-9007 Institutional research plan: CEZ:AV0Z10480505 Keywords : ASYMPTOTIC GIANT BRANCH * O-18 * ENERGIES Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 7.180, year: 2008

  13. Stereospecific assignments in proteins using exact NOEs

    Energy Technology Data Exchange (ETDEWEB)

    Orts, Julien; Vögeli, Beat; Riek, Roland, E-mail: roland.riek@phys.chem.ethz.ch [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry (Switzerland); Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

    2013-10-18

    Recently developed methods to measure distances in proteins with high accuracy by “exact” nuclear Overhauser effects (eNOEs) make it possible to determine stereospecific assignments, which are particularly important to fully exploit the accuracy of the eNOE distance measurements. Stereospecific assignments are determined by comparing the eNOE-derived distances to protein structure bundles calculated without stereospecific assignments, or an independently determined crystal structure. The absolute and relative CYANA target function difference upon swapping the stereospecific assignment of a diastereotopic group yields the respective stereospecific assignment. We applied the method to the eNOE data set that has recently been obtained for the third immunoglobulin-binding domain of protein G (GB3). The 884 eNOEs provide relevant data for 47 of the total of 75 diastereotopic groups. Stereospecific assignments could be established for 45 diastereotopic groups (96 %) using the X-ray structure, or for 27 diastereotopic groups (57 %) using structures calculated with the eNOE data set without stereospecific assignments, all of which are in agreement with those determined previously. The latter case is relevant for structure determinations based on eNOEs. The accuracy of the eNOE distance measurements is crucial for making stereospecific assignments because applying the same method to the traditional NOE data set for GB3 with imprecise upper distance bounds yields only 13 correct stereospecific assignments using the X-ray structure or 2 correct stereospecific assignments using NMR structures calculated without stereospecific assignments.

  14. Snake resonances

    International Nuclear Information System (INIS)

    Tepikian, S.

    1989-01-01

    Siberian Snakes provide a practical means of obtaining polarized proton beams in large accelerators. The effect of snakes can be understood by studying the dynamics of spin precession in an accelerator with snakes and a single spin resonance. This leads to a new class of energy independent spin depolarizing resonances, called snake resonances. In designing a large accelerator with snakes to preserve the spin polarization, there is an added constraint on the choice of the vertical betatron tune due to the snake resonances

  15. 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

  16. Influence of N-15 enrichment on neutronics, costs and C-14 production in nitride fuel cycle scenarios

    International Nuclear Information System (INIS)

    Wallenius, Janne; Arai, Yasuo; Minato, Kazuo

    2004-01-01

    The C-14 production for different closed fuel cycle scenarios has been investigated. If nitride fuel is used in fast reactors and ADSs dedicated to management of plutonium and minor actinides, an N-15 enrichment level of about 99% is required for the nitride cores to produce the same amount of C-14 as the oxide cores in the power park. The corresponding cost penalty for fuel fabrication is estimated to be larger than 25%. If reprocessing is included in the costs for fuel operations, the penalty is of the order of 5-10%, provided that a closed gas cycle is implemented for the fabrication. If nitride fuels are used only for minor actinide management in ADS, the required enrichment level is about 93%, and the cost penalty is less than 10%. (author)

  17. Biological nitrogen fixation by faba bean, pea and vetch, using isotopic techniques (N-15) and two reference crops

    International Nuclear Information System (INIS)

    Calvache, Marcelo; Bernal, Gustavo

    1991-01-01

    A field experiment was carried out on a Typic Dystrandept soil at Santa Catalina Experimental Station, Cutuglagua, Pichincha, Ecuador. The objectives were to quantify faba bean (Vicia faba) pea (Pisum sativum) and vetch (Vicia sativa) biological nitrogen fixation using N-15 isotopic technique and to evaluate suitability of reference crops for such quantification. Higher values of biological nitrogen fixation were obtained using maize (Zea mays L.) than using wheat (Triticum vurgare) as reference crops. The average values were 85 and 81 per cent for vetch; 73 and 69 per cent for faba bean; and 34 and 18 per cent for pea, respectively. It was assumed that nitrogen use efficiency should be the same for fixing and no fixing crop, but it was observed that a reference crop with low nitrogen use efficiency underestimates legume biological nitrogen fixation. Results suggest that greater caution is needed when selecting reference crops for legumes with low nitrogen fixation

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

    Science.gov (United States)

    Frueh, Dominique P.

    2014-01-01

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

  19. 849 RESONANCE | September 2013

    Indian Academy of Sciences (India)

    IAS Admin

    849. RESONANCE | September 2013. Page 2. 850. RESONANCE | September 2013. Page 3. 851. RESONANCE | September 2013. Page 4. 852. RESONANCE | September 2013. Page 5. 853. RESONANCE | September 2013. Page 6. 854. RESONANCE | September 2013. Page 7. 855. RESONANCE | September 2013.

  20. Nitrogen content and delta N-15 of marine algae and associated waters of Maui, Hawaii, from 2012-07-28 to 2014-04-01 (NCEI Accession 0156294)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set includes nutrient data related to algal and water samples collected between 2012 and 2014 on Maui, Hawaii. Algal tissue N%, C:N ratios, and delta N-15...

  1. Backbone and sidechain 1H, 13C and 15N resonance assignments of the human brain-type fatty acid binding protein (FABP7) in its apo form and the holo forms binding to DHA, oleic acid, linoleic acid and elaidic acid

    DEFF Research Database (Denmark)

    Oeemig, Jesper S; Jørgensen, Mathilde L; Hansen, Mikka S

    2009-01-01

    In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid.......In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid....

  2. Effect of Organic and Inorganic nitrogen Fertilizers on Salinity tolerance in Sorghum Plants Grown in sandy Soil Using N-15

    International Nuclear Information System (INIS)

    Ismail, M.M.

    2011-01-01

    A pot experiment was carried out in the green house to study the effect of compost, farmyard manure (FYM) and/or ammonium sulphate on salinity tolerance and nutrients-uptake by sorghum plants grown on sandy soil using N-15. Nitrogen was added at full dose of 100 mg N/kg soil. In general, dry matter accumulation as well as N, P and K-uptake by root and stalk of sorghum plants were significantly fluctuated between decrease and increase as influenced by the combined effect of water salinity levels and organic nitrogen source. The data showed that the application of organic sources decreased the adverse effect of salinity on dry matter yield of root and stalk of sorghum plants. The lowest dry matter yield was recorded when the plant received mineral fertilizer combined with irrigation of high concentration of diluted sea water. In the same time, root and stalk of sorghum plants were more dependent on N derived from organic sources than those derived from fertilizer. Fertilizer use efficiency (FUE %) was negatively affected by increasing water salinity levels under all treatments of organic and inorganic nitrogen fertilizer

  3. Biological nitrogen fixation in common beans(kidney); under fungicidal effects(vitavox), using N-15 isotopic methodology

    International Nuclear Information System (INIS)

    Gomez, Marco; Arahana, Venancio; Bernal, Gustavo

    1991-01-01

    This research was conducted in the EXPERIMENTAL EDUCATIONAL FIELD L a Tola , located in Tumbaco, Pichincha. The purpose was to evaluate the fixative efficiency of five strains of Rhizobium leguminosarum Bv. phaseoli under the effect of fungicidy, using the N-15 isotopic methodology. The experimental utilized desing was that of split plot with four replications. The area of the experimental plot in the assay was 2.4 Sq. m. (1.2 m x 2 m) and had three 0.60 m. appart furrows. The analized variables were: combined dry weight of stem and leaves and pods; total nitrogen of steam and leaves and pod; percentage and amount of fixed nitrogen (NFx per cent, QNFx); and the yield. The strains of greater nitrogen fixation were 1073 and 1020, with 40 NFx per cent and 31.0 kg NFx per ha. vitavax fungicidy had influence on all analized variables and did not affect the fixation of nitrogen of the strains for the yield of the Cargabello variety of bean

  4. Synchrobetatron resonances

    International Nuclear Information System (INIS)

    1977-03-01

    At the 1975 Particle Accelerator Conference it was reported that a class of resonances were observed in SPEAR II that had not appeared before in SPEAR I. While the existence of sideband resonances of the main betatron oscillation frequencies has been previously observed and analyzed, the resonances observed in SPEAR do not appear to be of the same variety. Experiments were performed at SPEAR to identify the mechanism believed to be the most likely explanation. Some of the current experimental knowledge and theoretical views on the source of these resonances are presented

  5. Snake resonances

    International Nuclear Information System (INIS)

    Tepikian, S.

    1988-01-01

    Siberian Snakes provide a practical means of obtaining polarized proton beams in large accelerators. The effect of snakes can be understood by studying the dynamics of spin precession in an accelerator with snakes and a single spin resonance. This leads to a new class of energy independent spin depolarizing resonances, called snake resonances. In designing a large accelerator with snakes to preserve the spin polarization, there is an added constraint on the choice of the vertical betatron tune due to the snake resonances. 11 refs., 4 figs

  6. 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…

  7. 7 CFR 784.15 - Assignments.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Assignments. 784.15 Section 784.15 Agriculture Regulations of the Department of Agriculture (Continued) FARM SERVICE AGENCY, DEPARTMENT OF AGRICULTURE SPECIAL PROGRAMS 2004 EWE LAMB REPLACEMENT AND RETENTION PAYMENT PROGRAM § 784.15 Assignments. Any person...

  8. 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

  9. 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…

  10. 24 CFR 221.770 - Assignment option.

    Science.gov (United States)

    2010-04-01

    ... MODERATE INCOME MORTGAGE INSURANCE-SAVINGS CLAUSE Contract Rights and Obligations-Moderate Income Projects... mortgagee's approved underwriter on or before November 30, 1983) has the option to assign, transfer and... direct the mortgagee to assign, transfer and deliver the original credit instrument, and the mortgage...

  11. Frequency assignment for satellite multilevel SCPC systems

    Science.gov (United States)

    Lau, Yuk-Hong; Skellern, D. J.

    1991-01-01

    A method for searching the frequency assignment for satellite multilevel SCPC systems is proposed based on the method for the case of equal carrier systems. The quality of assignment improves significantly on published results. The method requires only very short computations times.

  12. NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

    Science.gov (United States)

    Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R

    2011-05-01

    Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure-activity relationship, protein-protein and protein-ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement's (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB) , Berlin, Germany, April 10-13, pp. 176-187. ACM Press, New York, NY. J. Comp. Bio. , (2004), 11, pp. 277-298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR , 29, 111-138). Our approach uses NVR's scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs), instead of NH RDCs which NVR requires. We test our technique on NVR's data set as well as on four new proteins. Our results are comparable to NVR's assignment accuracy on NVR's test set, but higher on novel proteins. Our approach allows partial assignments. It is also complete and can return the optimum as well as near-optimum assignments. Furthermore, it allows us to analyze the information content of each data type and is easily extendable to accept new forms of input data, such as additional RDCs.

  13. Two new Ni(II) Schiff base complexes : X-ray absolute structure determination, synthesis of a N-15-labelled complex and full assignment of its H-1 NMR and C-13 NMR spectra

    NARCIS (Netherlands)

    Langer, Vratislav; Popkov, Alexander; Nadvornik, Milan; Lycka, Antonin

    2007-01-01

    The Ni(II) complex of the Schiff base of (S)-N-(2-benzoyl-4-chlorophenyl)-1-benzylpyrrolidine-2-carboxamide and glycine (1) [GKCI] and the hemihydrate of the Ni(II) complex of the Schiff base of (S)-N-(2-benzoylphenyl)-1-benzylpyrrolidine-2-carboxamide and 2-aminoisobutiric acid (2) Me(2)GK] were

  14. [Adenovirus-mediated killing of hepatocellular carcinoma HepG2 cells by heterogeneous fusion gene NT4p53(N15)Ant].

    Science.gov (United States)

    Li, Yue-ping; Qiu, Shu-dong; Song, Li-ping; Wang, Quan-ying; Yang, Guang-xiao

    2007-07-01

    OBJECTIVE To construct a recombinant adenovirus Ad.NT4p53(N15)Ant and explore its cytotoxic effect against hepatocellular carcinoma HepG2 cells in vitro. The recombinant adenovirus containing the fusion gene of neurotrophin 4 (NT4)signal peptide, N-terminal residues (12-26) of p53 and 17 amino acid Drosophila homeobox protein Antennapedia (Ant) was constructed by gene cloning protocol. The effect of this fusion gene on HepG2 cells was evaluated by MTT assay, PI staining and flow cytometry. The fusion gene Ad.NT4p53(N15)Ant was successfully constructed, as verified by restriction endonuclease digestion and PCR. Ad.NT4p53(N15)Ant could strongly suppress the growth of HepG2 cells (with a growth inhibition rate of 63.3% 48 h after infection) without affecting NIH-3T3 cells. Flow cytometry showed that Ad.NT4p53(N15)Ant could induce obvious apoptosis of HepG2 cells. The recombinant adenovirus containing NT4p53(N15)Ant fusion gene can inhibit the growth the of HepG2 cells in vitro partially by inducing cell apoptosis.

  15. 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

  16. Photothermal resonance

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention relates to a method for detecting photo-thermal absorbance of a material utilising a mechanically temperature sensitive resonator (20) and a sample being arrange in thermal communication with the temperature sensitive resonator. The present invention further relates...

  17. Optimal processor assignment for pipeline computations

    Science.gov (United States)

    Nicol, David M.; Simha, Rahul; Choudhury, Alok N.; Narahari, Bhagirath

    1991-01-01

    The availability of large scale multitasked parallel architectures introduces the following processor assignment problem for pipelined computations. Given a set of tasks and their precedence constraints, along with their experimentally determined individual responses times for different processor sizes, find an assignment of processor to tasks. Two objectives are of interest: minimal response given a throughput requirement, and maximal throughput given a response time requirement. These assignment problems differ considerably from the classical mapping problem in which several tasks share a processor; instead, it is assumed that a large number of processors are to be assigned to a relatively small number of tasks. Efficient assignment algorithms were developed for different classes of task structures. For a p processor system and a series parallel precedence graph with n constituent tasks, an O(np2) algorithm is provided that finds the optimal assignment for the response time optimization problem; it was found that the assignment optimizing the constrained throughput in O(np2log p) time. Special cases of linear, independent, and tree graphs are also considered.

  18. 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...

  19. The Assignment Game : The Reduced Game

    OpenAIRE

    Guillermo OWEN

    1992-01-01

    Let v be an assignment game. For a given reference payoff vector (x; y), and a coalition S, bargaining within the coalition can be represented by either the reduced game or the derived game. It is known that the reduced game need not be an assignment game (in fact, it need not be super additive) while the derived game is another assignment game, with modified reservation prices. We prove that, when the reference vector is in the core of the game, the derived game is the super additive cover o...

  20. Protein residue linking in a single spectrum for magic-angle spinning NMR assignment

    Energy Technology Data Exchange (ETDEWEB)

    Andreas, Loren B.; Stanek, Jan; Marchand, Tanguy Le; Bertarello, Andrea; Paepe, Diane Cala-De; Lalli, Daniela; Krejčíková, Magdaléna; Doyen, Camille; Öster, Carl [Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (CNRS, ENS Lyon, UCB Lyon 1) (France); Knott, Benno; Wegner, Sebastian; Engelke, Frank [Bruker Biospin (Germany); Felli, Isabella C.; Pierattelli, Roberta [University of Florence, Department of Chemistry “Ugo Schiff“and Magnetic Resonance Center (CERM) (Italy); Dixon, Nicholas E. [University of Wollongong, School of Chemistry (Australia); Emsley, Lyndon; Herrmann, Torsten; Pintacuda, Guido, E-mail: guido.pintacuda@ens-lyon.fr [Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (CNRS, ENS Lyon, UCB Lyon 1) (France)

    2015-07-15

    Here we introduce a new pulse sequence for resonance assignment that halves the number of data sets required for sequential linking by directly correlating sequential amide resonances in a single diagonal-free spectrum. The method is demonstrated with both microcrystalline and sedimented deuterated proteins spinning at 60 and 111 kHz, and a fully protonated microcrystalline protein spinning at 111 kHz, with as little as 0.5 mg protein sample. We find that amide signals have a low chance of ambiguous linkage, which is further improved by linking in both forward and backward directions. The spectra obtained are amenable to automated resonance assignment using general-purpose software such as UNIO-MATCH.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2000-07-01

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

  2. Homework assignments in couple and family therapy.

    Science.gov (United States)

    Dattilio, Frank M

    2002-05-01

    Homework has been cited as an integral part of a number of theoretical orientations and therapy formats; unfortunately, very little has been written about its use with couples and families. This is despite the fact that many couple and family therapists espouse the use of homework or out-of-session assignments in order to help the effects of therapy jell. This article reviews some of the empirical literature on homework assignments and their effectiveness in the domain of therapy for families and couples. It also highlights the effectiveness of and the need for out-of-session assignments in treatment. A case illustration is used to demonstrate how homework assignments may be used as a significant change agent in couple and family treatment. Copyright 2002 Wiley Periodicals, Inc.

  3. 12 CFR 25.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... of discriminatory or other illegal credit practices in any geography by the bank or in any assessment...) of this section on the bank's assigned rating, the OCC considers the nature, extent, and strength of...

  4. 12 CFR 228.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... evidence of discriminatory or other illegal credit practices in any geography by the bank or in any... described in paragraph (c)(1) of this section on the bank's assigned rating, the Board considers the nature...

  5. 12 CFR 345.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... credit practices in any geography by the bank or in any assessment area by any affiliate whose loans have... section on the bank's assigned rating, the FDIC considers the nature, extent, and strength of the evidence...

  6. 12 CFR 563e.28 - Assigned ratings.

    Science.gov (United States)

    2010-01-01

    ... practices in any geography by the savings association or in any assessment area by any affiliate whose loans...) of this section on the savings association's assigned rating, the OTS considers the nature, extent...

  7. Genetic algorithms for air traffic assignment

    OpenAIRE

    Delahaye , Daniel; Alliot , Jean-Marc; Schoenauer , Marc; Farges , Jean-Loup

    1994-01-01

    International audience; In this paper, we show how genetic algorithms can be used to compute automatically a traffic assignment of aircraft on the air network to increase Air Traffic Control capacity in high density areas.

  8. 12C/13C and 14N/15N isotopic ratios in HCN in the middle atmosphere of Titan from Cassini/CIRS data

    Science.gov (United States)

    Mathé, Christophe; Vinatier, Sandrine; Bézard, Bruno; Nixon, Conor A.

    2017-10-01

    Our study aims at constraining the 12C/13C and 14N/15N isotopic ratios in HCN, the most abundant nitrile in Titan’s atmosphere, which can provide information on physical and chemical process occurring during the formation and/or destruction of this molecule.Over the last decade, several estimations of the 12C/13C and 14N/15N isotopic ratios in HCN were performed from ground-based, Herschel and Cassini observations (Bézard et al,2014). The 14N/15N ratio lies in the range 56-76, which corresponds to half of the 14N/15N ratio in N2 (major N-bearing molecule in Titan’s atmosphere). This nitrogen isotopic fractionation mostly originates from the photodissociation of N2 (Liang et al, 2007). The 12C/13C ratio lies in the range 75-108, in agreement with the 12C/13C ratio in CH4 (major C-bearing molecule). Recent disk-averaged ALMA observations indicate 12C/13C and 14N/15N ratios equal to ˜90 and ˜72, respectively (Molter et al, 2016).Vinatier et al (2007) derived 14N/15N and 12C/13C ratios in two different regions (equator and north pole) from Cassini/CIRS (Composite InfraRed Spectrometer) observations at the beginning of the Cassini mission. 14N/15N was similar for both latitudes while the 12C/13C ratio displayed a possible enhancement at the equator.We present here a new study of the 12C/13C and 14N/15N isotopic ratios in HCN from CIRS. We analyzed limb observations (0.5 cm-1 resolution) from northern winter to early spring at poles, mid-latitudes and equator in order to investigate potential spatial and seasonal changes of these isotopic ratios in Titan’s middle atmosphere. These preliminary results will be presented and compared with previous observations.References:Bézard et al., Cambrigde University Press, 2014Liang et al., The Astrophysical Jounral Letters, 2007Molter et al., The Astronomical Journal, 2016Vinatier et al., Icarus, 2007

  9. Changes in mechanical properties of the OKh16N15M3B steel in the temperature range of radiation-induced swelling

    International Nuclear Information System (INIS)

    Neustroev, V.S.; Golovanov, V.N.; Povstyanko, A.V.; Shamardin, V.K.

    1986-01-01

    Presented are the results of investigations of both swelling and mechanical properties of the fuel element cans of BOR-60 reactor of the 0Kh16N15M3B steel after austenitization. The dose-temperature dependences have been plotted swelling and radiation-induced porosity parameters as well as for mechanical properties of the above steel. Interpretation of changes in some 0Kh16N15M3B steel mechanical properties with dose and temperature has been proposed based on Orovan's mechanism and on that for crack nucleation with voids present

  10. 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

  11. 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...

  12. 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.

  13. Physician in Triage Versus Rotational Patient Assignment.

    Science.gov (United States)

    Traub, Stephen J; Bartley, Adam C; Smith, Vernon D; Didehban, Roshanak; Lipinski, Christopher A; Saghafian, Soroush

    2016-05-01

    Physician in triage and rotational patient assignment are different front-end processes that are designed to improve patient flow, but there are little or no data comparing them. To compare physician in triage with rotational patient assignment with respect to multiple emergency department (ED) operational metrics. Design-Retrospective cohort review. Patients-Patients seen on 23 days on which we utilized a physician in triage with those patients seen on 23 matched days when we utilized rotational patient assignment. There were 1,869 visits during physician in triage and 1,906 visits during rotational patient assignment. In a simple comparison, rotational patient assignment was associated with a lower median length of stay (LOS) than physician in triage (219 min vs. 233 min; difference of 14 min; 95% confidence interval [CI] 5-27 min). In a multivariate linear regression incorporating multiple confounders, there was a nonsignificant reduction in the geometric mean LOS in rotational patient assignment vs. physician in triage (204 min vs. 217 min; reduction of 6.25%; 95% CI -3.6% to 15.2%). There were no significant differences between groups for left before being seen, left subsequent to being seen, early (within 72 h) returns, early returns with admission, or complaint ratio. In a single-site study, there were no statistically significant differences in important ED operational metrics between a physician in triage model and a rotational patient assignment model after adjusting for confounders. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. 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.

  15. Effects of NaCl salinity on N-15-nitrate fluxes and specific root length in the halophyte Plantago maritima L.

    NARCIS (Netherlands)

    Rubinigg, M; Posthumus, F; Ferschke, M; Elzenga, JTM; Stulen, [No Value

    The effect of salinity on nitrate influx, efflux, nitrate net uptake rate and net nitrogen translocation to the shoot was assessed in a N-15 steady state labelling experiment in the halophyte Plantago maritima L. raised for 14 days on solution supplied with 50, 100 and 200 mol m(-3) sodium chloride

  16. Genesis herschreven en geïnterpreteerd in het boek Jubileeën, nader toegelicht met een vergelijking van Genesis 17 en Jubileeën 15

    NARCIS (Netherlands)

    Ruiten, Jacques T.A.G.M. van

    2010-01-01

    Jacques T.A.G.M. van Ruiten, “Genesis herschreven en geïnterpreteerd in het boek Jubileeën, nader toegelicht met een vergelijking van Genesis 17 en Jubileeën 15,” Nederlands theologisch tijdschrift 64 (2010): 32-50.

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

    Directory of Open Access Journals (Sweden)

    de Brevern Alexandre G

    2005-09-01

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

  18. The Airport Gate Assignment Problem: A Survey

    Science.gov (United States)

    Ghaleb, Mageed A.; Salem, Ahmed M.

    2014-01-01

    The airport gate assignment problem (AGAP) is one of the most important problems operations managers face daily. Many researches have been done to solve this problem and tackle its complexity. The objective of the task is assigning each flight (aircraft) to an available gate while maximizing both conveniences to passengers and the operational efficiency of airport. This objective requires a solution that provides the ability to change and update the gate assignment data on a real time basis. In this paper, we survey the state of the art of these problems and the various methods to obtain the solution. Our survey covers both theoretical and real AGAP with the description of mathematical formulations and resolution methods such as exact algorithms, heuristic algorithms, and metaheuristic algorithms. We also provide a research trend that can inspire researchers about new problems in this area. PMID:25506074

  19. 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.

  20. Assignment Procedure Biases in Randomised Policy Experiments

    DEFF Research Database (Denmark)

    Aldashev, Gani; Kirchsteiger, Georg; Sebald, Alexander

    2017-01-01

    's propensity to act reciprocally. When people are motivated by reciprocity, the choice of assignment procedure influences the RCTs’ findings. We show that even credible and explicit randomisation procedures do not guarantee an unbiased prediction of the impact of policy interventions; however, they minimise......Randomised controlled trials (RCT) have gained ground as the dominant tool for studying policy interventions in many fields of applied economics. We analyse theoretically encouragement and resentful demoralisation in RCTs and show that these might be rooted in the same behavioural trait – people...... any bias relative to other less transparent assignment procedures....

  1. Optimization of Rated Officer Staff Assignments

    Science.gov (United States)

    2007-06-01

    determinant +1, -1 or 0, which holds for the assignment problem (Bazaraa et al., 1990). The Unimodularity Theorem states for an integer matrix A with...The constraints of the assignment problem, in matrix notation, are defined as in part (b) of the Unimodularity Theorem , therefore since the coefficient...ABM Match Flow output for cA Ac C∈ N = 1 2( , ),NCN N ,...,N where is the navigator Match Flow output for cN Nc C∈ P = 1 2( , ), PCP P ,...,P

  2. 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....

  3. Multiquark Resonances

    CERN Document Server

    Esposito, A.; Polosa, A.D.

    2016-01-01

    Multiquark resonances are undoubtedly experimentally observed. The number of states and the amount of details on their properties has been growing over the years. It is very recent the discovery of two pentaquarks and the confirmation of four tetraquarks, two of which had not been observed before. We mainly review the theoretical understanding of this sector of particle physics phenomenology and present some considerations attempting a coherent description of the so called X and Z resonances. The prominent problems plaguing theoretical models, like the absence of selection rules limiting the number of states predicted, motivate new directions in model building. Data are reviewed going through all of the observed resonances with particular attention to their common features and the purpose of providing a starting point to further research.

  4. Cognitive Function and 3-Tesla Magnetic Resonance Imaging Tractography of White Matter Hyperintensities in Elderly Persons

    Directory of Open Access Journals (Sweden)

    William Reginold

    2015-10-01

    Full Text Available Background/Aims: This study used 3-Tesla magnetic resonance imaging (MRI tractography to determine if there was an association between tracts crossing white matter hyperintensities (WMH and cognitive function in elderly persons. Methods: Brain T2-weighted fluid-attenuated inversion recovery (FLAIR and diffusion tensor MRI scans were acquired in participants above the age of 60 years. Twenty-six persons had WMH identified on T2 FLAIR scans. They completed a battery of neuropsychological tests and were classified as normal controls (n = 15 or with Alzheimer's dementia (n = 11. Tractography was generated by the Fiber Assignment by Continuous Tracking method. All tracts that crossed WMH were segmented. The average fractional anisotropy and average mean diffusivity of these tracts were quantified. We studied the association between cognitive test scores with the average mean diffusivity and average fractional anisotropy of tracts while controlling for age, total WMH volume and diagnosis. Results: An increased mean diffusivity of tracts crossing WMH was associated with worse performance on the Wechsler Memory Scale-III Longest Span Forward (p = 0.02. There was no association between the fractional anisotropy of tracts and performance on cognitive testing. Conclusion: The mean diffusivity of tracts crossing WMH measured by tractography is a novel correlate of performance on the Wechsler Memory Scale-III Longest Span Forward in elderly persons.

  5. Cognitive Function and 3-Tesla Magnetic Resonance Imaging Tractography of White Matter Hyperintensities in Elderly Persons.

    Science.gov (United States)

    Reginold, William; Luedke, Angela C; Tam, Angela; Itorralba, Justine; Fernandez-Ruiz, Juan; Reginold, Jennifer; Islam, Omar; Garcia, Angeles

    2015-01-01

    This study used 3-Tesla magnetic resonance imaging (MRI) tractography to determine if there was an association between tracts crossing white matter hyperintensities (WMH) and cognitive function in elderly persons. Brain T2-weighted fluid-attenuated inversion recovery (FLAIR) and diffusion tensor MRI scans were acquired in participants above the age of 60 years. Twenty-six persons had WMH identified on T2 FLAIR scans. They completed a battery of neuropsychological tests and were classified as normal controls (n = 15) or with Alzheimer's dementia (n = 11). Tractography was generated by the Fiber Assignment by Continuous Tracking method. All tracts that crossed WMH were segmented. The average fractional anisotropy and average mean diffusivity of these tracts were quantified. We studied the association between cognitive test scores with the average mean diffusivity and average fractional anisotropy of tracts while controlling for age, total WMH volume and diagnosis. An increased mean diffusivity of tracts crossing WMH was associated with worse performance on the Wechsler Memory Scale-III Longest Span Forward (p = 0.02). There was no association between the fractional anisotropy of tracts and performance on cognitive testing. The mean diffusivity of tracts crossing WMH measured by tractography is a novel correlate of performance on the Wechsler Memory Scale-III Longest Span Forward in elderly persons.

  6. Neuroaesthetic Resonance

    DEFF Research Database (Denmark)

    Brooks, Anthony Lewis

    2013-01-01

    tailored channeling of sensory stimulus aligned as ‘art-making’ and ‘game playing’ core experiences. Thus, affecting brain plasticity and human motoric-performance via the adaptability (plasticity) of digital medias result in closure of the human afferent-efferent neural feedback loop closure through...... the unencumbered motion-to-computer-generated activities - ‘Music Making’, ‘Painting’, ‘Robotic’ and ‘Video Game’ control. A focus of this position paper is to highlight how Aesthetic Resonance, in this context, relates to the growing body of research on Neuroaesthetics to evolve Neuroaesthetic Resonance....

  7. Repeatable Writing Assignments to Enhance Student Writing.

    Science.gov (United States)

    Wiebold, W. J.; And Others

    1990-01-01

    Discussed is the use of two short writing assignments and a peer review system in an undergraduate agronomy course to improve writing skills and the learning of agronomic principles. Provided is a course description and procedures used in the course. Student evaluation in the course is reviewed. (CW)

  8. Strategy-Proof Assignment Of Multiple Resources

    DEFF Research Database (Denmark)

    Erlanson, Albin; Szwagrzak, Karol

    2015-01-01

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

  9. Accounting for Sustainability: An Active Learning Assignment

    Science.gov (United States)

    Gusc, Joanna; van Veen-Dirks, Paula

    2017-01-01

    Purpose: Sustainability is one of the newer topics in the accounting courses taught in university teaching programs. The active learning assignment as described in this paper was developed for use in an accounting course in an undergraduate program. The aim was to enhance teaching about sustainability within such a course. The purpose of this…

  10. 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... requests for return of members to the United States for delivery to civilian authorities when the request...) Requests for return of members to the United States for delivery to civilian authorities when the request...

  11. Statistical aspects of optimal treatment assignment

    NARCIS (Netherlands)

    van der Linden, Willem J.

    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

  12. Influence Of Agricultural Education Students Home Assignments ...

    African Journals Online (AJOL)

    Four courses offered in the first semester were used and their raw scores in homework /assignments and class tests made up the data. Performance of students was relatively high in homework. However, there was no significant relationship in performance in homework and class test, since the correlation was almost ...

  13. 5 CFR 870.901 - Assignments permitted.

    Science.gov (United States)

    2010-01-01

    ..., corporations, or trustees, the insured individual must specify percentage shares, rather than dollar amounts or... increased insurance coverage under § 870.506 or during an open enrollment period, the increased coverage is considered included in the already existing assignment. The right to increase coverage remains with the...

  14. 7 CFR 1437.104 - Assigned production.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Assigned production. 1437.104 Section 1437.104 Agriculture Regulations of the Department of Agriculture (Continued) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS NONINSURED CROP DISASTER ASSISTANCE PROGRAM...

  15. Enhanced functional and structural domain assignments using ...

    Indian Academy of Sciences (India)

    The most populated families in MTB are involved in lipid metabolism, entry and survival of the bacillus in host. Interestingly, for 353 proteins, which we refer to as MTB-specific, no homologues have been identified. Numerous, previously unannotated, hypothetical proteins have been assigned domains and some of these ...

  16. income tax assignment under the ethiopian constitution

    African Journals Online (AJOL)

    eliasn

    Constitution from an income tax point of view. And finally, the article ends with some concluding remarks. 1. Theories of Fiscal Federalism In Income Tax Assignment. Few countries pursue the course of decentralization on grounds of its perceived economic efficiency or equity. Political, social, cultural or historical forces are.

  17. Enhanced functional and structural domain assignments using ...

    Indian Academy of Sciences (India)

    Unknown

    Superfamily relationships between families of unknown and known structures have increased structural in- formation by ~ 11%. Remote similarity detection methods have enabled domain assignments for 1325 'hypo- thetical proteins'. The most populated families in MTB are involved in lipid metabolism, entry and survival of.

  18. Dynamic traffic assignment on parallel computers

    Energy Technology Data Exchange (ETDEWEB)

    Nagel, K.; Frye, R.; Jakob, R.; Rickert, M.; Stretz, P.

    1998-12-01

    The authors describe part of the current framework of the TRANSIMS traffic research project at the Los Alamos National Laboratory. It includes parallel implementations of a route planner and a microscopic traffic simulation model. They present performance figures and results of an offline load-balancing scheme used in one of the iterative re-planning runs required for dynamic route assignment.

  19. Tabu search for target-radar assignment

    DEFF Research Database (Denmark)

    Hindsberger, Magnus; Vidal, Rene Victor Valqui

    2000-01-01

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

  20. 48 CFR 208.7002 - Assignment authority.

    Science.gov (United States)

    2010-10-01

    ... (MIPR) by a requiring activity and its acceptance by the contracting activity of another department, even though based on an oral communication, constitutes a one-time agreement. (ii) Consider repetitive... activities concerned. (b) Under the Integrated Materiel Management Program, assignments are made by the...

  1. Verifiable Task Assignment and Scheduling Controller

    Science.gov (United States)

    2017-07-01

    AFRL-RH-WP-TR-2017-0045 Verifiable Task Assignment and Scheduling Controller Clayton Rothwell Infoscitex Corporation...Chief, Supervisory Control Cognition Branch Supervisory Control and Cognition Branch Warfighter Interface Division //signed// KRISTOFFER A...information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD-MM

  2. 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…

  3. Teaching Historical Analysis through Creative Writing Assignments

    Science.gov (United States)

    Peterson, Janine Larmon; Graham, Lea

    2015-01-01

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

  4. 817 RESONANCE September 2013

    Indian Academy of Sciences (India)

    IAS Admin

    817. RESONANCE ⎜ September 2013. Page 2. 818. RESONANCE ⎜ September 2013. Page 3. 819. RESONANCE ⎜ September 2013. Page 4. 820. RESONANCE ⎜ September 2013. Page 5. 821. RESONANCE ⎜ September 2013. Page 6. 822. RESONANCE ⎜ September 2013. Page 7. 823. RESONANCE ⎜ September ...

  5. 996 RESONANCE November 2013

    Indian Academy of Sciences (India)

    IAS Admin

    996. RESONANCE. November 2013. Page 2. 997. RESONANCE. November 2013. Page 3. 998. RESONANCE. November 2013. Page 4. 999. RESONANCE. November 2013. Page 5. 1000. RESONANCE. November 2013. Page 6. 1001. RESONANCE. November 2013. Page 7. 1002. RESONANCE. November 2013 ...

  6. 369 RESONANCE April 2016

    Indian Academy of Sciences (India)

    IAS Admin

    369. RESONANCE ⎜ April 2016. Page 2. 370. RESONANCE ⎜ April 2016. Page 3. 371. RESONANCE ⎜ April 2016. Page 4. 372. RESONANCE ⎜ April 2016. Page 5. 373. RESONANCE ⎜ April 2016. Page 6. 374. RESONANCE ⎜ April 2016. Page 7. 375. RESONANCE ⎜ April 2016.

  7. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    Science.gov (United States)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

  8. Resonating Statements

    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 ...... as part of a feedback loop to re-attach the localized IT project to the broader national discourse. The paper concludes with reflections on how to actively build on resonating statements as a strategic resource for legitimizing IT projects...... 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. Autostereogram resonators

    Science.gov (United States)

    Leavey, Sean; Rae, Katherine; Murray, Adam; Courtial, Johannes

    2012-09-01

    Autostereograms, or "Magic Eye" pictures, are repeating patterns designed to give the illusion of depth. Here we discuss optical resonators that create light patterns which, when viewed from a suitable position by a monocular observer, are autostereograms of the three-dimensional shape of one of the mirror surfaces.

  10. Solving Quadratic Assignment Problem with Fixed Assignment (QAPFA) using Branch and Bound Approach

    Science.gov (United States)

    Shuthairah Syed-Abdullah, Sharifah; Abdul-Rahman, Syariza; Mauziah Benjamin, Aida; Wibowo, Antoni; Ku-Mahamud, Ku-Ruhana

    2018-01-01

    Quadratic Assignment Problem (QAP) has been a very popular problem to be solved among researchers due to its practical applications. Several variants of QAP have been proposed by researchers in the past in order to reflect the real situations of QAP. One of the real problems of QAP is related with facilities which are required to be assigned to certain locations due to its function. In solving this problem, a fixed assignment has to be made thus allowing for the complexity of the problem to be reduced. Hence, this study introduces Quadratic Assignment Problem with Fixed Assignment (QAPFA) with the objective to minimize the assignment cost between the facility and location. This assignment takes into account the flow and distance between facility and location. QAPFA represents the real-world situation of the problem especially in dealing with specific requirement of some facilities to specific locations. Dataset of QAPFA is introduced and is solved using branch and bound approach. As for validation, the results of QAPFA are compared with QAP in terms of objective function and running time. The computational results show that the solution quality of QAPFA is lower when compared with the QAP, while the running time for QAPFA is lower than the QAP. Since the complexity of the problem is reduced by fixing the assignment, thus there is possibility that QAPFA has lower quality than QAP due to the fixed assignment. Nevertheless, in terms of running time QAPFA is better than QAP. It can be concluded that this problem reflect the real problem and practical to be used.

  11. Assignation of limited resources in pediatrics

    Directory of Open Access Journals (Sweden)

    Garduño Espinosa Armando

    2014-07-01

    Full Text Available Limited resources assignation is fundamental in the development of health services and since they will never be enough, justice is- sues arise. Many distributive justice theories are discussed: liberal, equilable and utilitarian, as well as ethic principles and cost-benefit relation, that is, the consequences. Palliative medicine is suggested as a strategy to reduce the cost of hospitable care and to enhance its designation.

  12. Structural Encoding of Static Single Assignment Form

    DEFF Research Database (Denmark)

    Gal, Andreas; Probst, Christian; Franz, Michael

    2005-01-01

    Static Single Assignment (SSA) form is often used as an intermediate representation during code optimization in Java Virtual Machines. Recently, SSA has successfully been used for bytecode verification. However, constructing SSA at the code consumer is costly. SSAbased mobile code transport formats...... Java bytecode. While the resulting bytecode sequence can still be directly executed by traditional Virtual Machines, our novel VM can infer SSA form and confirm its safety with virtually no overhead....

  13. Protein secondary structure: category assignment and predictability

    DEFF Research Database (Denmark)

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

    2001-01-01

    In the last decade, the prediction of protein secondary structure has been optimized using essentially one and the same assignment scheme known as DSSP. We present here a different scheme, which is more predictable. This scheme predicts directly the hydrogen bonds, which stabilize the secondary......-forward neural network with one hidden layer on a data set identical to the one used in earlier work....

  14. Careerism, Committee Assignments and the Electoral Connection

    OpenAIRE

    Katz, Jonathan N.; Sala, Brian R.

    1996-01-01

    Most scholars agree that members of Congress are strongly motivated by their desire for reelection. This assumption implies that members of Congress adopt institutions, rules, and norms of behavior in part to serve their electoral interests. Direct tests of the electoral connection are rare, however, because significant, exogenous changes in the electoral environment are difficult to identify. We develop and test an electoral rationale for the norm of committee assignment "property rights...

  15. NMR backbone assignments of the tyrosine kinase domain of human fibroblast growth factor receptor 1.

    Science.gov (United States)

    Vajpai, Navratna; Schott, Anne-Kathrin; Vogtherr, Martin; Breeze, Alexander L

    2014-04-01

    Members of the fibroblast growth factor receptor tyrosine kinase family (FGFR1-4) play an important role in many signalling cascades. Although tightly regulated, aberrant activity of these enzymes may lead to, or become features of, disease pathologies including cancer. FGFR isoforms have been the subject of drug discovery programmes, with a number of kinase-domain inhibitors in pre-clinical and clinical development. Here, we present the first (83% complete) backbone resonance assignments of apo-FGFR1 kinase.

  16. 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

  17. Resonance Raman study of benzyl radical

    DEFF Research Database (Denmark)

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

    1992-01-01

    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...

  18. Effects of individualized assignments on biology achievement

    Science.gov (United States)

    Kremer, Philip L.

    A pretest-posttest, randomized, two groups, experimental, factorial design compared effects of detailed and nondetailed assignments on biology achievement over seven and a half months. Detailed assignments (favoring field independence and induction) employed block diagrams and stepwise directions. Nondetailed assignments (favoring field dependence and deduction) virtually lacked these. The accessible population was 101 tenth grade preparatory school male students. The 95 students enrolled in first year biology constituted the sample. Two by three ANOVA was done on residualized posttest score means of the students. Totally, the detailed students achieved significantly higher than the nondetailed students. This significantly higher achievement was only true of detailed students in the middle thirds of the deviation intelligence quotient (DIQ) range and of the grade point average (G.P.A.) range after the breakdown into upper, middle, and lower thirds of intellectual capability (ability and achievement). The upper third detailed DIQ grouping indirectly achieved higher than its peers, whereas the lower detailed DIQ third achieved lower than its peers. Thus, high capability students apparently benefit from flow and block diagrams, inductions, field independence, and high structure, whereas low capability students may be hindered by these.

  19. Capacity constrained assignment in spatial databases

    DEFF Research Database (Denmark)

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

    2008-01-01

    once) in M, (ii) the size of M is maximized (i.e., it comprises min{|P|, P q2Q q.k} pairs), and (iii) the total assignment cost (i.e., the sum of Euclidean distances within all pairs) is minimized. Thus, the CCA problem is to identify the assignment with the optimal overall quality; intuitively......, the quality of q's service to p in a given (q, p) pair is anti-proportional to their distance. Although max-flow algorithms are applicable to this problem, they require the complete distance-based bipartite graph between Q and P. For large spatial datasets, this graph is expensive to compute and it may be too...... large to fit in main memory. Motivated by this fact, we propose efficient algorithms for optimal assignment that employ novel edge-pruning strategies, based on the spatial properties of the problem. Additionally, we develop approximate (i.e., suboptimal) CCA solutions that provide a trade-off between...

  20. Resonant behavior of dielectric objects (electrostatic resonances).

    Science.gov (United States)

    Fredkin, D R; Mayergoyz, I D

    2003-12-19

    Resonant behavior of dielectric objects occurs at certain frequencies for which the object permittivity is negative and the free-space wavelength is large in comparison with the object dimensions. Unique physical features of these resonances are studied and a novel technique for the calculation of resonance values of permittivity, and hence resonance frequencies, is proposed. Scale invariance of resonance frequencies, unusually strong orthogonality properties of resonance modes, and a two-dimensional phenomenon of "twin" spectra are reported. The paper concludes with brief discussions of optical controllability of these resonances in semiconductor nanoparticles and a plausible, electrostatic resonance based, mechanism for nucleation and formation of ball lightning.

  1. Neuroaesthetic Resonance

    OpenAIRE

    Brooks, Anthony Lewis

    2013-01-01

    Neuroaesthetic Resonance emerged from a mature body of patient- centered gesture-control research investigating non-formal rehabilitation via ICT-enhanced-Art to question ‘Aesthetic Resonance’. Motivating participation, ludic engagement, and augmenting physical motion in non-formal (fun) treatment sessions are achieved via adaptive action-analyzed activities. These interactive virtual environments are designed to empower patients’ creative and/or playful expressions via digital feedback stimu...

  2. Efficient sequential assignments in proteins with reduced dimensionality 3D HN(CA)NH

    Energy Technology Data Exchange (ETDEWEB)

    Chandra, Kousik; Jaipuria, Garima; Shet, Divya; Atreya, Hanudatta S., E-mail: hsatreya@sif.iisc.ernet.in [Indian Institute of Science, NMR Research Centre (India)

    2012-02-15

    We present reduced dimensionality (RD) 3D HN(CA)NH for efficient sequential assignment in proteins. The experiment correlates the {sup 15}N and {sup 1}H chemical shift of a residue ('i') with those of its immediate N-terminal (i - 1) and C-terminal (i + 1) neighbors and provides four-dimensional chemical shift correlations rapidly with high resolution. An assignment strategy is presented which combines the correlations observed in this experiment with amino acid type information obtained from 3D CBCA(CO)NH. By classifying the 20 amino acid types into seven distinct categories based on {sup 13}C{sup {beta}} chemical shifts, it is observed that a stretch of five sequentially connected residues is sufficient to map uniquely on to the polypeptide for sequence specific resonance assignments. This method is exemplified by application to three different systems: maltose binding protein (42 kDa), intrinsically disordered domain of insulin-like growth factor binding protein-2 and Ubiquitin. Fast data acquisition is demonstrated using longitudinal {sup 1}H relaxation optimization. Overall, 3D HN(CA)NH is a powerful tool for high throughput resonance assignment, in particular for unfolded or intrinsically disordered polypeptides.

  3. 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.

  4. 1004 RESONANCE November 2013

    Indian Academy of Sciences (India)

    IAS Admin

    1004. RESONANCE │ November 2013. Page 2. 1005. RESONANCE │ November 2013. Page 3. 1006. RESONANCE │ November 2013. Page 4. 1007. RESONANCE │ November 2013. Page 5. 1008. RESONANCE │ November 2013. Page 6. 1009. RESONANCE │ November 2013. Page 7. 1010. RESONANCE ...

  5. Even order snake resonances

    International Nuclear Information System (INIS)

    Lee, S.Y.

    1993-01-01

    We found that the perturbed spin tune due to the imperfection resonance plays an important role in beam depolarization at snake resonances. We also found that even order snake resonances exist in the overlapping intrinsic and imperfection resonances. Due to the perturbed spin tune shift of imperfection resonances, each snake resonance splits into two

  6. NMR assignments and ligand-binding studies on a two-domain family GH19 chitinase allergen from Japanese cedar (Cryptomeria japonica) pollen.

    Science.gov (United States)

    Takashima, Tomoya; Ohnuma, Takayuki; Fukamizo, Tamo

    2017-04-01

    A two-domain family GH19 chitinase from Japanese cedar (Cryptomeria japonica) pollen, CJP-4, which consists of an N-terminal CBM18 domain and a GH19 catalytic domain, is known to be an important allergen, that causes pollinosis. We report here the resonance assignments of the NMR spectrum of CJP-4. The backbone resonances were almost completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of a chitin dimer to the enzyme solution perturbed the chemical shifts of the resonances of amino acid residues forming a long extended binding site spanning from the CBM18 domain to the GH19 catalytic domain.

  7. 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…

  8. 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...

  9. The core and related solution concepts for infinite assignment games

    NARCIS (Netherlands)

    Llorca, Natividad; Sanchez-Soriano, Joaquin; Tijs, Stef; Timmer, Judith B.

    2004-01-01

    Assignment problems where both sets of agents that have to be matched are countably infinite, the so-called infinite assignment problems, are studied as well as the related cooperative assignment games. Further, several solution concepts for these assignment games are studied. The first one is the

  10. Strategy-Proof Assignment Of Multiple Resources

    DEFF Research Database (Denmark)

    Erlanson, Albin; Szwagrzak, Karol

    2015-01-01

    by maximizing a separably concave function over a polyhedral extension of the set of Pareto-efficient allocations is strategy-proof. Moreover, these are the only strategy-proof, unanimous, consistent, and resource-monotonic mechanisms. These mechanisms generalize the parametric rationing mechanisms (Young, 1987......We examine the strategy-proof allocation of multiple resources; an application is the assignment of packages of tasks, workloads, and compensations among the members of an organization. In the domain of multidimensional single-peaked preferences, we find that any allocation mechanism obtained...

  11. Symmetric Logic Synthesis with Phase Assignment

    OpenAIRE

    Benschop, N. F.

    2001-01-01

    Decomposition of any Boolean Function BF_n of n binary inputs into an optimal inverter coupled network of Symmetric Boolean functions SF_k (k \\leq n) is described. Each SF component is implemented by Threshold Logic Cells, forming a complete and compact T-Cell Library. Optimal phase assignment of input polarities maximizes local symmetries. The "rank spectrum" is a new BF_n description independent of input ordering, obtained by mapping its minterms onto an othogonal n \\times n grid of (transi...

  12. ORTHO-TO-PARA ABUNDANCE RATIO (OPR) OF AMMONIA IN 15 COMETS: OPRs OF AMMONIA VERSUS 14N/15N RATIOS IN CN

    International Nuclear Information System (INIS)

    Shinnaka, Yoshiharu; Kawakita, Hideyo; Kobayashi, Hitomi; Jehin, Emmanuel; Manfroid, Jean; Hutsemekers, Damien; Arpigny, Claude

    2011-01-01

    The ortho-to-para abundance ratio (OPR) of cometary molecules is considered to be one of the primordial characteristics of cometary ices. We present OPRs of ammonia (NH 3 ) in 15 comets based on optical high-dispersion spectroscopic observations of NH 2 , which is a photodissociation product of ammonia in the gaseous coma. The observations were mainly carried out with the VLT/UVES. The OPR of ammonia is estimated from the OPR of NH 2 based on the observations of the NH 2 (0, 9, 0) vibronic band. The absorption lines by the telluric atmosphere are corrected and the cometary C 2 emission lines blended with NH 2 lines are removed in our analysis. The ammonia OPRs show a cluster between 1.1 and 1.2 (this corresponds to a nuclear spin temperature of ∼30 K) for all comets in our sample except for 73P/Schwassmann-Wachmann 3 (73P/SW3). Comet 73P/SW3 (both B- and C-fragments) shows the OPR of ammonia consistent with nuclear spin statistical weight ratio (1.0) that indicates a high-temperature limit as nuclear spin temperature. We compared the ammonia OPRs with other properties ( 14 N/ 15 N ratios in CN, D/H ratios of water, and mixing ratios of volatiles). Comet 73P/SW3 is clearly different from the other comets in the plot of ammonia OPRs versus 14 N/ 15 N ratios in CN. The ammonia OPRs of 1.0 and lower 15 N-fractionation of CN in comet 73P/SW3 imply that icy materials in this comet formed under warmer conditions than other comets. Comets may be classified into two groups in the plot of ammonia OPRs against 14 N/ 15 N ratios in CN.

  13. Spin-State-Dependent Ion-Molecule Chemistry as the Origin of N-15 and D Isotopic Anomalies in Primitive Matter.

    Science.gov (United States)

    Wirstrom, E. S.; Charnley, S. B.; Cordiner, M. A.; Milam, S. N.

    2012-01-01

    Many meteoritic and interplanetary dust particle (IDP) samples contain bulk enhancements and hotspots rich in N-15. Similarly low C(14)N/C(15)N ratios have been observed in numerous comets, An almost constant enrichment factor in comets from disti'nct formation zones in the nebular disk (i.e. both Jupiter Family and Oort Cloud comets), strongly suggests that this fractionation is primordial and was set in the protsolar cloud core. Deuterium enrichment is observed in both meteorites and IDPs

  14. 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...

  15. Optimization of demand assigned SCPC satellite networks

    Science.gov (United States)

    Laborde, E.

    1985-09-01

    This paper investigates various system aspects and price tradeoffs involved in providing cost-effective Demand Assignment (DA) satellite channel service. Those network characteristics which significantly affect the ultimate cost-based decision are discussed. The number of stations participating in the DA or PA system, the number of satellite channels, and the traffic are kept parametric within expected limits, covering most of the present and future applications. In particular, the interrelationships between the network requirements (e.g., grade of service) and network elements, and the impacts of different blocking assignment allocations on the number of modems in the network is examined. A cost model is then derived that allows the evaluation and comparison of both DA and PA networks. Absolute and differential costing of PA and DA networks is permitted using economic quantities available to the system planner. These include modem cost, satellite channel cost, network size, and defined efficiency factors. Based on the differential cost comparisons for several DA and PA network strategies, tradeoffs have been derived to aid the system designer in configuring the most cost-effective DA network.

  16. Assigned value improves memory of proper names.

    Science.gov (United States)

    Festini, Sara B; Hartley, Alan A; Tauber, Sarah K; Rhodes, Matthew G

    2013-01-01

    Names are more difficult to remember than other personal information such as occupations. The current research examined the influence of assigned point value on memory and metamemory judgements for names and occupations to determine whether incentive can improve recall of proper names. In Experiment 1 participants studied face-name and face-occupation pairs assigned 1 or 10 points, made judgements of learning, and were given a cued recall test. High-value names were recalled more often than low-value names. However, recall of occupations was not influenced by value. In Experiment 2 meaningless nonwords were used for both names and occupations. The name difficulty disappeared, and value influenced recall of both names and occupations. Thus value similarly influenced names and occupations when meaningfulness was held constant. In Experiment 3 participants were required to use overt rote rehearsal for all items. Value did not boost recall of high-value names, suggesting that differential processing could not be implemented to improve memory. Thus incentives may improve memory for proper names by motivating people to engage in selective rehearsal and effortful elaborative processing.

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

    Energy Technology Data Exchange (ETDEWEB)

    Volk, Jochen [ETH Zuerich, Institut fuer Molekularbiologie und Biophysik (Switzerland); Herrmann, Torsten [Universite de Lyon, CNRS/ENS Lyon/UCB-Lyon 1 (France); Wuethrich, Kurt [ETH Zuerich, Institut fuer Molekularbiologie und Biophysik (Switzerland)], E-mail: wuthrich@mol.biol.ethz.ch

    2008-07-15

    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.

  18. 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

  19. Cross comparison of the Collection 6 and Collection 6.1 Terra and Aqua MODIS Bands 1 and 2 using AVHRR N15 and N19

    Science.gov (United States)

    Chen, Xuexia; Wu, Aisheng; Xiong, Xiaoxiong J.; Chen, Na

    2017-09-01

    The Moderate Resolution Imaging Spectroradiometer (MODIS) is a key scientific instrument that was launched into Earth orbit by NASA in 1999 on board the Terra (EOS AM) satellite and in 2002 on board the Aqua (EOS PM) satellite. Terra and Aqua MODIS collect the entire Earth's images every 1 to 2 days in 36 spectral bands. MODIS band 1 (0.620- 0.670 μm) and band 2 (0.841-0.876 μm) have nadir spatial resolution of 250 m and their measurements are crucial to derive key land surface products. This study evaluates the performance of the Collection 6 (C6, and C6.1) L1B of both Terra and Aqua MODIS bands 1 and 2 using Simultaneous Nadir Overpass (SNO) data to compare with AVHRR/3 sensors. We examine the relative stability between Terra and Aqua MODIS in reference to NOAA N15 and N19 the Advanced Very High Resolution Radiometer (AVHRR/3). The comparisons for MODIS to AVHRR/3 are over a fifteenyear period from 2002 to 2017. Results from this study provide a quantitative assessment of Terra and Aqua MODIS band 1 and band 2 calibration stability and the relative differences through the NOAA N15 and N19 AVHRR/3 sensors.

  20. A multistage linear array assignment problem

    Science.gov (United States)

    Nicol, David M.; Shier, D. R.; Kincaid, R. K.; Richards, D. S.

    1988-01-01

    The implementation of certain algorithms on parallel processing computing architectures can involve partitioning contiguous elements into a fixed number of groups, each of which is to be handled by a single processor. It is desired to find an assignment of elements to processors that minimizes the sum of the maximum workloads experienced at each stage. This problem can be viewed as a multi-objective network optimization problem. Polynomially-bounded algorithms are developed for the case of two stages, whereas the associated decision problem (for an arbitrary number of stages) is shown to be NP-complete. Heuristic procedures are therefore proposed and analyzed for the general problem. Computational experience with one of the exact problems, incorporating certain pruning rules, is presented with one of the exact problems. Empirical results also demonstrate that one of the heuristic procedures is especially effective in practice.

  1. Rationalization of some genetic anticodonic assignments

    Science.gov (United States)

    Lacey, J. C., Jr.; Hall, L. M.; Mullins, D. W., Jr.

    1985-01-01

    The hydrophobicity of most amino acids correlates well with that of their anticodon nucleotides, with Trp, Tyr, Ile, and Ser being the exceptions to this rule. Using previous data on hydrophobicity and binding constants, and new data on rates of esterification of polyadenylic acid with several N-acetylaminoacyl imidazolides, several of the anticodon assignments are rationalized. Chemical reasons are shown supporting the idea of the inclusion of the Ile in the catalog of biological amino acids late in the evolution, through a mutation of the existing tRNA and its aminoacyl-tRNA-synthetase. It was found that an addition of hexane increases the incorporation of hydrophobic Ac-Phe into poly-A, in support of the Fox (1965) and Oparin (1965) emphasis on the biogenetic importance of phase-separated systems.

  2. Assignment of uncertainties to scientific data

    International Nuclear Information System (INIS)

    Froehner, F.H.

    1994-01-01

    Long-standing problems of uncertainty assignment to scientific data came into a sharp focus in recent years when uncertainty information ('covariance files') had to be added to application-oriented large libraries of evaluated nuclear data such as ENDF and JEF. Question arouse about the best way to express uncertainties, the meaning of statistical and systematic errors, the origin of correlation and construction of covariance matrices, the combination of uncertain data from different sources, the general usefulness of results that are strictly valid only for Gaussian or only for linear statistical models, etc. Conventional statistical theory is often unable to give unambiguous answers, and tends to fail when statistics is bad so that prior information becomes crucial. Modern probability theory, on the other hand, incorporating decision information becomes group-theoretic results, is shown to provide straight and unique answers to such questions, and to deal easily with prior information and small samples. (author). 10 refs

  3. Diagnosis code assignment: models and evaluation metrics.

    Science.gov (United States)

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

    2014-01-01

    The volume of healthcare data is growing rapidly with the adoption of health information technology. We focus on automated ICD9 code assignment from discharge summary content and methods for evaluating such assignments. We study ICD9 diagnosis codes and discharge summaries from the publicly available Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC II) repository. We experiment with two coding approaches: one that treats each ICD9 code independently of each other (flat classifier), and one that leverages the hierarchical nature of ICD9 codes into its modeling (hierarchy-based classifier). We propose novel evaluation metrics, which reflect the distances among gold-standard and predicted codes and their locations in the ICD9 tree. Experimental setup, code for modeling, and evaluation scripts are made available to the research community. The hierarchy-based classifier outperforms the flat classifier with F-measures of 39.5% and 27.6%, respectively, when trained on 20,533 documents and tested on 2282 documents. While recall is improved at the expense of precision, our novel evaluation metrics show a more refined assessment: for instance, the hierarchy-based classifier identifies the correct sub-tree of gold-standard codes more often than the flat classifier. Error analysis reveals that gold-standard codes are not perfect, and as such the recall and precision are likely underestimated. Hierarchy-based classification yields better ICD9 coding than flat classification for MIMIC patients. Automated ICD9 coding is an example of a task for which data and tools can be shared and for which the research community can work together to build on shared models and advance the state of the art.

  4. Applied neutron resonance theory

    International Nuclear Information System (INIS)

    Froehner, F.H.

    1978-07-01

    Utilisation of resonance theory in basic and applications-oriented neutron cross section work is reviewed. The technically important resonance formalisms, principal concepts and methods as well as representative computer programs for resonance parameter extraction from measured data, evaluation of resonance data, calculation of Doppler-broadened cross sections and estimation of level-statistical quantities from resonance parameters are described. (orig.) [de

  5. Neutron resonance spectroscopy of 113In and 115In

    International Nuclear Information System (INIS)

    Frankle, C.M.; Bowman, J.D.; Crawford, B.E.; Delheij, P.P.J.; Gould, C.R.; Haase, D.G.; Knudson, J.N.; Mitchell, G.E.; Patterson, S.S.; Penttilae, S.I.; Popov, Y.P.; Roberson, N.R.; Seestrom, S.J.; Sharapov, E.I.; Yen, Y.; Yoo, S.H.; Yuan, V.W.; Zhu, X.

    1993-01-01

    The neutron total cross section for natural indium was measured for E n =25--500 eV with the time-of-flight method at the Los Alamos Neutron Scattering Center. The neutron capture reaction was studied on a highly enriched sample (99.99%) of 115 In. A total of 47 previously unreported resonances were observed. The combination of the two measurements allowed assignment of the new resonances to 113 In or 115 In. Resonance parameters were extracted for all of the neutron resonances observed

  6. Mathematical Modeling and Optimizing ofin VitroHormonal Combination for G × N15 Vegetative Rootstock Proliferation Using Artificial Neural Network-Genetic Algorithm (ANN-GA).

    Science.gov (United States)

    Arab, Mohammad M; Yadollahi, Abbas; Ahmadi, Hamed; Eftekhari, Maliheh; Maleki, Masoud

    2017-01-01

    The efficiency of a hybrid systems method which combined artificial neural networks (ANNs) as a modeling tool and genetic algorithms (GAs) as an optimizing method for input variables used in ANN modeling was assessed. Hence, as a new technique, it was applied for the prediction and optimization of the plant hormones concentrations and combinations for in vitro proliferation of Garnem (G × N15) rootstock as a case study. Optimizing hormones combination was surveyed by modeling the effects of various concentrations of cytokinin-auxin, i.e., BAP, KIN, TDZ, IBA, and NAA combinations (inputs) on four growth parameters (outputs), i.e., micro-shoots number per explant, length of micro-shoots, developed callus weight (CW) and the quality index (QI) of plantlets. Calculation of statistical values such as R 2 (coefficient of determination) related to the accuracy of ANN-GA models showed a considerably higher prediction accuracy for ANN models, i.e., micro-shoots number: R 2 = 0.81, length of micro-shoots: R 2 = 0.87, CW: R 2 = 0.88, QI: R 2 = 0.87. According to the results, among the input variables, BAP (19.3), KIN (9.64), and IBA (2.63) showed the highest values of variable sensitivity ratio for proliferation rate. The GA showed that media containing 1.02 mg/l BAP in combination with 0.098 mg/l IBA could lead to the optimal proliferation rate (10.53) for G × N15 rootstock. Another objective of the present study was to compare the performance of predicted and optimized cytokinin-auxin combination with the best optimized obtained concentrations of our other experiments. Considering three growth parameters (length of micro-shoots, micro-shoots number, and proliferation rate), the last treatment was found to be superior to the rest of treatments for G × N15 rootstock in vitro multiplication. Very little difference between the ANN predicted and experimental data confirmed high capability of ANN-GA method in predicting new optimized protocols for plant in vitro propagation.

  7. MRI (Magnetic Resonance Imaging)

    Science.gov (United States)

    ... Medical Imaging MRI (Magnetic Resonance Imaging) MRI (Magnetic Resonance Imaging) Share Tweet Linkedin Pin it More sharing options Linkedin Pin it Email Print Magnetic Resonance Imaging (MRI) is a medical imaging procedure for ...

  8. 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...

  9. 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

  10. NMR resonance assignments of NarE, a putative ADP-ribosylating toxin from Neisseria meningitidis

    OpenAIRE

    Carlier, Ludovic; Koehler, Christian; Veggi, Daniele; Pizza, Mariagrazia; Soriani, Marco; Boelens, Rolf; Bonvin, Alexandre M. J. J.

    2010-01-01

    NarE is a 16 kDa protein identified from Neisseria meningitidis, one of the bacterial pathogens responsible for meningitis. NarE belongs to the ADP-ribosyltransferase family and catalyses the transfer of ADP-ribose moieties to arginine residues in target protein acceptors. Many pathogenic bacteria utilize ADP-ribosylating toxins to modify and alter essential functions of eukaryotic cells. NarE was proposed to bind iron through a Fe–S center which is supposed to be implied in catalysis. We hav...

  11. NMR resonance assignments of NarE, a putative ADP-ribosylating toxin from Neisseria meningitidis

    NARCIS (Netherlands)

    Carlier, L.P.A.; Köhler, Christian; Veggi, D.; Pizza, M.; Soriani, M.; Boelens, R.; Bonvin, A.M.J.J.

    2011-01-01

    NarE is a 16 kDa protein identified from Neisseria meningitidis, one of the bacterial pathogens responsible for meningitis. NarE belongs to the ADP-ribosyltransferase family and catalyses the transfer of ADP-ribose moieties to arginine residues in target protein acceptors. Many pathogenic bacteria

  12. Resonance assignment of PsbP: an extrinsic protein from photosystem II of Spinacia oleracea

    Czech Academy of Sciences Publication Activity Database

    Rathner, A.; Chandra, K.; Rathner, P.; Horničáková, M.; Schlagnitweit, J.; Kohoutová, Jaroslava; Ettrich, Rüdiger; Müller, N.

    2015-01-01

    Roč. 9, č. 2 (2015), s. 341-346 ISSN 1874-2718 Institutional support: RVO:61388971 Keywords : PsbP * Photosystem II * Oxygen evolving complex Subject RIV: EE - Microbiology, Virology Impact factor: 0.687, year: 2015

  13. 1H and 15N NMR resonance assignments and secondary structure of titin type I domains

    Energy Technology Data Exchange (ETDEWEB)

    Muhle-Goll, Claudia; Nilges, Michael; Pastore, Annalisa [European Molecular Biology Laboratory (Germany)

    1997-01-15

    Titin/connect in is a giant muscle protein with a highly modular architecture consisting of multiple repeats of two sequence motifs, named type I and type II. Type I modules have been suggested to be intracellular members of the fibronectin type III (Fn3) domain family. Along the titin sequence they are exclusively present in the region of the molecule located in the sarcomere A-band. This region has been shown to interact with myosin and C-protein. One of the most noticeable features of type I modules is that they are particularly rich in semiconserved prolines, since these residues account for about 8% of their sequence. We have determined the secondary structure of a representative type I domain (A71) by 15N and 1HNMR. We show that the type I domains of titin have the Fn3 fold as proposed, consisting of a three- and a four-stranded {beta}-sheet. When the two sheets are placed on top of each other to form the {beta}-sandwich characteristic of the Fn3 fold, 8 out of 10 prolines are found on the same side of the molecule and form an exposed hydrophobic patch. This suggests that the semiconserved prolines might be relevant for the function of type I modules, providing a surface for binding to other A-band proteins. The secondary structure of A71 was structurally aligned to other extracellular Fn3 modules of known 3D structure. The alignment shows that titin type I modules have closest similarity to the first Fn3 domain of Drosophila neuroglian.

  14. Backbone 1H, 13C, and 15N resonance assignments for lysozyme from bacteriophage lambda

    OpenAIRE

    Di Paolo, Alexandre; Duval, Val?rie; Matagne, Andr?; Redfield, Christina

    2010-01-01

    Lysozyme from lambda bacteriophage (? lysozyme) is an 18 kDa globular protein displaying some of the structural features common to all lysozymes; in particular, ? lysozyme consists of two structural domains connected by a helix, and has its catalytic residues located at the interface between these two domains. An interesting feature of ? lysozyme, when compared to the well-characterised hen egg-white lysozyme, is its lack of disulfide bridges; this makes ? lysozyme an interesting system for s...

  15. Regenerative feedback resonant circuit

    Science.gov (United States)

    Jones, A. Mark; Kelly, James F.; McCloy, John S.; McMakin, Douglas L.

    2014-09-02

    A regenerative feedback resonant circuit for measuring a transient response in a loop is disclosed. The circuit includes an amplifier for generating a signal in the loop. The circuit further includes a resonator having a resonant cavity and a material located within the cavity. The signal sent into the resonator produces a resonant frequency. A variation of the resonant frequency due to perturbations in electromagnetic properties of the material is measured.

  16. Cross sections and analyzing powers of 15N(p,n)15O at 200 MeV and 494 MeV

    International Nuclear Information System (INIS)

    Ciskowski, D.E.

    1989-11-01

    Differential cross sections and analyzing powers have been measured for the 15 N(p,n) 15 O(g.s.) reaction at bombarding energies of 200 MeV and 494 MeV. The 494 MeV data were obtained at the LAMPF Neutron Time-Of-Flight Facility on an 82 m flight path with a resolution of about 2.7 MeV. The 200 MeV data were obtained at IUCF on a 76m flight path with a resolution of about 1.1 MeV. At both energies, the measured analyzing power is small, the magnitude is less than .2 for momentum transfers of less than 1 fm -1 . In contrast, both Relativistic and standard DWIA calculations predict a maximum of A=-.7 near q=0.7 fm -1 . 53 refs., 44 figs

  17. 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…

  18. 7 CFR 1463.111 - Offsets and assignments.

    Science.gov (United States)

    2010-01-01

    ... assignment other than to: (i) A family member; or (ii) A party who had purchased a tobacco marketing quota... 7 Agriculture 10 2010-01-01 2010-01-01 false Offsets and assignments. 1463.111 Section 1463.111... Transition Payment Program § 1463.111 Offsets and assignments. (a) TTPP payments made to any person under...

  19. 42 CFR 405.912 - Assignment of appeal rights.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 2 2010-10-01 2010-10-01 false Assignment of appeal rights. 405.912 Section 405..., Reconsiderations, and Appeals Under Original Medicare (Part A and Part B) § 405.912 Assignment of appeal rights. (a... assignment of appeal rights from the beneficiary for that item or service. (b) Who may not be an assignee. An...

  20. Assessment of a Diversity Assignment in a PR Principles Course

    Science.gov (United States)

    Gallicano, Tiffany Derville; Stansberry, Kathleen

    2012-01-01

    This study assesses an assignment for incorporating diversity into the principles of public relations course. The assignment is tailored to the challenges of using an active learning approach in a large lecture class. For the assignment, students write a goal, objectives, strategies, an identification of tactics, and evaluation plans for either…

  1. 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

  2. Sequence-specific H NMR assignments and secondary structure in the sea anemone polypeptide Stichodactyla helianthus neurotoxin I

    International Nuclear Information System (INIS)

    Fogh, R.H.; Mabbutt, B.C.; Kem, W.R.; Norton, R.S.

    1989-01-01

    Sequence-specific assignments are reported for the 500-MHz H nuclear magnetic resonance (NMR) spectrum of the 48-residue polypeptide neurotoxin I from the sea anemone Stichodactyla helianthus (Sh I). Spin systems were first identified by using two-dimensional relayed or multiple quantum filtered correlation spectroscopy, double quantum spectroscopy, and spin lock experiments. Specific resonance assignments were then obtained from nuclear Overhauser enhancement (NOE) connectivities between protons from residues adjacent in the amino acid sequence. Of a total of 265 potentially observable resonances, 248 (i.e., 94%) were assigned, arising from 39 completely and 9 partially assigned amino acid spin systems. The secondary structure of Sh I was defined on the basis of the pattern of sequential NOE connectivities. NOEs between protons on separate strands of the polypeptide backbone, and backbone amide exchange rates. Sh I contains a four-stranded antiparallel β-sheet encompassing residues 1-5, 16-24, 30-33, and 40-46, with a β-bulge at residues 17 and 18 and a reverse turn, probably a type II β-turn, involving residues 27-30. No evidence of α-helical structure was found

  3. Stochastic resonance

    International Nuclear Information System (INIS)

    Wellens, Thomas; Shatokhin, Vyacheslav; Buchleitner, Andreas

    2004-01-01

    We are taught by conventional wisdom that the transmission and detection of signals is hindered by noise. However, during the last two decades, the paradigm of stochastic resonance (SR) proved this assertion wrong: indeed, addition of the appropriate amount of noise can boost a signal and hence facilitate its detection in a noisy environment. Due to its simplicity and robustness, SR has been implemented by mother nature on almost every scale, thus attracting interdisciplinary interest from physicists, geologists, engineers, biologists and medical doctors, who nowadays use it as an instrument for their specific purposes. At the present time, there exist a lot of diversified models of SR. Taking into account the progress achieved in both theoretical understanding and practical application of this phenomenon, we put the focus of the present review not on discussing in depth technical details of different models and approaches but rather on presenting a general and clear physical picture of SR on a pedagogical level. Particular emphasis will be given to the implementation of SR in generic quantum systems-an issue that has received limited attention in earlier review papers on the topic. The major part of our presentation relies on the two-state model of SR (or on simple variants thereof), which is general enough to exhibit the main features of SR and, in fact, covers many (if not most) of the examples of SR published so far. In order to highlight the diversity of the two-state model, we shall discuss several examples from such different fields as condensed matter, nonlinear and quantum optics and biophysics. Finally, we also discuss some situations that go beyond the generic SR scenario but are still characterized by a constructive role of noise

  4. Stochastic resonance

    Science.gov (United States)

    Wellens, Thomas; Shatokhin, Vyacheslav; Buchleitner, Andreas

    2004-01-01

    We are taught by conventional wisdom that the transmission and detection of signals is hindered by noise. However, during the last two decades, the paradigm of stochastic resonance (SR) proved this assertion wrong: indeed, addition of the appropriate amount of noise can boost a signal and hence facilitate its detection in a noisy environment. Due to its simplicity and robustness, SR has been implemented by mother nature on almost every scale, thus attracting interdisciplinary interest from physicists, geologists, engineers, biologists and medical doctors, who nowadays use it as an instrument for their specific purposes. At the present time, there exist a lot of diversified models of SR. Taking into account the progress achieved in both theoretical understanding and practical application of this phenomenon, we put the focus of the present review not on discussing in depth technical details of different models and approaches but rather on presenting a general and clear physical picture of SR on a pedagogical level. Particular emphasis will be given to the implementation of SR in generic quantum systems—an issue that has received limited attention in earlier review papers on the topic. The major part of our presentation relies on the two-state model of SR (or on simple variants thereof), which is general enough to exhibit the main features of SR and, in fact, covers many (if not most) of the examples of SR published so far. In order to highlight the diversity of the two-state model, we shall discuss several examples from such different fields as condensed matter, nonlinear and quantum optics and biophysics. Finally, we also discuss some situations that go beyond the generic SR scenario but are still characterized by a constructive role of noise.

  5. A Bayesian approach to simultaneously quantify assignments and linguistic uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Chavez, Gregory M [Los Alamos National Laboratory; Booker, Jane M [BOOKER SCIENTIFIC FREDERICKSBURG; Ross, Timothy J [UNM

    2010-10-07

    Subject matter expert assessments can include both assignment and linguistic uncertainty. This paper examines assessments containing linguistic uncertainty associated with a qualitative description of a specific state of interest and the assignment uncertainty associated with assigning a qualitative value to that state. A Bayesian approach is examined to simultaneously quantify both assignment and linguistic uncertainty in the posterior probability. The approach is applied to a simplified damage assessment model involving both assignment and linguistic uncertainty. The utility of the approach and the conditions under which the approach is feasible are examined and identified.

  6. 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.

  7. 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.

  8. Neutron resonance spectroscopy of 107Ag and 109Ag

    International Nuclear Information System (INIS)

    Lowie, L.Y.; Mitchell, G.E.; Stephenson, S.L.; Bowman, J.D.; Knudson, J.N.; Penttila, S.I.; Seestrom, S.J.; Yen, Y.; Yuan, V.W.; Crawford, B.E.; Roberson, N.R.; Delheij, P.P.; Haseyama, T.; Masaike, A.; Matsuda, Y.; Postma, H.; Sharapov, E.I.

    1997-01-01

    Parity violation has been observed in a number of previously unreported neutron resonances in silver. Analysis of these parity violation data requires improved neutron resonance spectroscopy. The neutron total cross section for natural silver was measured for E n =10 - 800 eV with the time-of-flight method at the Los Alamos Neutron Scattering Center. The neutron capture reaction was studied with both a natural silver target and a highly enriched sample (98.29%) of 107 Ag. A total of 38 previously unreported resonances were observed. The combination of the two measurements allowed assignment of the newly observed resonances to 107 Ag or to 109 Ag. Resonance parameters were determined for almost all of the neutron resonances observed. copyright 1997 The American Physical Society

  9. Residue-specific pK(a) determination of lysine and arginine side chains by indirect N-15 and C-13 NMR spectroscopy : Application to apo calmodulin

    NARCIS (Netherlands)

    Andre, Ingemar; Linse, Sara; Mulder, Frans A. A.

    2007-01-01

    Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants, We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on

  10. 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.

  11. Backbone chemical shifts assignments, secondary structure, and ligand binding of a family GH-19 chitinase from moss, Bryum coronatum.

    Science.gov (United States)

    Shinya, Shoko; Nagata, Takuya; Ohnuma, Takayuki; Taira, Toki; Nishimura, Shigenori; Fukamizo, Tamo

    2012-10-01

    Family GH19 chitinases have been recognized as important in the plant defense against fungal pathogens. However, their substrate-recognition mechanism is still unknown. We report here the first resonance assignment of NMR spectrum of a GH19 chitinase from moss, Bryum coronatum (BcChi-A). The backbone signals were nearly completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of the chitin dimer to the enzyme solution perturbed the chemical shifts of HSQC resonances of the amino acid residues forming the putative substrate-binding cleft. Further NMR analysis of the ligand binding to BcChi-A will improve understanding of the substrate-recognition mechanism of GH-19 enzymes.

  12. Studies of the efficiency of nitrogen placement methods and slow release nitrogen fertilizers for rice and wheat, using N-15 labelled fertilizers

    International Nuclear Information System (INIS)

    Shaukat, A.

    1979-12-01

    A series of experiments with rice and wheat were carried out to study the efficiency of nitrogen placement methods and slow-release nitrogen fertilizers for these two crops using N-15-labelled fertilizer. The results show that (1) reduced N levels, of the order of 75 percent of the full recommended dose, are equally efficient as the full dose for wheat. The yield of rice grain increased with the increased dose of nitrogen; (2) Point placement of fertilizers for rice was superior to broadcast application in terms of uptake and yield. For optimum yield of wheat grain, urea should perferably be applied as a single dose banded between the rows at 5 cm depth or by broadcasting and incorporation in the soil at the time of sowing; (3) Sulphur-coated urea (SCU) at a comparable dose and mode of application gave better yields of rice grain than the application of urea and IBDU (Isobutylidine Diurea); (4) More nitrogen was taken up by wheat when SCU was applied. The best uptake was when it was applied half at sowing and half at tillering. The nitrogen uptake from the SCU by point placement was better for rice plants than broadcast application and was higher in magnitude than the IBDU

  13. 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.)

  14. Resonance and Neck Length for a Spherical Resonator

    Directory of Open Access Journals (Sweden)

    Emily Corning

    2011-06-01

    Full Text Available The relationship between the neck length of a spherical resonator and its period of fundamental resonance was investigated. This was done by measuring the frequency of fundamental resonance of the resonator at 6 different neck lengths. It was found that its resonance resembled Helmholtz resonance but was not that of ideal Helmholtz resonance.

  15. 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.

  16. 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)

  17. {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)

  18. Neutron resonance spectroscopy of 106Pd and 108Pd from 20 to 2000 eV

    International Nuclear Information System (INIS)

    Crawford, B.E.; Roberson, N.R.; Bowman, J.D.; Knudson, J.N.; Penttilae, S.I.; Seestrom, S.J.; Yuan, V.W.; Delheij, P.P.; Haseyama, T.; Masaike, A.; Matsuda, Y.; Lowie, L.Y.; Mitchell, G.E.; Stephenson, S.L.; Postma, H.; Sharapov, E.I.

    1998-01-01

    Parity nonconserving asymmetries have been measured in p-wave resonances of 106 Pd and 108 Pd. The data analysis requires knowledge of the neutron resonance parameters. Transmission and capture γ-ray yields were measured for E n =20 - 2000 eV with the time-of-flight method at the Los Alamos Neutron Science Center (LANSCE). A total of 28 resonances in 106 Pd and 32 resonances in 108 Pd were studied. The resonance parameters for 106 Pd are new for all except one resonance. In 108 Pd six new resonances were observed and the precision improved for many of the resonance parameters. A Bayesian analysis was used to assign orbital angular momentum for the resonances studied. copyright 1998 The American Physical Society

  19. Partial 1H NMR assignments of the Escherichia coli dihydrofolate reductase complex with folate: Evidence for a unique conformation of bound folate

    International Nuclear Information System (INIS)

    Falzone, C.J.; Benkovic, S.J.; Wright, P.E.

    1990-01-01

    Sequence-specific 1 H assignments have been made for over 25% of the amino acid side chains of Escherichia coli dihydrofolate reductase complexed with folate by using a variety of two-dimensional techniques. Proton resonances were assigned by using a combination of site-directed mutagenesis and a knowledge of the X-ray crystal structure. Unique sets of NOE connectivities present in hydrophobic pockets were matched with the X-ray structure and used to assign many of the residues. Other residues, particularly those near or in the active site, were assigned by site-directed mutagenesis. The ability to assign unambiguosly the proton resonances of these catalytically important residues allowed for extensive networks of NOE connectivities to follow from these assignments. As a consequence of these assignments, the orientation of the pterin ring of folate could be determined, and its conformation is similar to that of the productive dihydrofolate complex. Under these experimental conditions, only one bound form of the pterin ring could be detected

  20. Evaluation of Automatically Assigned Job-Specific Interview Modules

    NARCIS (Netherlands)

    Friesen, Melissa C; Lan, Qing; Ge, Calvin; Locke, Sarah J; Hosgood, Dean; Fritschi, Lin; Sadkowsky, Troy; Chen, Yu-Cheng; Wei, Hu; Xu, Jun; Lam, Tai Hing; Kwong, Yok Lam; Chen, Kexin; Xu, Caigang; Su, Yu-Chieh; Chiu, Brian C H; Ip, Kai Ming Dennis; Purdue, Mark P; Bassig, Bryan A; Rothman, Nat; Vermeulen, Roel

    OBJECTIVE: In community-based epidemiological studies, job- and industry-specific 'modules' are often used to systematically obtain details about the subject's work tasks. The module assignment is often made by the interviewer, who may have insufficient occupational hygiene knowledge to assign the

  1. Determining Feasible Solutions of a Multicriteria Assignment Problem.

    African Journals Online (AJOL)

    This paper presents an important research tool in operations research as it applies to a particular structure of the multicriteria assignment problem. The paper addresses the problem of effectiveness of feasible solutions of a multicriteria assignment problem and this was done in two steps. In the first step, we determine ...

  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. An Algorithm for Protein Helix Assignment Using Helix Geometry.

    Science.gov (United States)

    Cao, Chen; Xu, Shutan; Wang, Lincong

    2015-01-01

    Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone Cα atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins.

  4. Conceptualizing Patient Barriers to Nonadherence with Homework Assignments

    Science.gov (United States)

    Kazantzis, Nikolaos; Shinkfield, Gregg

    2007-01-01

    Nonadherence with homework assignments and, by implication, "barriers" to homework assignments are a frequent occurrence in the practice of standard cognitive therapy (Beck, A. T., Rush, A. J., Shaw, B. F., Emery, G. (1979). "Cognitive therapy of depression." New York: The Guilford Press). The clinical examples in this article illustrate some of…

  5. Negotiating Languages and Cultures: Enacting Translingualism through a Translation Assignment

    Science.gov (United States)

    Kiernan, Julia; Meier, Joyce; Wang, Xiqiao

    2016-01-01

    This collaborative project explores the affordances of a translation assignment in the context of a learner-centered pedagogy that places composition students' movement among languages and cultures as both a site for inquiry and subject of analysis. The translation assignment asks students to translate scholarly articles or culture stories from…

  6. 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

  7. SKU assignment to unidirectional picking lines using correlations ...

    African Journals Online (AJOL)

    Dierent assignments of DBNs to picking lines are evaluated using three measures, namely total walking distance, the number of resulting small cartons and work balance. Several approaches to assign DBNs to picking lines have been in- vestigated in literature. All of these approaches seek to minimise walking distance ...

  8. 47 CFR 74.786 - Digital channel assignments.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Digital channel assignments. 74.786 Section 74... Translator, and TV Booster Stations § 74.786 Digital channel assignments. (a) An applicant for a new low... authorized digital station shall endeavor to select a channel on which its operation is not likely to cause...

  9. The Eco-Sculpture Assignment: Using Art to Scaffold Metacognition

    Science.gov (United States)

    Polegato, Rosemary

    2014-01-01

    The Eco-Sculpture Assignment demonstrates that art may be used as a conduit to scaffold metacognition in marketing courses. Theoretical underpinnings are drawn from the literature on pedagogy used in general, marketing, and art education contexts. The assignment is described in detail, followed by examples of learner response that illustrate…

  10. Key Issue: Teacher Hiring, Placement, and Assignment Practices

    Science.gov (United States)

    Behrstock, Ellen; Coggshall, Jane G.

    2009-01-01

    The literature on teacher hiring and assignment tends to omit definitions of these key terms. An exception in Cohen-Vogel and Osborne-Lampkin (277), who define teacher assignment as "the reciprocal process between school management and teachers to guide decisions about who will teach, where they will teach, and what they will teach." But the…

  11. Writing Assignments: What We Know We Don't Know.

    Science.gov (United States)

    Beene, LynnDianne

    Questions raised by the misinterpretations evidenced in the final examination essays of a freshman English class should lead teachers to a new understanding of how the phrasing of writing assignments influences what students write. Some of the questions included: (1) How detailed must an assignment be to communicate its goals? (2) What type of…

  12. 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... Consumer Product Safety Improvement Act, 15 U.S.C. 2087; the Patient Protection and Affordable Care Act...

  13. 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... (FLSA) in sections 1511 and 1512 of the Patient Protection and Affordable Care Act of 2010, Public Law...

  14. Parentage assignment of progeny in mixed milt fertilization of ...

    African Journals Online (AJOL)

    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. Effective population size of ...

  15. Frequency assignment with minimum intermodulation noise for satellite SCPC systems

    Science.gov (United States)

    Lau, Y.-H.; Skellern, D. J.

    1991-01-01

    A simple, fast, and effective procedure for quasi-optimum frequency assignment of equal carrier systems is given. The quality of assignments is marginally the same as published results. The computation time has been reduced greatly; a conservative estimate shows that the reduction factor can be greater than N/2.

  16. A tri-objective, dynamic weapon assignment model for surface ...

    African Journals Online (AJOL)

    In this paper, a tri-objective, dynamic weapon assignment model is proposed by modelling the weapon assignment problem as a multi-objective variation of the celebrated vehicle routing problem with time windows. A multi-objective, evolutionary metaheuristic for solving the vehicle routing problem with time windows is ...

  17. 48 CFR 1442.202 - Assignment of contract administration.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Assignment of contract administration. 1442.202 Section 1442.202 Federal Acquisition Regulations System DEPARTMENT OF THE INTERIOR CONTRACT MANAGEMENT CONTRACT ADMINISTRATION AND AUDIT SERVICES Contract Administration Services 1442.202 Assignment of contract administration. ...

  18. 48 CFR 1342.202 - Assignment of contract administration.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Assignment of contract administration. 1342.202 Section 1342.202 Federal Acquisition Regulations System DEPARTMENT OF COMMERCE CONTRACT MANAGEMENT CONTRACT ADMINISTRATION Contract Administration Services 1342.202 Assignment of contract administration. The designee authorized...

  19. Graduate Writing Assignments across Faculties in a Canadian University

    Science.gov (United States)

    Shi, Ling; Dong, Yanning

    2015-01-01

    This study examines 143 graduate assignments across 12 faculties or schools in a Canadian university in order to identify types of writing tasks. Based on the descriptions provided by the instructors, we identified nine types of assignments, with scholarly essay being the most common, followed by summary and response, literature review, project,…

  20. 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

  1. On the Use of Writing Assignments in Intermediate Microeconomic Theory

    Science.gov (United States)

    O'Neill, Patrick B.

    2009-01-01

    A typical writing assignment in upper level required courses is a term paper. However many economics majors, particularly those in business schools, need to develop skill at writing shorter pieces. In this paper I describe numerous examples of shorter writing assignments that I have incorporated into an Intermediate Microeconomic Theory course.…

  2. Students' Evaluation of Writing Assignments in an Abnormal Psychology Course.

    Science.gov (United States)

    Procidano, Mary E.

    1991-01-01

    Presents a study in which students in an abnormal psychology class rated the usefulness of drafts for two writing assignments. Reports that a research proposal was more effective than a case study in generating interest in psychology and opportunity for creativity. Concludes that writing assignments should reflect important aspects of a…

  3. 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,…

  4. 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...

  5. 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...

  6. 32 CFR 150.11 - Assignment of counsel.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Assignment of counsel. 150.11 Section 150.11 National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE REGULATIONS PERTAINING TO MILITARY JUSTICE COURTS OF CRIMINAL APPEALS RULES OF PRACTICE AND PROCEDURE § 150.11 Assignment of counsel...

  7. 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

  8. Nanomechanical resonance detector

    Science.gov (United States)

    Grossman, Jeffrey C; Zettl, Alexander K

    2013-10-29

    An embodiment of a nanomechanical frequency detector includes a support structure and a plurality of elongated nanostructures coupled to the support structure. Each of the elongated nanostructures has a particular resonant frequency. The plurality of elongated nanostructures has a range of resonant frequencies. An embodiment of a method of identifying an object includes introducing the object to the nanomechanical resonance detector. A resonant response by at least one of the elongated nanostructures of the nanomechanical resonance detector indicates a vibrational mode of the object. An embodiment of a method of identifying a molecular species of the present invention includes introducing the molecular species to the nanomechanical resonance detector. A resonant response by at least one of the elongated nanostructures of the nanomechanical resonance detector indicates a vibrational mode of the molecular species.

  9. Electron Paramagnetic Resonance Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    ARTICLE. Electron Paramagnetic Resonance Spectroscopy. Biological Applications. B G Hegde. Recently, electron paramagnetic resonance (EPR) spectros- copy has emerged as a powerful tool to study the structure and dynamics of biological macromolecules such as proteins, protein aggregates ... research interests are.

  10. Crossing simple resonances

    Energy Technology Data Exchange (ETDEWEB)

    Collins, T.

    1985-08-01

    A simple criterion governs the beam distortion and/or loss of protons on a fast resonance crossing. Results from numerical integrations are illustrated for simple sextupole, octupole, and 10-pole resonances.

  11. Crossing a Nonlinear Resonance

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 9. Crossing a Nonlinear Resonance: Adiabatic Invariants and the Melnikov-Arnold Integral. Sudhir R Jain. General Article Volume 19 Issue 9 September 2014 pp 797-813 ...

  12. Wavelength Assignment in Hybrid Quantum-Classical Networks.

    Science.gov (United States)

    Bahrani, Sima; Razavi, Mohsen; Salehi, Jawad A

    2018-02-22

    Optimal wavelength assignment in dense-wavelength-division-multiplexing (DWDM) systems that integrate both quantum and classical channels is studied. In such systems, weak quantum key distribution (QKD) signals travel alongside intense classical signals on the same fiber, where the former can be masked by the background noise induced by the latter. Here, we investigate how optimal wavelength assignment can mitigate this problem. We consider different DWDM structures and various sources of crosstalk and propose several near-optimal wavelength assignment methods that maximize the total secret key rate of the QKD channels. Our numerical results show that the optimum wavelength assignment pattern is commonly consisted of several interspersed quantum and classical bands. Using our proposed techniques, the total secret key rate of quantum channels can substantially be improved, as compared to conventional assignment methods, in the noise dominated regimes. Alternatively, we can maximize the number of QKD users supported under certain key rate constraints.

  13. 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.

  14. A NOVEL APPROACH TO MEASURE THE CROSS SECTION OF THE O-18(p, alpha)N-15 RESONANT REACTION IN THE 0-200 keV ENERGY RANGE

    Czech Academy of Sciences Publication Activity Database

    La Cognata, M.; Spitaleri, C.; Mukhamedzhanov, A. M.; Banu, A.; Cherubini, S.; Coc, A.; Crucilla, V.; Goldberg, V.; Gulino, M.; Irgaziev, B.; Kiss, G. G.; Lamia, L.; Mrázek, Jaromír; Pizzone, R. G.; Puglia, S. M. R.; Rapisarda, G. G.; Romano, S.; Sergi, M. L.; Tabacaru, G.; Trache, L.; Tribble, R. E.; Trzaska, W.; Tumino, A.

    2010-01-01

    Roč. 708, č. 1 (2010), s. 796-811 ISSN 0004-637X Institutional research plan: CEZ:AV0Z10480505 Keywords : nuclear reactions * nucleosynthesis * abundances Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 7.436, year: 2010

  15. Resonant thermonuclear reaction rate

    International Nuclear Information System (INIS)

    Haubold, H.J.; Mathai, A.M.

    1986-01-01

    Basic physical principles for the resonant and nonresonant thermonuclear reaction rates are applied to find their standard representations for nuclear astrophysics. Closed-form representations for the resonant reaction rate are derived in terms of Meijer's G-function. Analytic representations of the resonant and nonresonant nuclear reaction rates are compared and the appearance of Meijer's G-function is discussed in physical terms

  16. Resonance tongues in Hill's equations : A geometric approach

    NARCIS (Netherlands)

    Broer, H; Simo, C

    2000-01-01

    The geometry of resonance tongues is considered in, mainly reversible, versions of Hill's equation, close to the classical Mathieu case. Hill's map assigns to each value of the multiparameter the corresponding Poincare matrix. Dy an averaging method, the geometry of Hill's map locally can be

  17. Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family.

    Science.gov (United States)

    Buchko, Garry W; Sofia, Heidi J

    2008-06-01

    Cyanothece 51142 contains a 78-residue protein, cce_0567, that falls into the DUF683 family of proteins associated with nitrogen fixation. Here we report the assignment of most of the main chain and 13C(beta) side chain resonances of the approximately 40 kDa homo-tetramer.

  18. Ovenized microelectromechanical system (MEMS) resonator

    Science.gov (United States)

    Olsson, Roy H; Wojciechowski, Kenneth; Kim, Bongsang

    2014-03-11

    An ovenized micro-electro-mechanical system (MEMS) resonator including: a substantially thermally isolated mechanical resonator cavity; a mechanical oscillator coupled to the mechanical resonator cavity; and a heating element formed on the mechanical resonator cavity.

  19. Evaluation of Automatically Assigned Job-Specific Interview Modules.

    Science.gov (United States)

    Friesen, Melissa C; Lan, Qing; Ge, Calvin; Locke, Sarah J; Hosgood, Dean; Fritschi, Lin; Sadkowsky, Troy; Chen, Yu-Cheng; Wei, Hu; Xu, Jun; Lam, Tai Hing; Kwong, Yok Lam; Chen, Kexin; Xu, Caigang; Su, Yu-Chieh; Chiu, Brian C H; Ip, Kai Ming Dennis; Purdue, Mark P; Bassig, Bryan A; Rothman, Nat; Vermeulen, Roel

    2016-08-01

    In community-based epidemiological studies, job- and industry-specific 'modules' are often used to systematically obtain details about the subject's work tasks. The module assignment is often made by the interviewer, who may have insufficient occupational hygiene knowledge to assign the correct module. We evaluated, in the context of a case-control study of lymphoid neoplasms in Asia ('AsiaLymph'), the performance of an algorithm that provided automatic, real-time module assignment during a computer-assisted personal interview. AsiaLymph's occupational component began with a lifetime occupational history questionnaire with free-text responses and three solvent exposure screening questions. To assign each job to one of 23 study-specific modules, an algorithm automatically searched the free-text responses to the questions 'job title' and 'product made or services provided by employer' using a list of module-specific keywords, comprising over 5800 keywords in English, Traditional and Simplified Chinese. Hierarchical decision rules were used when the keyword match triggered multiple modules. If no keyword match was identified, a generic solvent module was assigned if the subject responded 'yes' to any of the three solvent screening questions. If these question responses were all 'no', a work location module was assigned, which redirected the subject to the farming, teaching, health professional, solvent, or industry solvent modules or ended the questions for that job, depending on the location response. We conducted a reliability assessment that compared the algorithm-assigned modules to consensus module assignments made by two industrial hygienists for a subset of 1251 (of 11409) jobs selected using a stratified random selection procedure using module-specific strata. Discordant assignments between the algorithm and consensus assignments (483 jobs) were qualitatively reviewed by the hygienists to evaluate the potential information lost from missed questions with using

  20. Quantum mechanical resonances

    International Nuclear Information System (INIS)

    Cisneros S, A.; McIntosh, H.V.

    1982-01-01

    A discussion of the nature of quantum mechanical resonances is presented from the point of view of the spectral theory of operators. In the case of Bohr-Feshbach resonances, graphs are presented to illustrate the theory showing the decay of a doubly excited metastable state and the excitation of the resonance by an incident particle with proper energy. A characterization of resonances is given as well as a procedure to determine widths using the spectral density function. A sufficient condition is given for the validity of the Breit-Wigner formula for Bohr-Feshbach resonances. (author)

  1. 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.

  2. 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

  3. 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

  4. Controlling Parametric Resonance

    DEFF Research Database (Denmark)

    Galeazzi, Roberto; Pettersen, Kristin Ytterstad

    2012-01-01

    if the system undergoing it could transform the large amplitude motion into, for example, energy. Therefore the development of control strategies to induce parametric resonance into a system can be as valuable as those which aim at stabilizing the resonant oscillations. By means of a mechanical equivalent......Parametric resonance is a resonant phenomenon which takes place in systems characterized by periodic variations of some parameters. While seen as a threatening condition, whose onset can drive a system into instability, this chapter advocates that parametric resonance may become an advantage...... the authors review the conditions for the onset of parametric resonance, and propose a nonlinear control strategy in order to both induce the resonant oscillations and to stabilize the unstable motion. Lagrange’s theory is used to derive the dynamics of the system and input–output feedback linearization...

  5. A note on the assignments of Rydberg states of COS

    Science.gov (United States)

    Wu, C. Y. R.

    1982-01-01

    Assignments of the Rydberg states which converge to the respective X-tilde and B-tilde ion states of the COS(+) ion are reported. The assignments were made based on previously established orderings for the quantum defects of isoelectronic molecules. The Rydberg series I and II, which converge to the X-tilde 2 Pi state of COS(+), and the series III, IV, V, VI and VII, which converge to the B-tilde 2 Sigma + state, are assigned to molecular orbitals characterized by predominant sulfur orbitals, in contrast to those converging to the C-tilde states, which are characterized by oxygen atomic orbitals.

  6. Assignments of autoionization states of O2-asterisk

    Science.gov (United States)

    Wu, C. Y. Robert

    1987-01-01

    Attention is given to the uncertainties that remain concerning the autoionization states of O2 leading to the a 4Pi(u) and A 2Pi(u) states of O2(+), as well as some of the assignments of the autoionization states and the determinations of effective quantum numbers and quantum defects. The former problems of vibrational assignments are unambiguously established in view of a study of isotopic oxygen molecules. A systematic examination of the known Rydberg series is conducted, and new assignments and interpretations for several autoionization states leading to the various states of O2(+) are suggested.

  7. 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....... during operations. We introduce a basic static model that can be adapted to the layout of different airports. Afterwards we show how a decision support system based on a MIP-model can be designed in a dynamic real world environment. The system supports the decisions of the dispatcher during daily...

  8. 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.

  9. Characterizing Sailor and Command Enlisted Placement and Assignment Preferences

    National Research Council Canada - National Science Library

    Butler, Virginia

    2002-01-01

    .... DON currently matches sailors to billets using a labor-intensive detailing process. With evolving information technology, the assignment process could be accomplished using intelligent agents and web-based markets...

  10. 48 CFR 1442.602 - Assignment and location.

    Science.gov (United States)

    2010-10-01

    ... MANAGEMENT CONTRACT ADMINISTRATION AND AUDIT SERVICES Corporate Administrative Contracting Officer 1442.602 Assignment and location. The BPC has the authority to approve the appointment of a Corporate Administrative...

  11. 47 CFR 63.24 - Assignments and transfers of control.

    Science.gov (United States)

    2010-10-01

    ... (CONTINUED) EXTENSION OF LINES, NEW LINES, AND DISCONTINUANCE, REDUCTION, OUTAGE AND IMPAIRMENT OF SERVICE BY..., is a sale of assets and shall be treated as an assignment, which requires prior Commission approval...

  12. ZAP: a distributed channel assignment algorithm for cognitive radio networks

    Directory of Open Access Journals (Sweden)

    Munaretto Anelise

    2011-01-01

    Full Text Available Abstract We propose ZAP, an algorithm for the distributed channel assignment in cognitive radio (CR networks. CRs are capable of identifying underutilized licensed bands of the spectrum, allowing their reuse by secondary users without interfering with primary users. In this context, efficient channel assignment is challenging as ideally it must be simple, incur acceptable communication overhead, provide timely response, and be adaptive to accommodate frequent changes in the network. Another challenge is the optimization of network capacity through interference minimization. In contrast to related work, ZAP addresses these challenges with a fully distributed approach based only on local (neighborhood knowledge, while significantly reducing computational costs and the number of messages required for channel assignment. Simulations confirm the efficiency of ZAP in terms of (i the performance tradeoff between different metrics and (ii the fast achievement of a suitable assignment solution regardless of network size and density.

  13. A singular value sensitivity approach to robust eigenstructure assignment

    DEFF Research Database (Denmark)

    Søgaard-Andersen, Per; Trostmann, Erik; Conrad, Finn

    1986-01-01

    A design technique for improving the feedback properties of multivariable state feedback systems designed using eigenstructure assignment is presented. Based on a singular value analysis of the feedback properties a design parameter adjustment procedure is outlined. This procedure allows...

  14. AMPO Travel Modeling Working Group Meeting on Dynamic Traffic Assignment

    Science.gov (United States)

    2016-03-01

    On December 17-18, 2015, the Association of Metropolitan Planning Organizations (AMPO) convened a travel modeling working group meeting for the purpose of discussing Dynamic Traffic Assignment (DTA). Participants discussed the uses of DTA, challenges...

  15. 7 CFR 400.305 - Assignment of Nonstandard Classifications.

    Science.gov (United States)

    2010-01-01

    ... Underwriting Classification System Regulations for the 1991 and Succeeding Crop Years § 400.305 Assignment of... a combination of person and identified acreage for a crop or crop practice, type, variety, or crop...

  16. Context-Aware Reviewer Assignment for Trust Enhanced Peer Review.

    Science.gov (United States)

    Li, Lei; Wang, Yan; Liu, Guanfeng; Wang, Meng; Wu, Xindong

    2015-01-01

    Reviewer assignment is critical to peer review systems, such as peer-reviewed research conferences or peer-reviewed funding applications, and its effectiveness is a deep concern of all academics. However, there are some problems in existing peer review systems during reviewer assignment. For example, some of the reviewers are much more stringent than others, leading to an unfair final decision, i.e., some submissions (i.e., papers or applications) with better quality are rejected. In this paper, we propose a context-aware reviewer assignment for trust enhanced peer review. More specifically, in our approach, we first consider the research area specific expertise of reviewers, and the institution relevance and co-authorship between reviewers and authors, so that reviewers with the right expertise are assigned to the corresponding submissions without potential conflict of interest. In addition, we propose a novel cross-assignment paradigm, and reviewers are cross-assigned in order to avoid assigning a group of stringent reviewers or a group of lenient reviewers to the same submission. More importantly, on top of them, we propose an academic CONtext-aware expertise relevanCe oriEnted Reviewer cross-assignmenT approach (CONCERT), which aims to effectively estimate the "true" ratings of submissions based on the ratings from all reviewers, even though no prior knowledge exists about the distribution of stringent reviewers and lenient reviewers. The experiments illustrate that compared with existing approaches, our proposed CONCERT approach can less likely assign more than one stringent reviewers or lenient reviewers to a submission simultaneously and significantly reduce the influence of ratings from stringent reviewers and lenient reviewers, leading to trust enhanced peer review and selection, no matter what kind of distributions of stringent reviewers and lenient reviewers are.

  17. 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.

  18. Neural Mechanisms of Credit Assignment in a Multicue Environment

    Science.gov (United States)

    Kolling, Nils; Brown, Joshua W.; Rushworth, Matthew

    2016-01-01

    In complex environments, many potential cues can guide a decision or be assigned responsibility for the outcome of the decision. We know little, however, about how humans and animals select relevant information sources that should guide behavior. We show that subjects solve this relevance selection and credit assignment problem by selecting one cue and its association with a particular outcome as the main focus of a hypothesis. To do this, we examined learning while using a task design that allowed us to estimate the focus of each subject's hypotheses on a trial-by-trial basis. When a prediction is confirmed by the outcome, then credit for the outcome is assigned to that cue rather than an alternative. Activity in medial frontal cortex is associated with the assignment of credit to the cue that is the main focus of the hypothesis. However, when the outcome disconfirms a prediction, the focus shifts between cues, and the credit for the outcome is assigned to an alternative cue. This process of reselection for credit assignment to an alternative cue is associated with lateral orbitofrontal cortex. SIGNIFICANCE STATEMENT Learners should infer which features of environments are predictive of significant events, such as rewards. This “credit assignment” problem is particularly challenging when any of several cues might be predictive. We show that human subjects solve the credit assignment problem by implicitly “hypothesizing” which cue is relevant for predicting subsequent outcomes, and then credit is assigned according to this hypothesis. This process is associated with a distinctive pattern of activity in a part of medial frontal cortex. By contrast, when unexpected outcomes occur, hypotheses are redirected toward alternative cues, and this process is associated with activity in lateral orbitofrontal cortex. PMID:26818500

  19. 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.

  20. Atlas of neutron resonances

    CERN Document Server

    Mughabghab, Said

    2018-01-01

    Atlas of Neutron Resonances: Resonance Properties and Thermal Cross Sections Z= 1-60, Sixth Edition, contains an extensive list of detailed individual neutron resonance parameters for Z=1-60, as well as thermal cross sections, capture resonance integrals, average resonance parameters and a short survey of the physics of thermal and resonance neutrons. The long introduction contains: nuclear physics formulas aimed at neutron physicists; topics of special interest such as valence neutron capture, nuclear level density parameters, and s-, p-, and d-wave neutron strength functions; and various comparisons of measured quantities with the predictions of nuclear models, such as the optical model. As in the last edition, additional features have been added to appeal to a wider spectrum of users. These include: spin-dependent scattering lengths that are of interest to solid-state physicists, nuclear physicists and neutron evaluators; calculated and measured Maxwellian average 5-keV and 30-keV capture cross sections o...

  1. Dynamically generated resonances

    International Nuclear Information System (INIS)

    Oset, E.; Vicente Vacas, M.J.; Gonzalez, P.; Martinez-Torres, A.; Ramos, A.; Sarkar, S.; Sun Baoxi; Vijande, J.; Jido, D.; Sekihara, T.; Khemchandani, K.

    2009-01-01

    In this talk I report on recent work related to the dynamical generation of baryonic resonances, some made up from pseudoscalar meson-baryon, others from vector meson-baryon and a third type from two meson-one baryon systems. We can establish a correspondence with known baryonic resonances, reinforcing conclusions previously drawn and bringing new light on the nature of some baryonic resonances of higher mass. (authors)

  2. 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.

  3. 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.

  4. Electron paramagnetic resonance

    CERN Document Server

    Al'tshuler, S A

    2013-01-01

    Electron Paramagnetic Resonance is a comprehensive text on the field of electron paramagnetic resonance, covering both the theoretical background and the results of experiment. This book is composed of eight chapters that cover theoretical materials and experimental data on ionic crystals, since these are the materials that have been most extensively studied by the methods of paramagnetic resonance. The opening chapters provide an introduction to the basic principles of electron paramagnetic resonance and the methods of its measurement. The next chapters are devoted to the theory of spectra an

  5. 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)

  6. 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)

  7. On open electromagnetic resonators: relation between interferometers and resonators

    International Nuclear Information System (INIS)

    Manenkov, Aleksandr A; Bykov, Vladimir P; Kuleshov, N V

    2010-01-01

    The physical difference between the concepts 'Fabry-Perot interferometer' and 'open resonator' is discussed. It is shown that the use of the term 'Fabry-Perot resonator' for open laser resonators is incorrect both from the historical viewpoint and from the viewpoint of the physical meaning of the processes occurring in these resonators. (laser beams and resonators)

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Protein subfamily assignment using the Conserved Domain Database

    Directory of Open Access Journals (Sweden)

    Marchler-Bauer Aron

    2008-11-01

    Full Text Available Abstract Background Domains, evolutionarily conserved units of proteins, are widely used to classify protein sequences and infer protein function. Often, two or more overlapping domain models match a region of a protein sequence. Therefore, procedures are required to choose appropriate domain annotations for the protein. Here, we propose a method for assigning NCBI-curated domains from the Curated Domain Database (CDD that takes into account the organization of the domains into hierarchies of homologous domain models. Findings Our analysis of alignment scores from NCBI-curated domain assignments suggests that identifying the correct model among closely related models is more difficult than choosing between non-overlapping domain models. We find that simple heuristics based on sorting scores and domain-specific thresholds are effective at reducing classification error. In fact, in our test set, the heuristics result in almost 90% of current misclassifications due to missing domain subfamilies being replaced by more generic domain assignments, thereby eliminating a significant amount of error within the database. Conclusion Our proposed domain subfamily assignment rule has been incorporated into the CD-Search software for assigning CDD domains to query protein sequences and has significantly improved pre-calculated domain annotations on protein sequences in NCBI's Entrez resource.

  14. Static assignment of complex stochastic tasks using stochastic majorization

    Science.gov (United States)

    Nicol, David; Simha, Rahul; Towsley, Don

    1992-01-01

    We consider the problem of statically assigning many tasks to a (smaller) system of homogeneous processors, where a task's structure is modeled as a branching process, and all tasks are assumed to have identical behavior. We show how the theory of majorization can be used to obtain a partial order among possible task assignments. Our results show that if the vector of numbers of tasks assigned to each processor under one mapping is majorized by that of another mapping, then the former mapping is better than the latter with respect to a large number of objective functions. In particular, we show how measurements of finishing time, resource utilization, and reliability are all captured by the theory. We also show how the theory may be applied to the problem of partitioning a pool of processors for distribution among parallelizable tasks.

  15. A Stone Resource Assignment Model under the Fuzzy Environment

    Directory of Open Access Journals (Sweden)

    Liming Yao

    2012-01-01

    to tackle a stone resource assignment problem with the aim of decreasing dust and waste water emissions. On the upper level, the local government wants to assign a reasonable exploitation amount to each stone plant so as to minimize total emissions and maximize employment and economic profit. On the lower level, stone plants must reasonably assign stone resources to produce different stone products under the exploitation constraint. To deal with inherent uncertainties, the object functions and constraints are defuzzified using a possibility measure. A fuzzy simulation-based improved simulated annealing algorithm (FS-ISA is designed to search for the Pareto optimal solutions. Finally, a case study is presented to demonstrate the practicality and efficiency of the model. Results and a comparison analysis are presented to highlight the performance of the optimization method, which proves to be very efficient compared with other algorithms.

  16. Task Assignment Heuristics for Parallel and Distributed CFD Applications

    Science.gov (United States)

    Lopez-Benitez, Noe; Djomehri, M. Jahed; Biswas, Rupak

    2003-01-01

    This paper proposes a task graph (TG) model to represent a single discrete step of multi-block overset grid computational fluid dynamics (CFD) applications. The TG model is then used to not only balance the computational workload across the overset grids but also to reduce inter-grid communication costs. We have developed a set of task assignment heuristics based on the constraints inherent in this class of CFD problems. Two basic assignments, the smallest task first (STF) and the largest task first (LTF), are first presented. They are then systematically costs. To predict the performance of the proposed task assignment heuristics, extensive performance evaluations are conducted on a synthetic TG with tasks defined in terms of the number of grid points in predetermined overlapping grids. A TG derived from a realistic problem with eight million grid points is also used as a test case.

  17. 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

  18. A New Resonance Tube

    Science.gov (United States)

    Bates, Alan

    2017-01-01

    The measurement of the speed of sound in air with the resonance tube is a popular experiment that often yields accurate results. One approach is to hold a vibrating tuning fork over an air column that is partially immersed in water. The column is raised and lowered in the water until the generated standing wave produces resonance: this occurs at…

  19. Nuclear Magnetic Resonance Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 1. Nuclear Magnetic Resonance Spectroscopy. Susanta Das. General Article Volume 9 Issue 1 January 2004 pp 34-49. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/009/01/0034-0049. Keywords.

  20. Resonance and Fractal Geometry

    NARCIS (Netherlands)

    Broer, Henk W.

    The phenomenon of resonance will be dealt with from the viewpoint of dynamical systems depending on parameters and their bifurcations. Resonance phenomena are associated to open subsets in the parameter space, while their complement corresponds to quasi-periodicity and chaos. The latter phenomena

  1. Electron Paramagnetic Resonance Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Electron Paramagnetic Resonance Spectroscopy: Biological Applications. B G Hegde. General Article Volume 20 Issue 11 November 2015 pp 1017-1032. Fulltext. Click here to view fulltext PDF. Permanent link:

  2. Laser magnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    Ferrari, C.A.

    1985-01-01

    The technique of laser resonance magnetic resonance allows one to study the high-resolution spectroscopy of transient paramagnetic species, viz, atoms, radicals, and molecular ions. This article is a brief exposition of the method, describing the principles, instrumentation and applicability of the IR and FIR-LMR and shows results of HF + . (Author) [pt

  3. Cardiac magnetic resonance imaging

    African Journals Online (AJOL)

    2011-03-06

    Mar 6, 2011 ... Cardiac magnetic resonance imaging. Cardiovascular magnetic resonance imaging is becoming a routine diagnostic technique. BRUCE s sPOTTiswOOdE, PhD. MRC/UCT Medical Imaging Research Unit, University of Cape Town, and Division of Radiology, Stellenbosch University. Bruce Spottiswoode ...

  4. Nuclear Magnetic Resonance Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 1. Nuclear Magnetic Resonance Spectroscopy. Susanta Das. General Article Volume 9 Issue 1 January 2004 pp 34-49. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/009/01/0034-0049. Keywords.

  5. Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

    Science.gov (United States)

    Akhmedov, Murodzhon; Çatay, Bülent; Apaydın, Mehmet Serkan

    2015-12-01

    Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results.

  6. Resonant snubber inverter

    Science.gov (United States)

    Lai, J.S.; Young, R.W. Sr.; Chen, D.; Scudiere, M.B.; Ott, G.W. Jr.; White, C.P.; McKeever, J.W.

    1997-06-24

    A resonant, snubber-based, soft switching, inverter circuit achieves lossless switching during dc-to-ac power conversion and power conditioning with minimum component count and size. Current is supplied to the resonant snubber branches solely by the main inverter switches. Component count and size are reduced by use of a single semiconductor switch in the resonant snubber branches. Component count is also reduced by maximizing the use of stray capacitances of the main switches as parallel resonant capacitors. Resonance charging and discharging of the parallel capacitances allows lossless, zero voltage switching. In one embodiment, circuit component size and count are minimized while achieving lossless, zero voltage switching within a three-phase inverter. 14 figs.

  7. Fundamentals of nanomechanical resonators

    CERN Document Server

    Schmid, Silvan; Roukes, Michael Lee

    2016-01-01

    This authoritative book introduces and summarizes the latest models and skills required to design and optimize nanomechanical resonators, taking a top-down approach that uses macroscopic formulas to model the devices. The authors cover the electrical and mechanical aspects of nano electromechanical system (NEMS) devices. The introduced mechanical models are also key to the understanding and optimization of nanomechanical resonators used e.g. in optomechanics. Five comprehensive chapters address: The eigenmodes derived for the most common continuum mechanical structures used as nanomechanical resonators; The main sources of energy loss in nanomechanical resonators; The responsiveness of micro and nanomechanical resonators to mass, forces, and temperature; The most common underlying physical transduction mechanisms; The measurement basics, including amplitude and frequency noise. The applied approach found in this book is appropriate for engineering students and researchers working with micro and nanomechanical...

  8. Resonant snubber inverter

    Science.gov (United States)

    Lai, Jih-Sheng; Young, Sr., Robert W.; Chen, Daoshen; Scudiere, Matthew B.; Ott, Jr., George W.; White, Clifford P.; McKeever, John W.

    1997-01-01

    A resonant, snubber-based, soft switching, inverter circuit achieves lossless switching during dc-to-ac power conversion and power conditioning with minimum component count and size. Current is supplied to the resonant snubber branches solely by the main inverter switches. Component count and size are reduced by use of a single semiconductor switch in the resonant snubber branches. Component count is also reduced by maximizing the use of stray capacitances of the main switches as parallel resonant capacitors. Resonance charging and discharging of the parallel capacitances allows lossless, zero voltage switching. In one embodiment, circuit component size and count are minimized while achieving lossless, zero voltage switching within a three-phase inverter.

  9. 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

  10. Statistical methods of spin assignment in compound nuclear reactions

    International Nuclear Information System (INIS)

    Mach, H.; Johns, M.W.

    1984-01-01

    Spin assignment to nuclear levels can be obtained from standard in-beam gamma-ray spectroscopy techniques and in the case of compound nuclear reactions can be complemented by statistical methods. These are based on a correlation pattern between level spin and gamma-ray intensities feeding low-lying levels. Three types of intensity and level spin correlations are found suitable for spin assignment: shapes of the excitation functions, ratio of intensity at two beam energies or populated in two different reactions, and feeding distributions. Various empirical attempts are examined and the range of applicability of these methods as well as the limitations associated with them are given. 12 references

  11. Statistical methods of spin assignment in compound nuclear reactions

    International Nuclear Information System (INIS)

    Mach, H.; Johns, M.W.

    1985-01-01

    Spin assignment to nuclear levels can be obtained from standard in-beam gamma-ray spectroscopy techniques and in the case of compound nuclear reactions can be complemented by statistical methods. These are based on a correlation pattern between level spin and gamma-ray intensities feeding low-lying levels. Three types of intensity and level spin correlations are found suitable for spin assignment: shapes of the excitation functions, ratio of intensity at two beam energies or populated in two different reactions, and feeding distributions. Various empirical attempts are examined and the range of applicability of these methods as well as the limitations associated with them are given

  12. Automated Negotiation for Resource Assignment in Wireless Surveillance Sensor Networks

    Science.gov (United States)

    de la Hoz, Enrique; Gimenez-Guzman, Jose Manuel; Marsa-Maestre, Ivan; Orden, David

    2015-01-01

    Due to the low cost of CMOS IP-based cameras, wireless surveillance sensor networks have emerged as a new application of sensor networks able to monitor public or private areas or even country borders. Since these networks are bandwidth intensive and the radioelectric spectrum is limited, especially in unlicensed bands, it is mandatory to assign frequency channels in a smart manner. In this work, we propose the application of automated negotiation techniques for frequency assignment. Results show that these techniques are very suitable for the problem, being able to obtain the best solutions among the techniques with which we have compared them. PMID:26610512

  13. Intermodulation interference-minimum frequency assignment for satellite SCPC systems

    Science.gov (United States)

    Okinaka, H.; Yasuda, Y.; Hirata, Y.

    1984-04-01

    This paper addresses frequency assignment for single-level and multilevel SCPC systems. In order to obtain the optimum channel allocation, where the influence of intermodulation noise on carriers is minimized, a practical and effective method is proposed. The quasi-optimum solutions obtained with the proposed method are presented for single-level SCPC systems, showing their advantage in intermodulation noise reduction. Concerning frequency assignment for multilevel SCPC systems, two strategies to realize the quasi-optimum channel allocation are compared with regard to the improvement in carrier-to-intermodulation noise power ratio. The performance of the obtained channel allocation indicates the effectiveness of the proposed optimization method.

  14. Evoked Feelings, Assigned Meanings and Constructed Knowledge Based on Mistakes

    Directory of Open Access Journals (Sweden)

    Luciane Guimarães Batistella Bianchini

    2017-09-01

    Full Text Available By means of Piaget's critical clinical method, the study investigated the meanings assigned to mistakes by four students in different activities and interactive situations. The research also analyzed the results of using self-regulatory situations in understanding mistakes initially committed by the students. Data collection instruments consisted of games, video recordings, diaries and interviews. Following intervention, the students were able to recognize their competence, establish positive interactions within the group, and avoid viewing mistakes as obstacles to learning. We concluded that the meanings assigned to mistakes depend on certain variables, among them feelings nurtured by the individuals about themselves, the other, and the object of knowledge.

  15. The use of meta-heuristics for airport gate assignment

    DEFF Research Database (Denmark)

    Cheng, Chun-Hung; Ho, Sin C.; Kwan, Cheuk-Lam

    2012-01-01

    Improper assignment of gates may result in flight delays, inefficient use of the resource, customer’s dissatisfaction. A typical metropolitan airport handles hundreds of flights a day. Solving the gate assignment problem (GAP) to optimality is often impractical. Meta-heuristics have recently been...... proposed to generate good solutions within a reasonable timeframe. In this work, we attempt to assess the performance of three meta-heuristics, namely, genetic algorithm (GA), tabu search (TS), simulated annealing (SA) and a hybrid approach based on SA and TS. Flight data from Incheon International Airport...

  16. Automated Negotiation for Resource Assignment in Wireless Surveillance Sensor Networks

    Directory of Open Access Journals (Sweden)

    Enrique de la Hoz

    2015-11-01

    Full Text Available Due to the low cost of CMOS IP-based cameras, wireless surveillance sensor networks have emerged as a new application of sensor networks able to monitor public or private areas or even country borders. Since these networks are bandwidth intensive and the radioelectric spectrum is limited, especially in unlicensed bands, it is mandatory to assign frequency channels in a smart manner. In this work, we propose the application of automated negotiation techniques for frequency assignment. Results show that these techniques are very suitable for the problem, being able to obtain the best solutions among the techniques with which we have compared them.

  17. Asymmetry in some common assignment algorithms: the dispersion factor solution

    OpenAIRE

    T de la Barra; B Pérez

    1986-01-01

    Many common assignment algorithms are based on Dial's original design to determine the paths that trip makers will follow from a given origin to destination centroids. The purpose of this paper is to show that the rules that have to be applied result in two unwanted properties. The first is that trips assigned from an origin centroid i to a destination j can be dramatically different to those resulting from centroid j to centroid i , even if the number of trips is the same and the network is ...

  18. Probing the Carbonyl Functionality of a Petroleum Resin and Asphaltene through Oximation and Schiff Base Formation in Conjunction with N-15 NMR.

    Directory of Open Access Journals (Sweden)

    Kevin A Thorn

    Full Text Available Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected.

  19. Probing the carbonyl functionality of a petroleum resin and asphaltene through oximation and schiff base formation in conjunction with N-15 NMR

    Science.gov (United States)

    Thorn, Kevin A.; Cox, Larry G.

    2015-01-01

    Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR) spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS) 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected.

  20. 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.

  1. Characterization of mu s-ms dynamics of proteins using a combined analysis of N-15 NMR relaxation and chemical shift: Conformational exchange in plastocyanin induced by histidine protonations

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Thuesen, Marianne Hallberg; Christensen, Hans Erik Mølager

    2004-01-01

    variabilis (A.v. PCu) (Ma, L.; Hass, M. A. S.; Vierick, N.; Kristensen, S. M.; Ulstrup, J.; Led, J. J. Biochemistry 2003, 42, 320-330). The R-1 and R-2 relaxation rates of the backbone N-15 nuclei were measured at a series of pH and temperatures on an 15N labeled sample of A.v. PCu, and the 15 N chemical...

  2. A study of 15N- 15N and 15N- 13C spin couplings in some 15N labeled mesoionic 1-oxa and 1-thia-2,3,4-triazoles

    Science.gov (United States)

    Jaźwiński, J.; Staszewska, O.; Stefaniak, L.; Webb, G. A.

    1996-03-01

    15N- 15N and 15N- 13C spin-spin couplings are reported for seven 15N labeled 1-oxa and 1-thia-2,3,4-triazoles and three sydnonimines. For the former class of compounds the spin-spin coupling data show a close similarity between the N2N3 and N3N4 bonds which had not previously been suspected from chemical shift measurements.

  3. Magnetic Resonance Imaging (MRI) -- Head

    Medline Plus

    Full Text Available ... Site Index A-Z Magnetic Resonance Imaging (MRI) - Head Magnetic resonance imaging (MRI) of the head uses ... of the Head? What is MRI of the Head? Magnetic resonance imaging (MRI) is a noninvasive medical ...

  4. (1)H, (13)C and (15)N chemical shift assignments for the cyclic-nucleotide binding homology domain of a KCNH channel.

    Science.gov (United States)

    Li, Qingxin; Ng, Hui Qi; Kang, CongBao

    2015-04-01

    The KCNH family of ion channels plays important roles in heart and nerve cells. The C-terminal region of the KCNH channel contains a cyclic-nucleotide binding homology domain (CNBHD) which is important for channel gating through interaction with the eag domain. To study the solution structure of CNBHD of the KCNH channel of zebrafish, we over-expressed and purified this domain from E. coli. We report the resonance assignments of the CNBHD. The assignments will allow us to perform structural and dynamic studies for this domain, which will shed light on its role in channel gating.

  5. Advances in magnetic resonance 10

    CERN Document Server

    Waugh, John S

    2013-01-01

    Advances in Magnetic Resonance, Volume 10, presents a variety of contributions to the theory and practice of magnetic resonance. The book contains three chapters that examine superoperators in magnetic resonance; ultrasonically modulated paramagnetic resonance; and the utility of electron paramagnetic resonance (EPR) and electron-nuclear double-resonance (ENDOR) techniques for studying low-frequency modes of atomic fluctuations and their significance for understanding the mechanism of structural phase transitions in solids.

  6. 5 CFR 9701.362 - Special assignment payments.

    Science.gov (United States)

    2010-01-01

    ... HUMAN RESOURCES MANAGEMENT SYSTEM Pay and Pay Administration Special Payments § 9701.362 Special... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Special assignment payments. 9701.362 Section 9701.362 Administrative Personnel DEPARTMENT OF HOMELAND SECURITY HUMAN RESOURCES MANAGEMENT...

  7. Threat evaluation and weapon assignment decision support: A ...

    African Journals Online (AJOL)

    ... stands within the context of a ground based air defence system (GBADS) at the turn of the twenty first century. However, much of the contents of the paper maye generalized to military environments other than a GBADS one. Keywords: Threat evaluation, weapon assignment, decision support. ORiON Vol. 23 (2) 2007: pp.

  8. The Influence of Consistent Assignment on Nursing Home Deficiency Citations

    Science.gov (United States)

    Castle, Nicholas G.

    2011-01-01

    Objective: The association of consistent assignment of nurse aides (NAs) with quality of care and quality of life of nursing home residents is examined (using 5 groups of deficiency citations). Methods: Data used came from a survey of nursing home administrators, the Online Survey Certification and Reporting data, and the Area Resource File. The…

  9. Protect Heterogeneous Environment Distributed Computing from Malicious Code Assignment

    Directory of Open Access Journals (Sweden)

    V. S. Gorbatov

    2011-09-01

    Full Text Available The paper describes the practical implementation of the protection system of heterogeneous environment distributed computing from malicious code for the assignment. A choice of technologies, development of data structures, performance evaluation of the implemented system security are conducted.

  10. 20 CFR 416.533 - Transfer or assignment of benefits.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Transfer or assignment of benefits. 416.533 Section 416.533 Employees' Benefits SOCIAL SECURITY ADMINISTRATION SUPPLEMENTAL SECURITY INCOME FOR THE AGED, BLIND, AND DISABLED Payment of Benefits, Overpayments, and Underpayments § 416.533 Transfer or...

  11. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    Science.gov (United States)

    Horowitz, Scott; Koldewey, Philipp; Bardwell, James C.

    2014-01-01

    Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the…

  12. ELECTRICAL AND ELECTRONIC INDUSTRIAL CONTROL. BASIC ELECTRICITY, UNIT 2, ASSIGNMENTS.

    Science.gov (United States)

    SUTTON, MACK C.

    THIS GUIDE IS FOR INDIVIDUAL STUDENT USE IN STUDYING BASIC ELECTRICAL FUNDAMENTALS IN ELECTRICAL-ELECTRONIC PROGRAMS. IT WAS DEVELOPED BY AN INSTRUCTIONAL MATERIALS SPECIALIST AND ADVISERS. THE COURSE OBJECTIVE IS TO DEVELOP AN UNDERSTANDING OF DIRECT CURRENT FUNDAMENTALS. EACH OF THE 15 ASSIGNMENT SHEETS PROVIDES THE LESSON SUBJECT, PURPOSE,…

  13. A new heuristic for the quadratic assignment problem

    OpenAIRE

    Zvi Drezner

    2002-01-01

    We propose a new heuristic for the solution of the quadratic assignment problem. The heuristic combines ideas from tabu search and genetic algorithms. Run times are very short compared with other heuristic procedures. The heuristic performed very well on a set of test problems.

  14. Asset Mapping: A Course Assignment and Community Assessment

    Science.gov (United States)

    Crozier, Mary; Melchior, Florence

    2013-01-01

    Asset mapping is a relatively new data collection strategy to identify services, staff capacity, programs, resources, values, and other protective factors in a geographic area that can be juxtaposed to risk factors when initiating community planning. A substance abuse prevention course for undergraduates added an assignment of assessing community…

  15. 48 CFR 1552.211-74 - Work assignments.

    Science.gov (United States)

    2010-10-01

    ... knowledge and belief, that all actual or potential organizational conflicts of interest have been reported... assignment or similar tasking document, the Contractor shall provide a conflict of interest certification... directly related to a site, the Contractor is only required to provide a conflict of interest certification...

  16. A multiobjective approach towards weapon assignment in a ground ...

    African Journals Online (AJOL)

    A typical ground-based air defence (GBAD) environment comprises defended assets on the ground which require protection from enemy aircraft entering the defended airspace. ... of computerised threat evaluation and weapon assignment (TEWA) decision support systems (DSSs) within the context of a GBAD system.

  17. Wavelength and fiber assignment problems on avionic networks

    DEFF Research Database (Denmark)

    Zhang, Jiang; An, Yi; Berger, Michael Stübert

    2011-01-01

    This paper solves the wavelength and fiber assignment problems with systems' isolation requirements on the avionic ring networks. The experiment results give a general glace of the numbers of the wavelengths and fibers are required under certain scale of networks. At the beginning of increasing...

  18. A multiobjective approach towards weapon assignment in a ground ...

    African Journals Online (AJOL)

    (TCI) and involves the classification of aircraft into different platform types such as rotary wing, fixed wing, cargo, .... After consulting with TEWA DSS experts Potgieter [14] and Roux [15], as well as military expert Visser [20], a survey ... in the responses. A total of fourteen factors influencing WA assignment decisions were.

  19. Using Clouds for MapReduce Measurement Assignments

    Science.gov (United States)

    Rabkin, Ariel; Reiss, Charles; Katz, Randy; Patterson, David

    2013-01-01

    We describe our experiences teaching MapReduce in a large undergraduate lecture course using public cloud services and the standard Hadoop API. Using the standard API, students directly experienced the quality of industrial big-data tools. Using the cloud, every student could carry out scalability benchmarking assignments on realistic hardware,…

  20. Comparison of Categorical Assignments of the BSRI and the PAQ.

    Science.gov (United States)

    Gaa, John P.; Liberman, Dov

    The degree of agreement between the Bem Sex Role Inventory (BSRI) and the Personality Attributes Questionnaire (PAQ) in assigning sex role categories was investigated by administering both instruments to undergraduate education majors. As a result of scoring, subjects were classified as androgynous, masculine, feminine, or undifferentiated. It was…

  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. Three results on frequency assignment in linear cellular networks

    Czech Academy of Sciences Publication Activity Database

    Chrobak, M.; Sgall, Jiří

    2010-01-01

    Roč. 411, č. 1 (2010), s. 131-137 ISSN 0304-3975 R&D Projects: GA MŠk(CZ) 1M0545; GA AV ČR IAA100190902 Keywords : frequency assignment * approximation algorithms * online algorithms Subject RIV: BA - General Mathematics Impact factor: 0.838, year: 2010 http://www.sciencedirect.com/science/article/pii/S0304397509006574

  3. 48 CFR 3042.202 - Assignment of contract administration.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 7 2010-10-01 2010-10-01 false Assignment of contract administration. 3042.202 Section 3042.202 Federal Acquisition Regulations System DEPARTMENT OF HOMELAND SECURITY, HOMELAND SECURITY ACQUISITION REGULATION (HSAR) CONTRACT MANAGEMENT CONTRACT ADMINISTRATION AND AUDIT SERVICES Contract Administration...

  4. Gamification for Non-Majors Mathematics: An Innovative Assignment Model

    Science.gov (United States)

    Leong, Siow Hoo; Tang, Howe Eng

    2017-01-01

    The most important ingredient of the pedagogy for teaching non-majors is getting their engagement. This paper proposes to use gamification to engage non-majors. An innovative game termed as Cover the Hungarian's Zeros is designed to tackle the common weakness of non-majors mathematics in solving the assignment problem using the Hungarian Method.…

  5. Understanding and Supporting the Career Implications of International Assignments

    Science.gov (United States)

    Collings, David G.; Doherty, Noeleen; Luethy, Madeleine; Osborn, Derek

    2011-01-01

    International assignments represent an important form of migration in the global economy. In contrast to most other migrants, international assignees enjoy a relatively privileged position in the labor market. Authored by a diverse team of academics and practitioners, this paper draws on insights from empirical research and unpublished examples…

  6. Assignments of rights and obligations under a gas sales contract

    International Nuclear Information System (INIS)

    Kowch, J.R.M.

    1996-01-01

    A general overview of the principles of assignment in a gas sales contract was presented. Assignment is a process wherein the rights or obligations under a contract are transferred from one of the contracting parties to a third party. It is, in other words, the introduction of a new party to the original contractual relationship. Under the rights and obligations of a gas sales contract, the most important right of the seller is to have its gas taken and to be paid. Likewise, the most important obligation of the buyer is to take the gas and pay for it. An assignment by either party has the potential to alter the original expectations of the parties or the basis of which they committed to the contract in the first place. Prior to deregulation and unbundling initiatives, gas sellers and buyers could enter a 20 year sales contract and deal exclusively with each other over the entire 20 year term. Since deregulation, there are more players, and a higher level of corporate acquisitions, divestitures, rationalizations, and restructuring. Today, there are greater chances than ever before that the original party to a contract may change, or that certain rights and obligations may be assigned to a third party and affect the expectations under the contract

  7. Error treatment in students' written assignments in Discourse Analysis

    African Journals Online (AJOL)

    ... is generally no consensus on how lecturers should treat students' errors in written assignments, observations in this study enabled the researcher to provide certain strategies that lecturers can adopt. Key words: Error treatment; error handling; corrective feedback, positive cognitive feedback; negative cognitive feedback; ...

  8. Automatic Functionality Assignment to AUTOSAR Multicore Distributed Architectures

    DEFF Research Database (Denmark)

    Maticu, Florin; Pop, Paul; Axbrink, Christian

    2016-01-01

    is modeled as a set of software components composed of subtasks, called runnables, in AUTOSAR terminology. We have proposed a Simulated Annealing metaheuristic optimization that decides: the (i) mapping of software components to multicore ECUs, (ii) the assignment of runnables to the ECU cores, (iii...

  9. 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…

  10. Submission of art studio-based assignments: Students experience ...

    African Journals Online (AJOL)

    In this study, the reasons why art students are reluctant to complete their studio assignments on time are critically examined. Both quantitative and qualitative data, derived from survey and interviews were used to examine students' attitudes and investigate their experience. The study revealed that although procrastination is ...

  11. 77 FR 8174 - EPAAR Prescription for Work Assignments

    Science.gov (United States)

    2012-02-14

    ... instructive language. The new policy language contained under 1511.011-74, Work Assignments (Deviation), will...) A small business that meets the definition of a small business found in the Small Business Act and..., Public Law 104-113, directs EPA to use voluntary consensus standards in it regulatory activities, unless...

  12. Single Assignment C (SAC): High Productivity meets High Performance

    NARCIS (Netherlands)

    Grelck, C.; Zsók, V.; Horváth, Z.; Plasmeijer, R.

    2012-01-01

    We present the ins and outs of the purely functional, data parallel programming language SaC (Single Assignment C). SaC defines state- and side-effect-free semantics on top of a syntax resembling that of imperative languages like C/C++/C# or Java: functional programming with curly brackets. In

  13. A Competitive and Experiential Assignment in Search Engine Optimization Strategy

    Science.gov (United States)

    Clarke, Theresa B.; Clarke, Irvine, III

    2014-01-01

    Despite an increase in ad spending and demand for employees with expertise in search engine optimization (SEO), methods for teaching this important marketing strategy have received little coverage in the literature. Using Bloom's cognitive goals hierarchy as a framework, this experiential assignment provides a process for educators who may be new…

  14. Nursing Distance Learning Course Comparison of Assignments and Examination Scores

    Science.gov (United States)

    Mundine, Jennifer

    2016-01-01

    Nursing programs have embraced distance learning in their curricula, but discussion is ongoing about course assignments and grading criteria to increase examination scores in nursing distance learning courses. Because course examinations are a predictor of success on the postgraduate licensing examination (NCLEX-RN), the purpose of this study was…

  15. 5 CFR 351.702 - Qualifications for assignment.

    Science.gov (United States)

    2010-01-01

    .... This determination includes recency of experience, when appropriate. (b) The sex of an employee may not be considered in determining whether an employee is qualified for a position, except for positions... as provided in § 351.703, an employee is qualified for assignment under § 351.701 if the employee: (1...

  16. Towards Next Generation Rubrics: An Automated Assignment Feedback System

    Directory of Open Access Journals (Sweden)

    Nilupulee Nathawitharana

    2017-11-01

    Full Text Available As the use of blended learning environments and digital technologies become integrated into the higher education sector, rich technologies such as analytics have shown promise in facilitating teaching and learning. One popular application of analytics is Automated Writing Evaluation (AWE systems. Such systems can be used in a formative way; for example, by providing students with feedback on digitally submitted assignments. This paper presents work on the development of an AWE software tool for an Australian university using advanced text analytics techniques. The tool was designed to provide students with timely feedback on their initial assignment drafts, for revision and further improvement. Moreover, it could also assist academics in better understanding students’ assignment performance so as to inform future teaching activities. The paper provides details on the methodology used for development of the software, and presents the results obtained from the analysis of text-based assignments submitted in two subjects. The results are discussed, highlighting how the tool can provide practical value, followed by insights into existing challenges and possible future directions.

  17. The Rescue Mission: Assigning Guilt to a Chaotic Scene.

    Science.gov (United States)

    Procter, David E.

    1987-01-01

    Seeks to identify rhetorical distinctiveness of the rescue mission as a form of belligerency--examining presidential discourse justifying the 1985 Lebanon intervention, the 1965 Dominican intervention, and the 1983 Grenada intervention. Argues that the distinction is in guilt narrowly assigned to a chaotic scene and the concomitant call for…

  18. submission of art studio-based assignments: students experience

    African Journals Online (AJOL)

    PUBLICATIONS1

    on web-based language learners performance and motivation. CALICO Journal, 27(2): 298. -310. Chin, C. and Brown, D. E. (2000). Learning in science: A comparison of deep and surface approaches. Journal of Research in Science. Teaching, 37(2): 109-138. Darbyshire, P. (2000). Distributed Web-Based. Assignment ...

  19. Identifying clinical cases among patients assigned to psychoanalytic treatment

    NARCIS (Netherlands)

    Berghout, Caspar C; Zevalkink, D.J.

    2008-01-01

    The present study compared 89 patients assigned to long-term psychoanalytic psychotherapy or psychoanalysis in the Netherlands with psychiatric and nonclinical norm groups with regard to symptoms and personality pathology as assessed with six instruments. Patients filled in four self-report

  20. Using Portfolio Assignments to Assess Students' Mathematical Thinking

    Science.gov (United States)

    Fukawa-Connelly, Timothy; Buck, Stephen

    2010-01-01

    Writing in mathematics can improve procedural knowledge and communication skills and may also help students better understand and then remember problems. The majority of mathematics teachers know that they ought to include some writing assignments in their instructional plans, but the challenge of covering the curriculum and the time required to…

  1. A storage assignment model for batch preparation in process industries

    NARCIS (Netherlands)

    Ashayeri, J.; Selen, W.

    2013-01-01

    Purpose – The purpose of this paper is to develop new model formulation for reducing the workload in pre‐batching at a manufacturer of flavors and fragrances, by optimally assigning ingredients to different storage types, taking into account past usage of ingredients and several restrictions about

  2. Integrating Video Documentary into the Classroom: A Community Assessment Assignment

    Science.gov (United States)

    Levinson, Samantha G.; Caldwell, Keith; Petracchi, Helen E.; Wexler, Sandra; Engel, Rafael

    2016-01-01

    Community assessment is a strategy commonly taught to social work students to identify a community's strengths and challenges. This article describes the value of using video documentary as part of a community assessment assignment. We identify the advantages of using video documentary in the assessment process and the reporting of findings. We…

  3. The Quadratic Assignment Problem is Easy for Robinsonian Matrices

    NARCIS (Netherlands)

    Laurent, M.; Seminaroti, M.

    2014-01-01

    We present a new polynomially solvable case of the Quadratic Assignment Problem in Koopmans-Beckman form QAP(A;B), by showing that the identity permutation is optimal when A and B are respectively a Robinson similarity and dissimilarity matrix and one of A or B is a Toeplitz matrix. A Robinson

  4. A bilinear programming solution to the quadratic assignment problem

    NARCIS (Netherlands)

    J.F. Kaashoek (Johan); J.H.P. Paelinck (Jean)

    1999-01-01

    textabstractThe quadratic assignment problem (QAP) or maximum acyclical graph problem is well documented (see e.g. Pardalos and Wolkowicz, 1994). One of the authors has published some material, in which it was tried, by structuring the problem additionally, to bring it as closely as possible in the

  5. The quadratic assignment problem is easy for robinsonian matrices

    NARCIS (Netherlands)

    Laurent, M.; Seminaroti, M.

    We present a new polynomially solvable case of the Quadratic Assignment Problem in Koopmans–Beckman form QAP(A,B), by showing that the identity permutation is optimal when AA and BB are respectively a Robinson similarity and dissimilarity matrix and one of AA or BB is a Toeplitz matrix. A Robinson

  6. Bandit-Inspired Memetic Algorithms for Solving Quadratic Assignment Problems

    NARCIS (Netherlands)

    Puglierin, Francesco; Drugan, Madalina M.; Wiering, Marco

    2013-01-01

    In this paper we propose a novel algorithm called the Bandit-Inspired Memetic Algorithm (BIMA) and we have applied it to solve different large instances of the Quadratic Assignment Problem (QAP). Like other memetic algorithms, BIMA makes use of local search and a population of solutions. The novelty

  7. Assigning Main Orientation to an EOH Descriptor on Multispectral Images

    Directory of Open Access Journals (Sweden)

    Yong Li

    2015-07-01

    Full Text Available This paper proposes an approach to compute an EOH (edge-oriented histogram descriptor with main orientation. EOH has a better matching ability than SIFT (scale-invariant feature transform on multispectral images, but does not assign a main orientation to keypoints. Alternatively, it tends to assign the same main orientation to every keypoint, e.g., zero degrees. This limits EOH to matching keypoints between images of translation misalignment only. Observing this limitation, we propose assigning to keypoints the main orientation that is computed with PIIFD (partial intensity invariant feature descriptor. In the proposed method, SIFT keypoints are detected from images as the extrema of difference of Gaussians, and every keypoint is assigned to the main orientation computed with PIIFD. Then, EOH is computed for every keypoint with respect to its main orientation. In addition, an implementation variant is proposed for fast computation of the EOH descriptor. Experimental results show that the proposed approach performs more robustly than the original EOH on image pairs that have a rotation misalignment.

  8. 37 CFR 1.46 - Assigned inventions and patents.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Assigned inventions and patents. 1.46 Section 1.46 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES National Processing Provisions Who May Apply...

  9. 32 CFR 150.15 - Assignments of error and briefs.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Assignments of error and briefs. 150.15 Section 150.15 National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE REGULATIONS PERTAINING TO MILITARY JUSTICE COURTS OF CRIMINAL APPEALS RULES OF PRACTICE AND PROCEDURE § 150.15...

  10. Python Source Code Plagiarism Attacks on Introductory Programming Course Assignments

    Science.gov (United States)

    Karnalim, Oscar

    2017-01-01

    This paper empirically enlists Python plagiarism attacks that have been found on Introductory Programming course assignments for undergraduate students. According to our observation toward 400 plagiarism-suspected cases, there are 35 plagiarism attacks that have been conducted by students. It starts with comment & whitespace modification as…

  11. Properties of spiral resonators

    International Nuclear Information System (INIS)

    Haeuser, J.

    1989-10-01

    The present thesis deals with the calculation and the study of the application possibilities of single and double spiral resonators. The main aim was the development and the construction of reliable and effective high-power spiral resonators for the UNILAC of the GSI in Darmstadt and the H - -injector for the storage ring HERA of DESY in Hamburg. After the presentation of the construction and the properties of spiral resonators and their description by oscillating-circuit models the theoretical foundations of the bunching are presented and some examples of a rebuncher and debuncher and their influence on the longitudinal particle dynamics are shown. After the description of the characteristic accelerator quantities by means of an oscillating-circuit model and the theory of an inhomogeneous λ/4 line it is shown, how the resonance frequency and the efficiency of single and double spiral resonators can be calculated from the geometrical quantities of the structure. In the following the dependence of the maximal reachable resonator voltage in dependence on the gap width and the surface of the drift tubes is studied. Furthermore the high-power resonators are presented, which were built for the different applications for the GSI in Darmstadt, DESY in Hamburg, and for the FOM Institute in Amsterdam. (orig./HSI) [de

  12. Children's (Pediatric) Magnetic Resonance Imaging

    Medline Plus

    Full Text Available ... and Media Catheter Angiography Magnetic Resonance, Functional (fMRI) - Brain Children's (Pediatric) CT (Computed Tomography) Magnetic Resonance Imaging (MRI) Safety Contrast Materials Children ...

  13. Magnetic Resonance Force Microscopy System

    Data.gov (United States)

    Federal Laboratory Consortium — The Magnetic Resonance Force Microscopy (MRFM) system, developed by ARL, is the world's most sensitive nuclear magnetic resonance (NMR) spectroscopic analysis tool,...

  14. 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

  15. ¹H, ¹³C and ¹⁵N chemical shift assignments of Na-FAR-1, a helix-rich fatty acid and retinol binding protein of the parasitic nematode Necator americanus.

    Science.gov (United States)

    Rey-Burusco, M Florencia; Ibañez-Shimabukuro, Marina; Cooper, Alan; Kennedy, Malcolm W; Córsico, Betina; Smith, Brian O

    2014-04-01

    The fatty acid and retinol-binding (FAR) proteins are a family of unusual helix-rich lipid binding proteins found exclusively in nematodes, and are secreted by a range of parasites of humans, animals and plants. Na-FAR-1 is from the parasitic nematode Necator americanus, an intestinal blood-feeding parasite of humans. Sequence-specific (1)H, (13)C and (15)N resonance assignments have been obtained for the recombinant 170 amino acid protein, using three-dimensional triple-resonance heteronuclear magnetic resonance experiments. Backbone assignments have been obtained for 99.3% of the non-proline HN/N pairs (146 out of 147). The amide resonance of T45 was not observed, probably due to rapid exchange with solvent water. A total of 96.9% of backbone resonances were identified, while 97.7% assignment of amino acid sidechain protons is complete. All Hα(166), Hβ(250) and Hγ(160) and 98.4% of the Hδ (126 out of 128) atoms were assigned. In addition, 99.4% Cα (154 out of 155) and 99.3% Cβ (143 out of 144) resonances have been assigned. No resonances were observed for the NH(n) groups of R93 NεHε, arginine, N(η1)H2, N(η2)H2, histidine N(δ1)H(δ1), N(ε1)H(ε1) and lysine N(ζ3)H3. Na-FAR-1 has a similar overall arrangement of α-helices to Ce-FAR-7 of the free-living Caeorhabditis elegans, but with an extra C-terminal helix.

  16. Resonant power converters

    CERN Document Server

    Kazimierczuk, Marian K

    2012-01-01

    This book is devoted to resonant energy conversion in power electronics. It is a practical, systematic guide to the analysis and design of various dc-dc resonant inverters, high-frequency rectifiers, and dc-dc resonant converters that are building blocks of many of today's high-frequency energy processors. Designed to function as both a superior senior-to-graduate level textbook for electrical engineering courses and a valuable professional reference for practicing engineers, it provides students and engineers with a solid grasp of existing high-frequency technology, while acquainting them wit

  17. Tunable multiwalled nanotube resonator

    Science.gov (United States)

    Jensen, Kenneth J; Girit, Caglar O; Mickelson, William E; Zettl, Alexander K; Grossman, Jeffrey C

    2013-11-05

    A tunable nanoscale resonator has potential applications in precise mass, force, position, and frequency measurement. One embodiment of this device consists of a specially prepared multiwalled carbon nanotube (MWNT) suspended between a metal electrode and a mobile, piezoelectrically controlled contact. By harnessing a unique telescoping ability of MWNTs, one may controllably slide an inner nanotube core from its outer nanotube casing, effectively changing its length and thereby changing the tuning of its resonance frequency. Resonant energy transfer may be used with a nanoresonator to detect molecules at a specific target oscillation frequency, without the use of a chemical label, to provide label-free chemical species detection.

  18. Doubly resonant multiphoton ionization

    International Nuclear Information System (INIS)

    Crance, M.

    1978-01-01

    A particular case of doubly resonant multiphoton ionization is theoretically investigated. More precisely, two levels quasi-resonant with two successive harmonics of the field frequency are considered. The method used is based on the effective operator formalism first introduced for this problem by Armstrong, Beers and Feneuille. The main result is to show the possibility of observing large interference effects on the width of the resonances. Moreover this treatment allows us to make more precise the connection between effective operator formalism and standard perturbation theory

  19. Dihadronic and dileptonic resonances

    International Nuclear Information System (INIS)

    Gareev, F.A.; Barabanov, M.Yu.; Kazacha, G.S.

    1997-01-01

    Simple phenomenological rules are suggested for calculation of dihadron and dilepton resonance masses. A general interpretation is given for different exotic resonances in nuclear physics: Darmstadt-effect, dibaryon, dipion and other resonances. Information about the inner structure of e ± , proton, neutron, pions and so on can be obtained from the usual reactions of the type e + + e - =>γγ, e ± +γ=>e ± γ, e ± μ ± , e ± N... at low, intermediate and high energies using existing experimental devices

  20. 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.)