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Sample records for rapid chemical shift

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

    Science.gov (United States)

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

    2017-12-01

    Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

  2. Rapid chemical shift encoding with single-acquisition single-slab 3D GRASE.

    Science.gov (United States)

    Kim, Hahnsung; Kim, Dong-Hyun; Sohn, Chul-Ho; Park, Jaeseok

    2017-11-01

    To investigate the feasibility of chemical shift encoded, single-slab 3D GRASE for rapid fat-water separation within a single acquisition. The proposed method incorporates signal-to-noise-ratio-optimal chemical shift encoding into single-slab 3D GRASE with variable flip angles. Chemical shift induced phase information was encoded in succession to different positions in k-space by inserting phase encoding blips between adjacent lobes of the oscillating readout gradients. To enhance imaging efficiency, signal prescription-based variable flip angles were used in the long refocusing pulse train. After echo-independent phase correction, missing signals in k-echo space were interpolated using convolution kernels that span over all echoes. Fat-water separation in a single acquisition was performed using both multi-echo fast spin echo and GRASE as compared to conventional multiacquisition fast spin echo with echo shifts. The proposed single-slab 3D GRASE shows superior performance in accurately delineating cartilage structures compared to its counterpart, multi-echo 3D fast spin echo. Compared with multiacquisition fast spin echo with three echo shifts (63 min), the proposed method substantially speeds up imaging time (7 min), and achieves 0.6 mm isotropic resolution in knee imaging with reduced artifacts and noise. We successfully demonstrated the feasibility of rapid chemical shift encoding and separation using the proposed, single-acquisition single-slab 3D GRASE for high resolution isotropic imaging within clinically acceptable time. Magn Reson Med 78:1852-1861, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  3. Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement.

    Science.gov (United States)

    Jakovkin, Igor; Klipfel, Marco; Muhle-Goll, Claudia; Ulrich, Anne S; Luy, Burkhard; Sternberg, Ulrich

    2012-09-21

    Although difficult to analyze, NMR chemical shifts provide detailed information on protein structure. We have adapted the semi-empirical bond polarization theory (BPT) to protein chemical shift calculation and chemical shift driven protein structure refinement. A new parameterization for BPT amide nitrogen chemical shift calculation has been derived from MP2 ab initio calculations and successfully evaluated using crystalline tripeptides. We computed the chemical shifts of the small globular protein ubiquitin, demonstrating that BPT calculations can match the results obtained at the DFT level of theory at very low computational cost. In addition to the calculation of chemical shift tensors, BPT allows the calculation of chemical shift gradients and consequently chemical shift driven geometry optimizations. We applied chemical shift driven protein structure refinement to the conformational analysis of a set of Trypanosoma brucei (the causative agent of African sleeping sickness) tryparedoxin peroxidase Px III structures. We found that the interaction of Px III with its reaction partner Tpx seems to be governed by conformational selection rather than by induced fit.

  4. Protein Chemical Shift Prediction

    CERN Document Server

    Larsen, Anders S

    2014-01-01

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

  5. Rapid chemical separations

    CERN Document Server

    Trautmann, N

    1976-01-01

    A survey is given on the progress of fast chemical separation procedures during the last few years. Fast, discontinuous separation techniques are illustrated by a procedure for niobium. The use of such techniques for the chemical characterization of the heaviest known elements is described. Other rapid separation methods from aqueous solutions are summarized. The application of the high speed liquid chromatography to the separation of chemically similar elements is outlined. The use of the gas jet recoil transport method for nuclear reaction products and its combination with a continuous solvent extraction technique and with a thermochromatographic separation is presented. Different separation methods in the gas phase are briefly discussed and the attachment of a thermochromatographic technique to an on-line mass separator is shown. (45 refs).

  6. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...... is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  7. Rapid Hydrogen Shift Reactions in Acyl Peroxy Radicals

    DEFF Research Database (Denmark)

    Knap, Hasse Christian; Jørgensen, Solvejg

    2017-01-01

    We have used quantum mechanical chemical calculations (CCSD(T)-F12a/cc-pVDZ-F12//M06-2X/aug-cc-pVTZ) to investigate the hydrogen shift (H-shift) reactions in acyl peroxy and hydroperoxy acyl peroxy radicals. We have focused on the H-shift reactions from a hydroperoxy group (OOH) (1,X-OOH H...

  8. Random coil chemical shift for intrinsically disordered proteins

    DEFF Research Database (Denmark)

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

    2011-01-01

    Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical....... Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series...... shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970-2978, 2001). The chemical shifts are determined at neutral pH in order to match the conditions of most studies of intrinsically disordered proteins...

  9. Rapid Chemical Exposure and Dose Research

    Science.gov (United States)

    EPA evaluates the potential risks of the manufacture and use of thousands of chemicals. To assist with this evaluation, EPA scientists developed a rapid, automated model using off the shelf technology that predicts exposures for thousands of chemicals.

  10. Improving 3D structure prediction from chemical shift data

    NARCIS (Netherlands)

    van der Schot, G.; Zhang, Z.; Vernon, R.; Shen, Y.; Vranken, W.F.; Baker, D.; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238; Lange, O.F.

    2013-01-01

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CSRosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts

  11. Calculations of proton chemical shifts in olefins and aromatics

    CERN Document Server

    Escrihuela, M C

    2000-01-01

    induced reagents on alpha,beta unsaturated ketones has also been investigated in order to deduce molecular structures and to obtain the assignment of the spectra of these molecules. A semi-empirical calculation of the partial atomic charges in organic compounds based on molecular dipole moments (CHARGE3) was developed into a model capable of predicting proton chemical shifts in a wide variety of organic compounds to a reasonable degree of accuracy. The model has been modified to include condensed aromatic hydrocarbons and substituted benzenes, alkenes, halo-monosubstituted benzenes and halo-alkenes. Within the aromatic compounds the influence of the pi electron densities and the ring current have been investigated, along with the alpha, beta and gamma effects. The model gives the first accurate calculation of the proton chemical shifts of condensed aromatic compounds and the proton substituent chemical shifts (SCS) in the benzene ring. For the data set of 55 proton chemical shifts spanning 3 ppm the rms error...

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

    Science.gov (United States)

    Berjanskii, Mark V; Wishart, David S

    2017-11-01

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

  13. NightShift: NMR shift inference by general hybrid model training - a framework for NMR chemical shift prediction

    Science.gov (United States)

    2013-01-01

    Background NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking results can profit from efficient and accurate chemical shift estimation from a three-dimensional model. A variety of NMR chemical shift prediction approaches have been presented in the past, but nearly all of these rely on laborious manual data set preparation and the training itself is not automatized, making retraining the model, e.g., if new data is made available, or testing new models a time-consuming manual chore. Results In this work, we present the framework NightShift (NMR Shift Inference by General Hybrid Model Training), which enables automated data set generation as well as model training and evaluation of protein NMR chemical shift prediction. In addition to this main result – the NightShift framework itself – we describe the resulting, automatically generated, data set and, as a proof-of-concept, a random forest model called Spinster that was built using the pipeline. Conclusion By demonstrating that the performance of the automatically generated predictors is at least en par with the state of the art, we conclude that automated data set and predictor generation is well-suited for the design of NMR chemical shift estimators. The framework can be downloaded from https://bitbucket.org/akdehof/nightshift. It requires the open source Biochemical Algorithms Library (BALL), and is available under the conditions of the GNU Lesser General Public License (LGPL). We additionally offer a browser-based user interface to our NightShift instance employing the Galaxy framework via https://ballaxy.bioinf.uni-sb.de/. PMID:23496927

  14. NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction.

    Science.gov (United States)

    Dehof, Anna Katharina; Loew, Simon; Lenhof, Hans-Peter; Hildebrandt, Andreas

    2013-03-16

    NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking results can profit from efficient and accurate chemical shift estimation from a three-dimensional model.A variety of NMR chemical shift prediction approaches have been presented in the past, but nearly all of these rely on laborious manual data set preparation and the training itself is not automatized, making retraining the model, e.g., if new data is made available, or testing new models a time-consuming manual chore. In this work, we present the framework NightShift (NMR Shift Inference by General Hybrid Model Training), which enables automated data set generation as well as model training and evaluation of protein NMR chemical shift prediction.In addition to this main result - the NightShift framework itself - we describe the resulting, automatically generated, data set and, as a proof-of-concept, a random forest model called Spinster that was built using the pipeline. By demonstrating that the performance of the automatically generated predictors is at least en par with the state of the art, we conclude that automated data set and predictor generation is well-suited for the design of NMR chemical shift estimators.The framework can be downloaded from https://bitbucket.org/akdehof/nightshift. It requires the open source Biochemical Algorithms Library (BALL), and is available under the conditions of the GNU Lesser General Public License (LGPL). We additionally offer a browser-based user interface to our NightShift instance employing the Galaxy framework via https://ballaxy.bioinf.uni-sb.de/.

  15. Counterion influence on chemical shifts in strychnine salts

    Energy Technology Data Exchange (ETDEWEB)

    Metaxas, Athena E.; Cort, John R.

    2013-05-01

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

  16. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim

    2015-01-01

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

  17. [Shift-work and cardiovascular diseases among chemical industry workers].

    Science.gov (United States)

    Meloni, M; Marchi, R; Broi, M; Avataneo, G; Sanna Randaccio, F

    2003-01-01

    In order to assess the prevalence of cardiovascular abnormalities among shift workers, who were free from such abnormalities at the time of hiring, compared to day workers and ex-shift workers, we studied the QTc interval and several cardiovascular risk factors in 61 chemical workers, including 40 shift workers, 11 day workers, and 10 ex-shift workers. We found a high prevalence rate of ischemic heart disease and conduction abnormalities among ex-shift workers (5/10, 50%). We did not observe variations in the QTc interval among the three groups. The occurrence of cardiovascular disease is a reason for moving workers to day work. Therefore, the shift workers group in our study might have been selected among subjects with a healthier lifestyle preventing side effects on their cardiovascular system.

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

    Science.gov (United States)

    Koes, David R; Vries, John K

    2017-10-01

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

  19. Chemical Stockpile Disposal Program rapid accident assessment

    Energy Technology Data Exchange (ETDEWEB)

    Chester, C.V.

    1990-08-01

    This report develops a scheme for the rapid assessment of a release of toxic chemicals resulting from an accident in one of the most chemical weapon demilitarization plants or storage areas. The system uses such inputs as chemical and pressure sensors monitoring the plant and reports of accidents radioed to the Emergency Operations Center by work parties or monitoring personnel. A size of release can be estimated from previous calculations done in the risk analysis, from back calculation from an open-air chemical sensor measurement, or from an estimated percentage of the inventory of agent at the location of the release. Potential consequences of the estimated release are calculated from real-time meteorological data, surrounding population data, and properties of the agent. In addition to the estimated casualties, area coverage and no-death contours vs time would be calculated. Accidents are assigned to one of four categories: community emergencies, which are involve a threat to off-site personnel; on-post emergencies, which involve a threat only to on-site personnel; advisory, which involves a potential for threat to on-site personnel; and chemical occurrence, which can produce an abnormal operating condition for the plant but no immediate threat to on-site personnel. 9 refs., 20 tabs.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand......We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level......-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3) JNC' ) spin-spin coupling constants that are in excellent agreement with experiment. We show...

  1. Chemical shift of UL 3 edges in different uranium compounds ...

    Indian Academy of Sciences (India)

    Home; Journals; Bulletin of Materials Science; Volume 37; Issue 3. Chemical shift of U L3 edges in different uranium compounds obtained by X-ray absorption spectroscopy with synchrotron radiation. D Joseph C Nayak P Venu Babu S N Jha D Bhattacharyya. Volume 37 Issue 3 May 2014 pp 643-647 ...

  2. Chemical shift and coupling constant analysis of dibenzyloxy disulfides.

    Science.gov (United States)

    Stoutenburg, Eric G; Gryn'ova, Ganna; Coote, Michelle L; Priefer, Ronny

    2015-02-05

    Dialkoxy disulfides have found applications in the realm of organic synthesis as an S2 or alkoxy donor, under thermal and photolytic decompositions conditions, respectively. Spectrally, dibenzyloxy disulfides possess an ABq in the (1)H NMR, which can shift by over 1.1ppm depending on the substituents present on the aromatic ring, as well as the solvent employed. The effect of the said substituents and solvent were analyzed and compared to the center of the ABq, geminal coupling, and the differences in chemical shifts of the individual doublets. Additionally, quantum-chemical calculations demonstrated the intramolecular H-bonding arrangement, found within the dibenzyloxy disulfides. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Ligand binding analysis and screening by chemical denaturation shift.

    Science.gov (United States)

    Schön, Arne; Brown, Richard K; Hutchins, Burleigh M; Freire, Ernesto

    2013-12-01

    The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Toward this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Because ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities, and the ligand rank order obtained at denaturation temperatures (≥60°C) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations where binding changes the cooperativity of the unfolding transition. In this article, we develop the basic analytical equations and provide several experimental examples. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Rapid Shifts in Soil Nutrients and Decomposition Enzyme Activity in Early Succession Following Forest Fire

    OpenAIRE

    Knelman, Joseph E.; Graham, Emily B; Scott Ferrenberg; Aurélien Lecoeuvre; Amanda Labrado; Darcy, John L.; Nemergut, Diana R; Schmidt, Steven K.

    2017-01-01

    While past research has studied forest succession on decadal timescales, ecosystem responses to rapid shifts in nutrient dynamics within the first months to years of succession after fire (e.g., carbon (C) burn-off, a pulse in inorganic nitrogen (N), accumulation of organic matter, etc.) have been less well documented. This work reveals how rapid shifts in nutrient availability associated with fire disturbance may drive changes in soil enzyme activity on short timescales in forest secondary s...

  5. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts

    DEFF Research Database (Denmark)

    Eriksen, Janus Juul; Olsen, Jógvan Magnus Haugaard; Aidas, Kestutis

    2011-01-01

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

  6. Theoretical Modeling of 99 Tc NMR Chemical Shifts

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Gabriel B.; Andersen, Amity; Washton, Nancy M.; Chatterjee, Sayandev; Levitskaia, Tatiana G.

    2016-09-06

    Technetium (Tc) displays a rich chemistry due to the wide range of oxidation states (from -I to +VII) and ability to form coordination compounds. Determination of Tc speciation in complex mixtures is a major challenge, and 99Tc NMR spec-troscopy is widely used to probe chemical environments of Tc in odd oxidation states. However interpretation of the 99Tc NMR data is hindered by the lack of reference compounds. DFT computations can help fill this gap, but to date few com-putational studies have focused on 99Tc NMR of compounds and complexes. This work systematically evaluates the inclu-sion small percentages of Hartree-Fock exchange correlation and relativistic effects in DFT computations to support in-terpretation of the 99Tc NMR spectra. Hybrid functionals are found to perform better than their pure GGA counterparts, and non-relativistic calculations have been found to generally show a lower mean absolute deviation from experiment. Overall non-relativistic PBE0 and B3PW91 calculations are found to most accurately predict 99Tc NMR chemical shifts.

  7. Chemical shift encoded imaging of hyperpolarized (13) C pyruvate.

    Science.gov (United States)

    Wiens, Curtis N; Friesen-Waldner, Lanette J; Wade, Trevor P; Sinclair, Kevin J; McKenzie, Charles A

    2015-12-01

    To demonstrate a reconstruction technique for separating signal from different hyperpolarized carbon-13 metabolites. A reconstruction method is described for chemical shift encoded separation of the signal from pyruvate and its downstream metabolites. This method uses consistency of the data with the signal model rather than an additional free-induction decay (FID) acquisition to estimate the B0 offset. Compressed sensing was also integrated into the reconstruction allowing reconstruction of metabolite images from undersampled datasets. The performance of the reconstruction was assessed using thermal phantoms, digital phantoms, and in vivo hyperpolarized [1-(13) C] pyruvate experiments. Thermal and digital phantoms indicate that metabolite separation is feasible given Signal-to-noise ratio > 5 and an initial B0 offset estimate within -105 Hz to 90 Hz of the actual B0 offset. In vivo comparisons to an existing FID calibrated reconstruction show improved fidelity in regions with significant field map inhomogeneity provided that these field map variations are accounted for using an additional proton acquisition. Prospectively and retrospectively undersampled studies show acceleration factors of 2 are feasible using compressed sensing. A reconstruction framework for the separation of signal from pyruvate and its downstream metabolites is shown. This reconstruction eliminates the need to acquire additional calibration FID acquisition and allows acceleration through compressed sensing. © 2014 Wiley Periodicals, Inc.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-11-15

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

  9. Two-dimensional concurrent HMQC-COSY as an approach for small molecule chemical shift assignment and compound identification

    Energy Technology Data Exchange (ETDEWEB)

    Hu Kaifeng; Westler, William M.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison (United States)

    2011-04-15

    Chemical shift assignment is the first step toward the structure elucidation of natural products and other chemical compounds. We propose here the use of 2D concurrent HMQC-COSY as an experiment for rapid chemical shift assignment of small molecules. This experiment provides well-dispersed {sup 1}H-{sup 13}C peak patterns that are distinctive for different functional groups plus {sup 1}H-{sup 1}H COSY connectivities that serve to identify adjacent groups. The COSY diagonal peaks, which are phased to be absorptive, resemble {sup 1}H-{sup 13}C HMQC cross peaks. We demonstrate the applicability of this experiment for rapidly and unambiguously establishing correlations between different functional groups through the analysis of the spectrum of a metabolite (jasmonic acid) dissolved in CDCl{sub 3}. In addition, we show that the experiment can be used to assign spectra of compounds in a mixture of metabolites in D{sub 2}O.

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

    Science.gov (United States)

    Sanz-Hernández, Máximo; De Simone, Alfonso

    2017-11-08

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

  11. Ocean warming, a rapid distributional shift, and the hybridization of a coastal fish species.

    Science.gov (United States)

    Potts, Warren M; Henriques, Romina; Santos, Carmen V; Munnik, Kate; Ansorge, Isabelle; Dufois, Francois; Booth, Anthony J; Kirchner, Carola; Sauer, Warwick H H; Shaw, Paul W

    2014-09-01

    Despite increasing awareness of large-scale climate-driven distribution shifts in the marine environment, no study has linked rapid ocean warming to a shift in distribution and consequent hybridization of a marine fish species. This study describes rapid warming (0.8 °C per decade) in the coastal waters of the Angola-Benguela Frontal Zone over the last three decades and a concomitant shift by a temperature sensitive coastal fish species (Argyrosomus coronus) southward from Angola into Namibia. In this context, rapid shifts in distribution across Economic Exclusive Zones will complicate the management of fishes, particularly when there is a lack of congruence in the fisheries policy between nations. Evidence for recent hybridization between A. coronus and a congener, A. inodorus, indicate that the rapid shift in distribution of A. coronus has placed adults of the two species in contact during their spawning events. Ocean warming may therefore revert established species isolation mechanisms and alter the evolutionary history of fishes. While the consequences of the hybridization on the production of the resource remain unclear, this will most likely introduce additional layers of complexity to their management. © 2014 John Wiley & Sons Ltd.

  12. Rapid mixing chemical oxidative polymerization: an easy route to ...

    Indian Academy of Sciences (India)

    Administrator

    (catalyst)-coated silicon wafer was used as the substrate. After placing the substrate in the furnace of the .... monomer. This type of interaction is evident from Raman analysis (red shift in C=N Raman band corresponding to. PANI). Remaining aniline molecules get dispersed in the aq. HCl suspension. At the moment of rapid ...

  13. More rapid shift to a benthic niche in larger Gadus morhua juveniles.

    Science.gov (United States)

    Ólafsdóttir, G Á; Gunnarsson, G S; Karlsson, H

    2015-08-01

    Trophic use by Atlantic cod Gadus morhua juveniles was examined early and late in the shift from pelagic to benthic habitats. Changes in the proportion of pelagic copepods, estimates of benthic prey indicated by isotope mixing models and stable-isotope values between sample periods suggested a gradual shift towards a benthic niche. Values of the trophic proxies, however, changed most markedly in the largest juvenile group, suggesting a more rapid trophic niche shift, and in turn competitive advantage, of larger juveniles. © 2015 The Fisheries Society of the British Isles.

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

    Science.gov (United States)

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

    2017-07-06

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

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

    Science.gov (United States)

    Wang, Liya; Markley, John L

    2009-06-01

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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  17. Rapid Detection of Glycogen Synthase Kinase-3 Activity in Mouse Sperm Using Fluorescent Gel Shift Electrophoresis

    National Research Council Canada - National Science Library

    Choi, Hoseok; Choi, Bomi; Seo, Ju Tae; Lee, Kyung Jin; Gye, Myung Chan; Kim, Young-Pil

    2016-01-01

    .... The GSK3 activity in mouse testes and sperm were quantifiable by gel shift assay with low sample consumption and were significantly correlated with the expression levels of GSK3 and p-GSK3. We suggest that our assay can be used for reliable and rapid detection of GSK3 activity in cells and tissue extracts.

  18. Aromatic interactions in model peptide β-hairpins: ring current effects on proton chemical shifts.

    Science.gov (United States)

    Rajagopal, Appavu; Aravinda, Subrayashastry; Raghothama, Srinivasarao; Shamala, Narayanaswamy; Balaram, Padmanabhan

    2012-01-01

    Crystal structures of eight peptide β-hairpins in the sequence Boc-Leu-Phe-Val-Xxx-Yyy-Leu-Phe-Val-OMe revealed that the Phe(2) and Phe(7) aromatic rings are in close spacial proximity, with the centroid-centroid distance (R(cen)) of 4.4-5.4 Å between the two phenyl rings. Proton NMR spectra in chloroform and methanol solution reveal a significant upfield shift of the Phe(7) C(δ,δ') H(2) protons (6.65-7.04 ppm). Specific assignments of the aromatic protons have been carried out in the peptide Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (6). The anticipated ring current shifts have been estimated from the aromatic ring geometrics observed in crystals for all eight peptides. Only one of the C(δ,δ') H proton lies in the shielding zone with rapid ring flipping, resulting in averaging between the two extreme chemical shifts. An approximate estimate of the population of conformations, which resemble crystal state orientation, may be obtained. Key nuclear Overhauser effects (NOEs) between facing Phe side chains provide support for close similarity between the solid state and solution conformation. Temperature dependence of aromatic ring proton chemical shift and line widths for peptide 6 (Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe) and the control peptide Boc-Leu-Val-Val-(D)Pro-Gly-Leu-Phe-Val-OMe establish an enhanced barrier to ring flipping when the two Phe rings are in proximity. Modeling studies suggest that small, conformational adjustment about C(α)-C(β) (χ(1) ) and C(β)-C(γ) (χ(2) ) bonds of both the Phe residues may be required in order to permit unhindered, uncorrelated flipping of both the Phe rings. The maintenance of the specific aromatic ring orientation in organic solvents provides evidence for significant stabilizing interaction. Copyright © 2012 Wiley Periodicals, Inc.

  19. NMR chemical shift data and ab initio shielding calculations : emerging tools for protein structure determination

    NARCIS (Netherlands)

    Mulder, Frans A. A.; Filatov, Michael

    2010-01-01

    In this tutorial review, we discuss the utilization of chemical shift information as well as ab initio calculations of nuclear shieldings for protein structure determination. Both the empirical and computational aspects of the chemical shift are reviewed and the role of molecular dynamics and the

  20. Fluorine Chemical Shift Imaging by Nuclear Magnetic Resonance

    Science.gov (United States)

    Lee, Heung Kyu

    1990-01-01

    One of the difficulties encountered in ^{19}F NMR imaging of fluorinated blood substitutes is that these compounds often exhibit complex multi-peak spectra. These peaks result in chemical shift artifacts along the readout direction (mis-registration). In addition, each peak excites a different slice (mis-selection) when a slice selection gradient is applied. Another difficulty is due to its low concentration in the human body. Even after injecting a fluorinated compound into a living system up to the safest level, the concentration still does not appear to be enough to give a sufficient SNR. To solve the inherent problem of mis-selection, a simultaneous multislice method has been developed. The essence of this method is to use the two strongest peaks of the spectrum to excite different multiple slices simultaneously in a controlled fashion, with or without a slice gap. The images corresponding to the two spectral lines are then separated from in and out of phase images (Dixon method). A signed magnitude method is proposed in conjunction with the simultaneous multislice method. Corrected images are obtained from the magnitude of the measured images using the sign determined from the phase images. The method was tested in the presence of phase error, such as static magnetic field inhomogeneity. As alternatives, two deconvolution methods have been devised to eliminate the mis-registration artifacts and utilize the multiple spectral lines. The reblurring deconvolution method, an iterative deconvolution method, is utilized without serious noise amplifications. A pseudo parametric Wiener filter, a variation of the Wiener filter combined with a constrained least square filter, is also devised. Since the point spread function and 2D or 3D object data are already available in the time domain as the FID data, the computational overhead for either method is negligible. To enhance the signal to noise ratio and solve the problems of mis-registration and mis

  1. Ab Initio Calculation of Nuclear Magnetic Resonance Chemical Shift Anisotropy Tensors 1. Influence of Basis Set on the Calculation of 31P Chemical Shifts

    Energy Technology Data Exchange (ETDEWEB)

    Alam, T.M.

    1998-09-01

    The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.

  2. A robustness screen for the rapid assessment of chemical reactions.

    Science.gov (United States)

    Collins, Karl D; Glorius, Frank

    2013-07-01

    In contrast to the rapidity with which scientific information is published, the application of new knowledge often remains slow, and we believe this to be particularly true of newly developed synthetic organic chemistry methodology. Consequently, methods to assess and identify robust chemical reactions are desirable, and would directly facilitate the application of newly reported synthetic methodology to complex synthetic problems. Here, we describe a simple process for assessing the likely scope and limitations of a chemical reaction beyond the idealized reaction conditions initially reported. Using simple methods and common analytical techniques we demonstrate a rapid assessment of an established chemical reaction, and also propose a simplified analysis that may be reported alongside new synthetic methodology.

  3. Rapid Shifts in Soil Nutrients and Decomposition Enzyme Activity in Early Succession Following Forest Fire

    Directory of Open Access Journals (Sweden)

    Joseph E. Knelman

    2017-09-01

    Full Text Available While past research has studied forest succession on decadal timescales, ecosystem responses to rapid shifts in nutrient dynamics within the first months to years of succession after fire (e.g., carbon (C burn-off, a pulse in inorganic nitrogen (N, accumulation of organic matter, etc. have been less well documented. This work reveals how rapid shifts in nutrient availability associated with fire disturbance may drive changes in soil enzyme activity on short timescales in forest secondary succession. In this study, we evaluate soil chemistry and decomposition extracellular enzyme activity (EEA across time to determine whether rapid shifts in nutrient availability (1–29 months after fire might control microbial enzyme activity. We found that, with advancing succession, soil nutrients correlate with C-targeting β-1,4-glucosidase (BG EEA four months after the fire, and with N-targeting β-1,4-N-acetylglucosaminidase (NAG EEA at 29 months after the fire, indicating shifting nutrient limitation and decomposition dynamics. We also observed increases in BG:NAG ratios over 29 months in these recently burned soils, suggesting relative increases in microbial activity around C-cycling and C-acquisition. These successional dynamics were unique from seasonal changes we observed in unburned, forested reference soils. Our work demonstrates how EEA may shift even within the first months to years of ecosystem succession alongside common patterns of post-fire nutrient availability. Thus, this work emphasizes that nutrient dynamics in the earliest stages of forest secondary succession are important for understanding rates of C and N cycling and ecosystem development.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found to be nega...... with calculated OH stretching frequencies. Isotope effects on chemical shifts are calculated for systems with OH exchanged by OD. Hydrogen bond potentials are discussed. New and more soluble nitro derivatives are synthesized.......Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found...... to be negative, indicating transmission via the hydrogen bond. In addition unusual long-range effects are seen. Structures, NMR chemical shifts and changes in nuclear shieldings upon deuteriation are calculated using DFT methods. Two-bond deuterium isotope effects on 13C chemical shifts are correlated...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-15

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

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

    Science.gov (United States)

    Karp, Jerome M; Eryilmaz, Ertan; Erylimaz, Ertan; Cowburn, David

    2015-01-01

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

  7. Empirical Correlation Between Protein Backbone 15N And 13C Secondary Chemical Shifts and its Application to Nitrogen Chemical Shift Re-referencing

    OpenAIRE

    Wang, Liya; Markley, John L.

    2009-01-01

    The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting 13C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to 15N NMR data from proteins, so as to ena...

  8. Determination of Water Content in THF Based on Chemical Shift Differences in Solution NMR

    Energy Technology Data Exchange (ETDEWEB)

    Jun, Jae Kyung; Park, Hey Rhee; Lee, Yunhee; Choi, Myung Gil; Chang, Suk-Kyu; Ahn, Sangdoo [Chung-Ang University, Seoul (Korea, Republic of)

    2016-03-15

    In this study, H NMR chemical shift differences were used as a probe for water content in organic solvents. Changes in chemical shift differences reflecting the competition for hydrogen bondings between fluoride ions and water were linearly proportional to water content within certain ranges. Comparison between the results obtained using the developed sensor and Karl Fischer showed that this method could be useful to understand water sensing mechanisms of dye and that the probes were sensitive to water content in organic solvents. NMR spectroscopy is one of the most powerful and versatile analytical techniques for the analysis of molecular structures and properties. Chemical shifts can be regarded as the most important information that can be obtained from NMR in regard to molecular structures. Changes in chemical and/or physical environments affecting electronic distributions result in alterations in the chemical shifts of the nuclei involved.

  9. 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.

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

    DEFF Research Database (Denmark)

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

    2018-01-01

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

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

    OpenAIRE

    M. Motamedzade; S. Ghazaiee

    2003-01-01

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

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

    DEFF Research Database (Denmark)

    Beeren, Sophie; Meier, Sebastian

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-09-01

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

  14. Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera

    Science.gov (United States)

    Sweet, M. J.; Brown, B. E.; Dunne, R. P.; Singleton, I.; Bulling, M.

    2017-09-01

    Shifts in the microbiome of the intertidal coral Coelastrea aspera (formally known as Goniastrea aspera) from Phuket, Thailand, were noted over the course of a 4-d period of spring tides. During this time, corals were naturally exposed to high temperatures, intense solar radiation, sub-aerial exposure and tidally induced water fluxes. Analysis of the 16S microbiome highlighted that the corals harbored both `core or stable' communities and those which appeared to be more `transient or sporadic.' Only relatively few microbial associates were classified as core microbes; the majority were transient or sporadic. Such transient associates were likely to have been governed by tidally induced variations in mucus thickness and water fluxes. Here we report strong shifts in the bacterial community of C. aspera over a short temporal scale. However, we also show significant differences in the timing of shifts between the two age groups of corals studied. More rapid changes (within 2 d of sub-aerial exposure) occurred within the 4-yr-old colonies, but a slightly delayed response was observed in the 10-yr-old colonies, whereby the microbial associates only changed after 4 d. We hypothesize that these shifts are age related and could be influenced by the observed baseline differences in the microbiome of the 4- and 10-yr-old corals, bacteria-bacteria interactions, and/or host energetics.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-04-15

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

  16. Dynamic habitat suitability modelling reveals rapid poleward distribution shift in a mobile apex predator.

    Science.gov (United States)

    Hill, Nicholas J; Tobin, Andrew J; Reside, April E; Pepperell, Julian G; Bridge, Tom C L

    2016-03-01

    Many taxa are undergoing distribution shifts in response to anthropogenic climate change. However, detecting a climate signal in mobile species is difficult due to their wide-ranging, patchy distributions, often driven by natural climate variability. For example, difficulties associated with assessing pelagic fish distributions have rendered fisheries management ill-equipped to adapt to the challenges posed by climate change, leaving pelagic species and ecosystems vulnerable. Here, we demonstrate the value of citizen science data for modelling the dynamic habitat suitability of a mobile pelagic predator (black marlin, Istiompax indica) within the south-west Pacific Ocean. The extensive spatial and temporal coverage of our occurrence data set (n = 18 717), collected at high resolution (~1.85 km(2) ), enabled identification of suitable habitat at monthly time steps over a 16-year period (1998-2013). We identified considerable monthly, seasonal and interannual variability in the extent and distribution of suitable habitat, predominately driven by chlorophyll a and sea surface height. Interannual variability correlated with El Nino Southern Oscillation (ENSO) events, with suitable habitat extending up to ~300 km further south during La Nina events. Despite the strong influence of ENSO, our model revealed a rapid poleward shift in the geometric mean of black marlin habitat, occurring at 88.2 km decade(-1) . By incorporating multiple environmental factors at monthly time steps, we were able to demonstrate a rapid distribution shift in a mobile pelagic species. Our findings suggest that the rapid velocity of climate change in the south-west Pacific Ocean is likely affecting mobile pelagic species, indicating that they may be more vulnerable to climate change than previously thought. © 2015 John Wiley & Sons Ltd.

  17. Errors in the Calculation of 27Al Nuclear Magnetic Resonance Chemical Shifts

    Directory of Open Access Journals (Sweden)

    Hui Zhao

    2012-11-01

    Full Text Available Computational chemistry is an important tool for signal assignment of 27Al nuclear magnetic resonance spectra in order to elucidate the species of aluminum(III in aqueous solutions. The accuracy of the popular theoretical models for computing the 27Al chemical shifts was evaluated by comparing the calculated and experimental chemical shifts in more than one hundred aluminum(III complexes. In order to differentiate the error due to the chemical shielding tensor calculation from that due to the inadequacy of the molecular geometry prediction, single-crystal X-ray diffraction determined structures were used to build the isolated molecule models for calculating the chemical shifts. The results were compared with those obtained using the calculated geometries at the B3LYP/6-31G(d level. The isotropic chemical shielding constants computed at different levels have strong linear correlations even though the absolute values differ in tens of ppm. The root-mean-square difference between the experimental chemical shifts and the calculated values is approximately 5 ppm for the calculations based on the X-ray structures, but more than 10 ppm for the calculations based on the computed geometries. The result indicates that the popular theoretical models are adequate in calculating the chemical shifts while an accurate molecular geometry is more critical.

  18. Further conventions for NMR shielding and chemical shifts IUPAC recommendations 2008.

    Science.gov (United States)

    Harris, Robin K; Becker, Edwin D; Cabral De Menezes, Sonia M; Granger, Pierre; Hoffman, Roy E; Zilm, Kurt W

    2008-03-01

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

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

    Science.gov (United States)

    Harris, Robin K; Becker, Edwin D; De Menezes, Sonia M Cabral; Granger, Pierre; Hoffman, Roy E; Zilm, Kurt W

    2008-06-01

    IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the (1)H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3-(trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating (13)C NMR chemical shifts in solids to the scales used for high-resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. Copyright (c) 2008 John Wiley & Sons, Ltd

  20. Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

    Science.gov (United States)

    Koes, David R; Vries, John K

    2017-01-01

    Accurate chemical shifts for the atoms in molecular mechanics (MD) trajectories can be obtained from quantum mechanical (QM) calculations that depend solely on the coordinates of the atoms in the localized regions surrounding atoms of interest. If these coordinates are correct and the sample size is adequate, the ensemble average of these chemical shifts should be equal to the chemical shifts obtained from NMR spectroscopy. If this is not the case, the coordinates must be incorrect. We have utilized this fact to quantify the errors associated with the backbone atoms in MD simulations of proteins. A library of regional conformers containing 169,499 members was constructed from 6 model proteins. The chemical shifts associated with the backbone atoms in each of these conformers was obtained from QM calculations using density functional theory at the B3LYP level with a 6-311+G(2d,p) basis set. Chemical shifts were assigned to each backbone atom in each MD simulation frame using a template matching approach. The ensemble average of these chemical shifts was compared to chemical shifts from NMR spectroscopy. A large systematic error was identified that affected the 1H atoms of the peptide bonds involved in hydrogen bonding with water molecules or peptide backbone atoms. This error was highly sensitive to changes in electrostatic parameters. Smaller errors affecting the 13Ca and 15N atoms were also detected. We believe these errors could be useful as metrics for comparing the force-fields and parameter sets used in MD simulation because they are directly tied to errors in atomic coordinates.

  1. Rapid Detection of Glycogen Synthase Kinase-3 Activity in Mouse Sperm Using Fluorescent Gel Shift Electrophoresis.

    Science.gov (United States)

    Choi, Hoseok; Choi, Bomi; Seo, Ju Tae; Lee, Kyung Jin; Gye, Myung Chan; Kim, Young-Pil

    2016-04-16

    Assaying the glycogen synthase kinase-3 (GSK3) activity in sperm is of great importance because it is closely implicated in sperm motility and male infertility. While a number of studies on GSK3 activity have relied on labor-intensive immunoblotting to identify phosphorylated GSK3, here we report the simple and rapid detection of GSK3 activity in mouse sperm using conventional agarose gel electrophoresis and a fluorescent peptide substrate. When a dye-tethered and prephosphorylated (primed) peptide substrate for GSK3 was employed, a distinct mobility shift in the fluorescent bands on the agarose was observed by GSK3-induced phosphorylation of the primed peptides. The GSK3 activity in mouse testes and sperm were quantifiable by gel shift assay with low sample consumption and were significantly correlated with the expression levels of GSK3 and p-GSK3. We suggest that our assay can be used for reliable and rapid detection of GSK3 activity in cells and tissue extracts.

  2. Rapid Detection of Glycogen Synthase Kinase-3 Activity in Mouse Sperm Using Fluorescent Gel Shift Electrophoresis

    Directory of Open Access Journals (Sweden)

    Hoseok Choi

    2016-04-01

    Full Text Available Assaying the glycogen synthase kinase-3 (GSK3 activity in sperm is of great importance because it is closely implicated in sperm motility and male infertility. While a number of studies on GSK3 activity have relied on labor-intensive immunoblotting to identify phosphorylated GSK3, here we report the simple and rapid detection of GSK3 activity in mouse sperm using conventional agarose gel electrophoresis and a fluorescent peptide substrate. When a dye-tethered and prephosphorylated (primed peptide substrate for GSK3 was employed, a distinct mobility shift in the fluorescent bands on the agarose was observed by GSK3-induced phosphorylation of the primed peptides. The GSK3 activity in mouse testes and sperm were quantifiable by gel shift assay with low sample consumption and were significantly correlated with the expression levels of GSK3 and p-GSK3. We suggest that our assay can be used for reliable and rapid detection of GSK3 activity in cells and tissue extracts.

  3. Rapidly shifting environmental baselines among fishers of the Gulf of California

    Science.gov (United States)

    Sáenz-Arroyo, Andrea; Roberts, Callum M; Torre, Jorge; Cariño-Olvera, Micheline; Enríquez-Andrade, Roberto R

    2005-01-01

    Shifting environmental baselines are inter-generational changes in perception of the state of the environment. As one generation replaces another, people's perceptions of what is natural change even to the extent that they no longer believe historical anecdotes of past abundance or size of species. Although widely accepted, this phenomenon has yet to be quantitatively tested. Here we survey three generations of fishers from Mexico's Gulf of California (N=108), where fish populations have declined steeply over the last 60 years, to investigate how far and fast their environmental baselines are shifting. Compared to young fishers, old fishers named five times as many species and four times as many fishing sites as once being abundant/productive but now depleted (Kruskal–Wallis tests, both p<0.001) with no evidence of a slowdown in rates of loss experienced by younger compared to older generations (Kruskal–Wallis test, n.s. in both cases). Old fishers caught up to 25 times as many Gulf grouper Mycteroperca jordani as young fishers on their best ever fishing day (regression r2=0.62, p<0.001). Despite times of plentiful large fish still being within living memory, few young fishers appreciated that large species had ever been common or nearshore sites productive. Such rapid shifts in perception of what is natural help explain why society is tolerant of the creeping loss of biodiversity. They imply a large educational hurdle in efforts to reset expectations and targets for conservation. PMID:16191603

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

    Science.gov (United States)

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-03-15

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

  6. Density functional calculations of {sup 15}N chemical shifts in solvated dipeptides

    Energy Technology Data Exchange (ETDEWEB)

    Cai Ling; Fushman, David, E-mail: fushman@umd.edu; Kosov, Daniel S. [University of Maryland, Department of Chemistry and Biochemistry (United States)], E-mail: dkosov@umd.edu

    2008-06-15

    We performed density functional calculations to examine the effects of solvation, hydrogen bonding, backbone conformation, and the side chain on {sup 15}N chemical shielding in proteins. We used N-methylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) as model systems. In addition, calculations were performed for selected fragments from protein GB3. The conducting polarizable continuum model was employed to include the effect of solvent in the density functional calculations. Our calculations for NMA show that the augmentation of the polarizable continuum model with the explicit water molecules in the first solvation shell has a significant influence on isotropic {sup 15}N chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard {beta}-sheet and {alpha}-helical conformations ranges from 0.8 to 6.2 ppm depending on the residue type, with the mean of 2.7 ppm. This is in good agreement with the experimental chemical shifts averaged over a database of 36 proteins containing >6100 amino acid residues. The orientation of the {sup 15}N chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins.

  7. Deuterium isotope effects on 13C chemical shifts of negatively charged NH.N systems

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Pietrzak, Mariusz; Grech, Eugeniusz

    2013-01-01

    ” and equilibrium cases. NMR assignments of the former have been revised. The NH proton is deuteriated. The isotope effects on 13C chemical shifts are rather unusual in these strongly hydrogen bonded systems between a NH and a negatively charged nitrogen atom. The formal four-bond effects are found to be negative......Deuterium isotope effects on 13C chemical shifts are investigated in anions of 1,8-bis(4-toluenesulphonamido)naphthalenes together with N,N-(naphthalene-1,8-diyl)bis(2,2,2-trifluoracetamide) all with bis(1,8-dimethylamino)napthaleneH+ as counter ion. These compounds represent both “static...... indicating transmission via the hydrogen bond. In addition, unusual long range effects are seen. Structures, 1H and 13C NMR chemical shifts and changes in nuclear shieldings upon deuteriation are calculated using density functional theory methods...

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

    Science.gov (United States)

    Hansen, Poul Erik

    2015-01-30

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

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

    DEFF Research Database (Denmark)

    Hansen, Poul Erik

    2015-01-01

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

  10. 13C-detection in RNA bases: revealing structure-chemical shift relationships.

    Science.gov (United States)

    Farès, Christophe; Amata, Irene; Carlomagno, Teresa

    2007-12-26

    The chemical shifts of the unprotonated carbons in the proton-deficient nucleobases of RNA are rarely reported, despite the valuable information that they contain about base-pairing and base-stacking. We have developed 13C-detected 2D-experiments to identify the unprotonated 13C in the RNA bases and have assigned all the base nuclei of uniformly 13C,15N-labeled HIV-2 TAR-RNA. The 13C chemical shift distributions revealed perturbations correlated with the base-pairing and base-stacking properties of all four base-types. From this work, we conclude that the information contained in the chemical shift perturbations within the base rings can provide valuable restraint information for solving RNA structures, especially in conformational averaged regions, where NOE-based information is not available.

  11. CSI 2.0: a significantly improved version of the Chemical Shift Index.

    Science.gov (United States)

    Hafsa, Noor E; Wishart, David S

    2014-11-01

    Protein chemical shifts have long been used by NMR spectroscopists to assist with secondary structure assignment and to provide useful distance and torsion angle constraint data for structure determination. One of the most widely used methods for secondary structure identification is called the Chemical Shift Index (CSI). The CSI method uses a simple digital chemical shift filter to locate secondary structures along the protein chain using backbone (13)C and (1)H chemical shifts. While the CSI method is simple to use and easy to implement, it is only about 75-80% accurate. Here we describe a significantly improved version of the CSI (2.0) that uses machine-learning techniques to combine all six backbone chemical shifts ((13)Cα, (13)Cβ, (13)C, (15)N, (1)HN, (1)Hα) with sequence-derived features to perform far more accurate secondary structure identification. Our tests indicate that CSI 2.0 achieved an average identification accuracy (Q3) of 90.56% for a training set of 181 proteins in a repeated tenfold cross-validation and 89.35% for a test set of 59 proteins. This represents a significant improvement over other state-of-the-art chemical shift-based methods. In particular, the level of performance of CSI 2.0 is equal to that of standard methods, such as DSSP and STRIDE, used to identify secondary structures via 3D coordinate data. This suggests that CSI 2.0 could be used both in providing accurate NMR constraint data in the early stages of protein structure determination as well as in defining secondary structure locations in the final protein model(s). A CSI 2.0 web server (http://csi.wishartlab.com) is available for submitting the input queries for secondary structure identification.

  12. On the stochastic nature of the rapid climate shifts during the last ice age

    DEFF Research Database (Denmark)

    Ditlevsen, Peter Dalager; Ditlevsen, Ove Dalager

    2009-01-01

    The rapid climate shifts observed in the glacial climate are analysed. The transitions into the warm interstadial states, the onsets, are easy identifiable in the record. The distribution of waiting times between consecutive onsets is well fitted assuming the remaining residence time in each state...... to exponential distributions with mean waiting times of around 800 y in the warm state and around 1600 y in the cold state. This observation is an important piece in the climate puzzle, since the fact that the climate is a no memory process indicates that the transitions are noise induced and the mean residence...... to be independent on the past. That implies that it has a simple no memory exponential waiting time distribution, but with mean waiting time depending on the climate state. The mean waiting time from one onset to the next is around 2400 y. The most likely (maximum likelihood) distribution derived solely from...

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

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen

    In this thesis, my work involving dierent aspects of protein structure determination by computer modeling is presented. Determination of several protein's native fold were carried out with Markov chain Monte Carlo simulations in the PHAISTOS protein structure simulation framework, utilizing...... to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...

  14. Using chemical shifts to assess transient secondary structure and generate ensemble structures of intrinsically disordered proteins.

    Science.gov (United States)

    Kashtanov, Stepan; Borcherds, Wade; Wu, Hongwei; Daughdrill, Gary W; Ytreberg, F Marty

    2012-01-01

    The chemical shifts of backbone atoms in polypeptides are sensitive to the dihedral angles phi and psi and can be used to estimate transient secondary structure and to generate structural ensembles of intrinsically disordered proteins (IDPs). In this chapter, several of the random coil reference databases used to estimate transient secondary structure are described, and the procedure is outlined for using these databases to estimate transient secondary structure. A new protocol is also presented for generating a diverse ensemble of structures for an IDP and reweighting these structures to optimize the fit between simulated and experimental chemical shift values.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-15

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

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

    Directory of Open Access Journals (Sweden)

    M. Motamedzade

    2003-04-01

    Full Text Available This study was conducted to determine the combined effects of noise and shift work on physiological parameters including body temperature, heart rate and blood pressure. This study was performed in a chemical industry in Tehran in 1993. The workers’ physiological parameters was recorded at the beginning and at the end of all work shifts. Groups under study included : day workers (n=115 , day workers with continuous noise exposure (n=44 , two-shift workers without noise exposure (n=180 , three-shift workers without noise exposure and three-shift workers with continous noise exposure (n=216. In workers with continuous noise exposure, noise dosimetry was performed using B & K noise dose meter type 4428. The results showed that noise and shift work hove more effects on systolic and diastolic blood pressure than body temperature. The statistical analysis showed that in 3-shift workers, combined effects of noise and shift work on systolic and diastolic blood pressure caused considerable differences between exposed and control group. In general, regarding research design of this study to determine probable combined effects of noise and shiftwork on physiological parameters, our findings confirmed the additive effects of noise and shiftwork on systolic and diastolic blood pressure in which the effect of noise was more significant. Our findings showed that combined exposure to shiftwork and noise may be regarded as a risk factor for cardiovascular diseases because it is responsible for increasing blood pressure in exposed workers.

  17. Mycobacteria mobility shift assay: a method for the rapid identification of Mycobacterium tuberculosis and nontuberculous mycobacteria

    Directory of Open Access Journals (Sweden)

    Letícia Muraro Wildner

    2014-06-01

    Full Text Available The identification of mycobacteria is essential because tuberculosis (TB and mycobacteriosis are clinically indistinguishable and require different therapeutic regimens. The traditional phenotypic method is time consuming and may last up to 60 days. Indeed, rapid, affordable, specific and easy-to-perform identification methods are needed. We have previously described a polymerase chain reaction-based method called a mycobacteria mobility shift assay (MMSA that was designed for Mycobacterium tuberculosis complex (MTC and nontuberculous mycobacteria (NTM species identification. The aim of this study was to assess the MMSA for the identification of MTC and NTM clinical isolates and to compare its performance with that of the PRA-hsp65 method. A total of 204 clinical isolates (102 NTM and 102 MTC were identified by the MMSA and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing fragments of the 16S rRNA and hsp65 genes. Both methods correctly identified all MTC isolates. Among the NTM isolates, the MMSA alone assigned 94 (92.2% to a complex or species, whereas the PRA-hsp65 method assigned 100% to a species. A 91.5% agreement was observed for the 94 NTM isolates identified by both methods. The MMSA provided correct identification for 96.8% of the NTM isolates compared with 94.7% for PRA-hsp65. The MMSA is a suitable auxiliary method for routine use for the rapid identification of mycobacteria.

  18. Rapid and Profound Shifts in the Vaginal Microbiota Following Antibiotic Treatment for Bacterial Vaginosis.

    Science.gov (United States)

    Mayer, Bryan T; Srinivasan, Sujatha; Fiedler, Tina L; Marrazzo, Jeanne M; Fredricks, David N; Schiffer, Joshua T

    2015-09-01

    Bacterial vaginosis (BV) is a common polymicrobial disease associated with numerous negative reproductive health outcomes, including an increased risk of human immunodeficiency virus acquisition. BV is treatable with antibiotics, but relapse is common. A more detailed understanding of bacterial dynamics during antibiotic therapy for BV could identify conditions that favor establishment, maintenance, and eradication of BV-associated bacterial species, thereby improving treatment outcomes. We used mathematical models to analyze daily quantitative measurements of 11 key bacterial species during metronidazole treatment for 15 cases of BV. We identified complete reorganization of vaginal bacterial composition within a day of initiating therapy. Although baseline bacterial levels predicted a longer time to clearance, all anaerobic species were eliminated rapidly within a median of 3 days. However, reemergence of BV-associated species was common following treatment cessation. Gardnerella vaginalis, a facultative anaerobe, was cleared more slowly than anaerobic BV-associated species, and levels of G. vaginalis often rebounded during treatment. We observed gradual Lactobacillus species growth, indicating that untargeted microbes fill the transient vacuum formed during treatment. Under antibiotic pressure, the human microbiome can undergo rapid shifts on a scale of hours. When treatment is stopped, BV-associated bacteria quickly reemerge, suggesting a possible role for intermittent prophylactic treatment. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. Mycobacteria mobility shift assay: a method for the rapid identification of Mycobacterium tuberculosis and nontuberculous mycobacteria.

    Science.gov (United States)

    Wildner, Letícia Muraro; Bazzo, Maria Luiza; Liedke, Susie Coutinho; Nogueira, Christiane Lourenço; Segat, Gabriela; Senna, Simone Gonçalves; Schlindwein, Aline Daiane; Oliveira, Jaquelline Germano de; Rovaris, Darcita B; Bonjardim, Claudio A; Kroon, Erna G; Ferreira, Paulo C P

    2014-06-01

    The identification of mycobacteria is essential because tuberculosis (TB) and mycobacteriosis are clinically indistinguishable and require different therapeutic regimens. The traditional phenotypic method is time consuming and may last up to 60 days. Indeed, rapid, affordable, specific and easy-to-perform identification methods are needed. We have previously described a polymerase chain reaction-based method called a mycobacteria mobility shift assay (MMSA) that was designed for Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) species identification. The aim of this study was to assess the MMSA for the identification of MTC and NTM clinical isolates and to compare its performance with that of the PRA-hsp65 method. A total of 204 clinical isolates (102 NTM and 102 MTC) were identified by the MMSA and PRA-hsp65. For isolates for which these methods gave discordant results, definitive species identification was obtained by sequencing fragments of the 16S rRNA and hsp65 genes. Both methods correctly identified all MTC isolates. Among the NTM isolates, the MMSA alone assigned 94 (92.2%) to a complex or species, whereas the PRA-hsp65 method assigned 100% to a species. A 91.5% agreement was observed for the 94 NTM isolates identified by both methods. The MMSA provided correct identification for 96.8% of the NTM isolates compared with 94.7% for PRA-hsp65. The MMSA is a suitable auxiliary method for routine use for the rapid identification of mycobacteria.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-17

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

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

    DEFF Research Database (Denmark)

    Lægsgaard, Jesper

    2001-01-01

    The chemical shifts of the K alpha radiation line from Al, Si, and Ge ions between their elemental and oxide forms are calculated within the framework of density functional theory using ultrasoft pseudopotentials. It is demonstrated that this theoretical approach yields quantitatively accurate...

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

    Energy Technology Data Exchange (ETDEWEB)

    Trautwein, Matthias; Fredriksson, Kai [Eberhard Karls Universität Tübingen, Institute of Pharmacy (Germany); Möller, Heiko M. [University of Potsdam, Institute of Chemistry (Germany); Exner, Thomas E., E-mail: thomas.exner@uni-konstanz.de [Eberhard Karls Universität Tübingen, Institute of Pharmacy (Germany)

    2016-08-15

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

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

    Directory of Open Access Journals (Sweden)

    Costa V.E.U.

    1999-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Feng YongE

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

  5. NMR Nomenclature: Nuclear Spin Properties and Conventions for Chemical Shifts. IUPAC Recommendations 2001.

    Science.gov (United States)

    Harris, Robin K.; Becker, Edwin D.; Cabral de Menezes, Sonia M.; Goodfellow, Robin; Granger, Pierre

    2002-12-01

    A unified scale is recommended for reporting the NMR chemical shifts of all nuclei relative to the (1)H resonance of tetramethylsilane. The unified scale is designed to provide a precise ratio, Xi, of the resonance frequency of a given nuclide to that of the primary reference, the (1)H resonance of tetramethylsilane (TMS) in dilute solution (volume fraction, varphi<1%) in chloroform. Referencing procedures are discussed, including matters of practical application of the unified scale. Special attention is paid to recommended reference samples, and values of Xi for secondary references on the unified scale are listed, many of which are the results of new measurements. Some earlier recommendations relating to the reporting of chemical shifts are endorsed. The chemical shift, delta, is redefined to avoid previous ambiguities but to leave practical usage unchanged. Relations between the unified scale and recently published recommendations for referencing in aqueous solutions (for specific use in biochemical work) are discussed, as well as the special effects of working in the solid state with magic-angle spinning. In all, nine new recommendations relating to chemical shifts are made. Standardised nuclear spin data are also presented in tabular form for the stable (and some unstable) isotopes of all elements with non-zero quantum numbers. The information given includes quantum numbers, isotopic abundances, magnetic moments, magnetogyric ratios, and receptivities, together with quadrupole moments and line-width factors (where appropriate).

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

    NARCIS (Netherlands)

    Sijens, PE; Oudkerk, M

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

  7. Next generation chemical proteomic tools for rapid enzyme profiling.

    Science.gov (United States)

    Uttamchandani, Mahesh; Lu, Candy H S; Yao, Shao Q

    2009-08-18

    Sequencing of the human genome provided a wealth of information about the genomic blueprint of a cell. But genes do not tell the entire story of life and living processes; identifying the roles of enzymes and mapping out their interactions is also crucial. Enzymes catalyze virtually every cellular process and metabolic exchange. They not only are instrumental in sustaining life but also are required for its regulation and diversification. Diseases such as cancer can be caused by minor changes in enzyme activities. In addition, the unique enzymes of pathogenic organisms are ripe targets for combating infections. Consequently, nearly one-third of all current drug targets are enzymes. An estimated 18-29% of eukaryotic genes encode enzymes, but only a limited proportion of enzymes have thus far been characterized. Therefore, little is understood about the physiological roles, substrate specificity, and downstream targets of the vast majority of these important proteins. A key step toward the biological characterization of enzymes, as well as their adoption as drug targets, is the development of global solutions that bridge the gap in understanding these proteins and their interactions. We herein present technological advances that facilitate the study of enzymes and their properties in a high-throughput manner. Over the years, our group has introduced and developed a variety of such enabling platforms for many classes of enzymes, including kinases, phosphatases, and proteases. For each of these different types of enzymes, specific design considerations are required to develop the appropriate chemical tools to characterize each class. These tools include activity-based probes and chemical compound libraries, which are rapidly assembled using efficient combinatorial synthesis or "click chemistry" strategies. The resulting molecular assortments may then be screened against the target enzymes in high-throughput using microplates or microarrays. These techniques offer

  8. A geometrical parametrization of C1'-C5' RNA ribose chemical shifts calculated by density functional theory

    Science.gov (United States)

    Suardíaz, Reynier; Sahakyan, Aleksandr B.; Vendruscolo, Michele

    2013-07-01

    It has been recently shown that NMR chemical shifts can be used to determine the structures of proteins. In order to begin to extend this type of approach to nucleic acids, we present an equation that relates the structural parameters and the 13C chemical shifts of the ribose group. The parameters in the equation were determined by maximizing the agreement between the DFT-derived chemical shifts and those predicted through the equation for a database of ribose structures. Our results indicate that this type of approach represents a promising way of establishing quantitative and computationally efficient analytical relationships between chemical shifts and structural parameters in nucleic acids.

  9. [Metabolic syndrome and shift work: study of the relationship in workers of a chemical plant].

    Science.gov (United States)

    Taino, Giuseppe; Gazzoldi, Tiziana; Brevi, Marco; Giorgi, Marco; Imbriani, Paola

    2011-01-01

    Metabolic syndrome is defined by several metabolic factors, related to one another, which induce atherosclerotic pathology. These factors are: visceral obesity, atherogenic dyslipidemia, high blood pressure, hyperglycemia, proinflammatory and prothrombotic state. Shift work is known to be related to a series of organic changes, including increased cardiovascular risk independent factors. The aim of our study is to assess if shift work might be a cofactor inducing metabolic syndrome. 119 workers of a chemical industry have been examinated and been divided in two groups: shift workers and daytime workers. We checked if workers were affected by metabolic syndrome, following the ATP III criteria. The results have been statistically compared. The prevalence of metabolic syndrome is significantly higher in night shift workers comparing to other workers. Among night shift workers metabolic syndrome was found in 28 out of 77 (36,36%); in daytime workers the syndrome was observed in 8 workers out of 42 (19,05%) (DR: 2, 43; 95% CI 0,99 - 5,98; p=0,049). This difference is stronger when only over 40 years old subjects were considered. Our results show an association between metabolic syndrome and night shift work. It is therefore necessary, as primary health safety measure, to verify the presence of metabolic syndrome in night shift workers. All aspects of the syndrome should be studied to prevent disease and its clinical complications. The primary prevention activity should be based on specific information and education programs, particulary aimed at learning about a correct lifestyle.

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

    Science.gov (United States)

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

    2016-02-24

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

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

    Science.gov (United States)

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

    2016-08-01

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

  12. Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard.

    Science.gov (United States)

    Campbell-Staton, Shane C; Cheviron, Zachary A; Rochette, Nicholas; Catchen, Julian; Losos, Jonathan B; Edwards, Scott V

    2017-08-04

    Extreme environmental perturbations offer opportunities to observe the effects of natural selection in wild populations. During the winter of 2013-2014, the southeastern United States endured an extreme cold event. We used thermal performance, transcriptomics, and genome scans to measure responses of lizard populations to storm-induced selection. We found significant increases in cold tolerance at the species' southern limit. Gene expression in southern survivors shifted toward patterns characteristic of northern populations. Comparing samples before and after the extreme winter, 14 genomic regions were differentiated in the surviving southern population; four also exhibited signatures of local adaptation across the latitudinal gradient and implicate genes involved in nervous system function. Together, our results suggest that extreme winter events can rapidly produce strong selection on natural populations at multiple biological levels that recapitulate geographic patterns of local adaptation. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  13. 13C solid-state NMR chemical shift anisotropy analysis of the anomeric carbon in carbohydrates.

    Science.gov (United States)

    Chen, Ying-Ying; Luo, Shun-Yuan; Hung, Shang-Cheng; Chan, Sunney I; Tzou, Der-Lii M

    2005-03-21

    (13)C NMR solid-state structural analysis of the anomeric center in carbohydrates was performed on six monosaccharides: glucose (Glc), mannose (Man), galactose (Gal), galactosamine hydrochloride (GalN), glucosamine hydrochloride (GlcN), and N-acetyl-glucosamine (GlcNAc). In the 1D (13)C cross-polarization/magic-angle spinning (CP/MAS) spectrum, the anomeric center C-1 of these carbohydrates revealed two well resolved resonances shifted by 3-5ppm, which were readily assigned to the anomeric alpha and beta forms. From this experiment, we also extracted the (13)C chemical shift anisotropy (CSA) tensor elements of the two forms from their spinning sideband intensities, respectively. It was found out that the chemical shift tensor for the alpha anomer was more axially symmetrical than that of the beta form. A strong linear correlation was obtained when the ratio of the axial asymmetry of the (13)C chemical shift tensors of the two anomeric forms was plotted in a semilogarithmic plot against the relative population of the two anomers. Finally, we applied REDOR spectroscopy to discern whether or not there were any differences in the sugar ring conformation between the anomers. Identical two-bond distances of 2.57A (2.48A) were deduced for both the alpha and beta forms in GlcNAc (GlcN), suggesting that the two anomers have essentially identical sugar ring scaffolds in these sugars. In light of these REDOR distance measurements and the strong correlation observed between the ratio of the axial asymmetry parameters of the (13)C chemical shift tensors and the relative population between the two anomeric forms, we concluded that the anomeric effect arises principally from interaction of the electron charge clouds between the C-1-O-5 and the C-1-O-1 bonds in these monosaccharides.

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

    Science.gov (United States)

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

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

  15. Large area super-resolution chemical imaging via rapid dithering of a nanoprobe

    Science.gov (United States)

    Languirand, Eric R.; Cullum, Brian M.

    2015-05-01

    Super-resolution chemical imaging via Raman spectroscopy provides a significant ability to simultaneously or pseudosimultaneously monitor numerous label-free analytes while elucidating their spatial distribution on the surface of the sample. However, spontaneous Raman is an inherently weak phenomenon making trace detection and thus superresolution imaging extremely difficult, if not impossible. To circumvent this and allow for trace detection of the few chemical species present in any sub-diffraction limited resolution element of an image, we have developed a surface enhanced Raman scattering (SERS) coherent fiber-optic imaging bundle probe consisting of 30,000 individual fiber elements. When the probes are tapered, etched and coated with metal, they provide circular Raman chemical images of a sample with a field of view of approximately 20μm (i.e. diameter) via the array of 30,000 individual 50 nm fiber elements. An acousto-optic tunable filter is used to rapidly scan or select discrete frequencies for multi- or hyperspectral analysis. Although the 50nm fiber element dimensions of this probe inherently provide spatial resolutions of approximately 100nm, further increases in the spatial resolution can be achieved by using a rapid dithering process. Using this process, additional images are obtained one-half fiber diameter translations in the x- and y- planes. A piezostage drives the movement, providing the accurate and reproducible shifts required for dithering. Optimal probability algorithms are then used to deconvolute the related images producing a final image with a three-fold increase in spatial resolution. This paper describes super-resolution chemical imaging using these probes and the dithering method as well as its potential applications in label-free imaging of lipid rafts and other applications within biology and forensics.

  16. Uniform fat suppression in hands and feet through the use of two-point Dixon chemical shift MR imaging

    NARCIS (Netherlands)

    Maas, M.; Dijkstra, P. F.; Akkerman, E. M.

    1999-01-01

    To assess the potential of two-point Dixon chemical shift magnetic resonance imaging to achieve uniform fat suppression in the distal parts of the extremities. Two-point Dixon chemical shift imaging was performed in 31 consecutive patients clinically suspected to have bone marrow disease. In some

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

    Energy Technology Data Exchange (ETDEWEB)

    Lee, In-Sook Han; Jeon, Hyun Ju; Yu, Ji Sook; Lee, Chang Kiu [Kangwon National University, Chuncheon (Korea, Republic of)

    2010-06-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-10-15

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Karl-Heinz Böhm

    2014-04-01

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

  1. Rapid determination of fumigant and industrial chemical residues in food.

    Science.gov (United States)

    Daft, J L

    1988-01-01

    A gas chromatographic (GC) method is described for the determination of 22 fumigant and industrial chemical residues in a variety of foods. The fumigants and industrial chemicals determined are methyl bromide, methylene chloride, carbon disulfide, chloroform, 1,1-dichloroethane, ethylene dichloride, methyl chloroform, carbon tetrachloride, methylene bromide, propylene dichloride, 2,3-dichloropropene, trichloroethylene, 1,3-dichloropropylene, 1,1,2-trichloroethane, chloropicrin, ethylene dibromide, tetrachloroethylene, propylene dibromide, 1,1,2,2-tetrachloroethane, p-dichlorobenzene, o-dichlorobenzene, and 1,2-dibromo-3-chloropropane. Except for the latter three, the fumigants are determined at 90 degrees C on 3.6 m 20% loaded OV-101 columns with electron-capture and Hall-electroconductivity detectors. The other 3 compounds (o-dichlorobenzene, p-dichlorobenzene, and 1,2-dibromo-3-chloropropane), which elute beyond 30 min on the above columns, are determined at 90 degrees C on 1.8 m 5% loaded OV-101 columns with the same detectors. The ng/g-level fortifications have an overall mean analyte recovery of 70% and a coefficient of variation of 40%. The variety of foods examined includes both fatty and nonfatty food types (e.g., off-the-shelf cooked and uncooked grain-based items, dairy products, fresh and canned fruits and vegetables, and meats). Samples are extracted and cleaned up according to fat content and food type. Samples containing less than 71% fat are extracted by using an aqueous: nonaqueous shakeout (20% acetone solution under isooctane). Most extracts (isooctanes) are analyzed directly. Extracts from samples containing from 21 to 70% fat (e.g., ground beef, pecans, and corn chips) are cleaned up further on micro-Florisil columns to remove excess fat. A few other samples containing more than 71% fat or oil (e.g., butter, salad dressing, and vegetable oil) are diluted directly in isooctane and, depending on the degree of dilution, can be cleaned up further on

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

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin

    2011-01-01

    . The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we......Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues...... use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes...

  3. Semiempirical calculations of ESCA chemical shifts by the SCC-AMEP model

    Science.gov (United States)

    Maksic, Z. B.; Rupnik, K.

    1986-03-01

    ESCA chemical shifts give a direct insight into the charge redistribution accompanying formation of chemical bonds. This remarkable feature follows directly from a finding that inner-shell binding energies are closely related to the potentials exerted on the nuclei in question. We have provided extensive evidence which conclusively shows that electrostatic potentials (EP), evaluated in the atomic monopole (AM) approximation, by using the self-consistent charge (SCC-MO) densities, reproduce observed ESCA data in a surprisingly successful way. This approach, abbreviated heretofore the SCC-AMEP model, has also a considerable predictive power. The results have usually an accuracy which is placed in between the chemical and moderate precision. Hence, the salient features of the basic ESCA lines are well described within the AMEP approximation. Finally, the role of the relaxation energy is briefly discussed.

  4. Systemic range shift lags among a pollinator species assemblage following rapid climate change

    DEFF Research Database (Denmark)

    Bedford, Felicity E.; Whittaker, Robert J.; Kerr, Jeremy T.

    2012-01-01

    Contemporary climate change is driving widespread geographical range shifts among many species. If species are tracking changing climate successfully, then leading populations should experience similar climatic conditions through time as new populations establish beyond historical range margins. ...

  5. Quantum mechanical calculations of conformationally relevant 1H and 13C NMR chemical shifts of calixarene systems.

    Science.gov (United States)

    Bifulco, Giuseppe; Gomez-Paloma, Luigi; Riccio, Raffaele; Gaeta, Carmine; Troisi, Francesco; Neri, Placido

    2005-12-22

    [graphs: see text] QM GIAO calculations of 13C and 1H chemical shift values of the ArCH2Ar group have been performed, using the hybrid DFT functional MPW1PW91 and the 6-31G(d,p) basis set, on some representative calixarenes and on a series of simplified calixarene models allowing derivation of chemical shift surfaces versus phi and chi dihedral angles. A good reproduction of experimental data was obtained. The applicability of chemical shift surfaces in the study of calixarene conformational features is illustrated.

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

    DEFF Research Database (Denmark)

    Schripsema, Jan; Danigno, Denise

    1996-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-15

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

  8. Xenon NMR: Chemical Shifts of a General Anesthetic in Common Solvents, Proteins, and Membranes

    Science.gov (United States)

    Miller, Keith W.; Reo, Nicholas V.; Schoot Uiterkamp, Antonius J. M.; Stengle, Diane P.; Stengle, Thomas R.; Williamson, Kenneth L.

    1981-08-01

    The rare gas xenon contains two NMR-sensitive isotopes in high natural abundance. The nuclide 129Xe has a spin of {textstyle1/2}; 131Xe is quadrupolar with a spin of {textstyle3/2}. The complementary NMR characteristics of these nuclei provide a unique opportunity for probing their environment. The method is widely applicable because xenon interacts with a useful range of condensed phases including pure liquids, protein solutions, and suspensions of lipid and biological membranes. Although xenon is chemically inert, it does interact with living systems; it is an effective general anesthetic. We have found that the range of chemical shifts of 129Xe dissolved in common solvents is ca. 200 ppm, which is 30 times larger than that found for 13C in methane dissolved in various solvents. Resonances were also observed for 131Xe in some systems; they were broader and exhibited much greater relaxation rates than did 129Xe. The use of 129Xe NMR as a probe of biological systems was investigated. Spectra were obtained from solutions of myoglobin, from suspensions of various lipid bilayers, and from suspensions of the membranes of erythrocytes and of the acetylcholine receptor-rich membranes of Torpedo californica. These systems exhibited a smaller range of chemical shifts. In most cases there was evidence of a fast exchange of xenon between the aqueous and organic environments, but the exchange was slow in suspensions of dimyristoyl lecithin vesicles.

  9. Effects of crystallinity and chemical variation on apparent band-gap shift in polycrystalline indium nitride

    Energy Technology Data Exchange (ETDEWEB)

    Chen, P.P.-T., E-mail: patrick.chen@mq.edu.a [Department of Physics and Astronomy, Faculty of Science, Macquarie University, Sydney, NSW 2109 (Australia); Downes, J.E.; Fernandes, A.J.; Butcher, K.S.A.; Wintrebert-Fouquet, M. [Department of Physics and Astronomy, Faculty of Science, Macquarie University, Sydney, NSW 2109 (Australia); Wuhrer, R.; Phillips, M.R. [Microstructural Analysis Unit, Faculty of Science, University of Technology, Sydney, Broadway, NSW 2007 (Australia)

    2011-01-03

    The nature of the apparent band-gap shift in polycrystalline indium nitride thin-films, grown by remote-plasma-enhanced chemical vapour deposition at 535 {+-} 10 {sup o}C, has been investigated separately in relation to growth temperature dependent crystallinity and chemical variation. Substrates of sapphire and gallium nitride on sapphire were used to study the effect of a stress-reduced template on indium nitride crystallite quality and apparent band-gap. To mimic surface growth temperature variations two glass substrates of differing thickness and thermal conductivity were intentionally used for the same growth conditions. The samples were characterised using optical transmission, scanning electron microscope, X-ray diffraction, and high-resolution X-ray photoelectron spectroscopy. The results indicate that the apparent band-gap shift in polycrystalline narrow band-gap indium nitride thin-films is not primarily determined by the quality of indium nitride crystallites but rather it is associated with growth temperature dependent chemical variations in the films.

  10. Investigating lipids as a source of chemical exchange-induced MRI frequency shifts.

    Science.gov (United States)

    Shmueli, K; Dodd, S J; van Gelderen, P; Duyn, J H

    2017-04-01

    While magnetic susceptibility is a major contributor to NMR resonance frequency variations in the human brain, a substantial contribution may come from the chemical exchange of protons between water and other molecules. Exchange-induced frequency shifts fe have been measured in tissue and protein solutions, but relatively lipid-rich white matter (WM) has a larger fe than gray matter, suggesting that lipids could contribute. Galactocerebrosides (GC) are a prime candidate as they are abundant in WM and susceptible to exchange. To investigate this, fe was measured in a model of WM lipid membranes in the form of multilamellar vesicles (MLVs), consisting of a 1:2 molar ratio of GC and phospholipids (POPC), and in MLVs with POPC only. Chemical shift imaging with 15% volume fraction of dioxane, an internal reference whose protons are assumed not to undergo chemical exchange, was used to remove susceptibility-induced frequency shifts in an attempt to measure fe in MLVs at several lipid concentrations. Initial analysis of these measurements indicated a necessity to correct for small unexpected variations in dioxane concentration due to its effect on the water frequency shift. To achieve this, the actual dioxane concentration was inferred from spectral analysis and its additional contribution to fe was removed through separate experiments which showed that the water-dioxane frequency shift depended linearly on the dioxane concentration at low concentrations with a proportionality constant of -0.021 ± 0.002 ppb/mM in agreement with published experiments. Contrary to expectations and uncorrected results, for GC + POPC vesicles, the dependence of the corrected fe on GC concentration was insignificant (0.023 ± 0.037 ppb/mM; r(2)  = 0.085, p > 0.57), whereas for the POPC-only vesicles a small but significant linear increase with POPC concentration was found: 0.044 ± 0.008 ppb/mM (r(2)  = 0.877, p lipids to frequency contrast in WM may be

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    . This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on 15N nuclear shielding, 1Δ15N......Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation...

  12. Thymic hyperplasia and thymus gland tumors: differentiation with chemical shift MR imaging.

    Science.gov (United States)

    Inaoka, Tsutomu; Takahashi, Koji; Mineta, Masayuki; Yamada, Tomonori; Shuke, Noriyuki; Okizaki, Atsutaka; Nagasawa, Kenichi; Sugimori, Hiroyuki; Aburano, Tamio

    2007-06-01

    To prospectively evaluate chemical shift magnetic resonance (MR) imaging for differentiating thymic hyperplasia from tumors of the thymus gland. The institutional review board approved this study; informed consent was obtained and patient confidentiality was protected. The authors assessed 41 patients (17 male, 24 female; age range, 16-78 years) in whom thymic lesions were seen at chest computed tomography. Patients were assigned to a hyperplasia group (n=23) (18 patients with hyperplastic thymus associated with Graves disease and five with rebound thymic hyperplasia) and a tumor group (n=18) (seven patients with thymomas, four with invasive thymomas, five with thymic cancers, and two with malignant lymphomas). T2-weighted fast spin-echo and T1-weighted in-phase and opposed-phase MR images were obtained in all patients and visually assessed. A chemical shift ratio (CSR), determined by comparing the signal intensity of the thymus gland with that of the paraspinal muscle, was calculated for quantitative analysis. Mean CSRs for the patient groups and subgroups were analyzed by using Welch t and Newman-Keuls tests. Pthymus gland had homogeneous signal intensity in all 23 patients in the hyperplasia group and in 12 of the 18 patients in the tumor group. The mean CSR (+/- standard deviation) was 0.614 +/- 0.130 in the hyperplasia group and 1.026 +/- 0.039 in the tumor group. Mean CSRs in the patients with a hyperplastic thymus and Graves disease, rebound thymic hyperplasia, thymoma, invasive thymoma, thymic cancer, and malignant lymphoma were 0.594 +/- 0.120, 0.688 +/- 0.154, 1.033 +/- 0.043, 1.036 +/- 0.040, 1.020 +/- 0.044, and 0.997 +/- 0.010, respectively. The difference in CSR between the hyperplasia and tumor groups was significant (Pthymus gland signal intensity at chemical shift MR imaging; no tumor group patients had a decrease in thymus gland signal intensity. Chemical shift MR imaging can be used to differentiate thymic hyperplasia from thymic tumors. (c) RSNA

  13. Sclerosing liposarcoma of epididymis: Role of chemical shift magnetic resonance imaging

    Directory of Open Access Journals (Sweden)

    Subramaniyan Ramanathan

    2016-01-01

    Full Text Available Sclerosing liposarcoma of epididymis is a rare extratesticular scrotal tumor with variable prognosis. Ultrasonography is the initial imaging modality of choice for the evaluation of scrotal mass and helps to differentiate testicular and extratesticular masses, thereby narrowing down the differential diagnosis. Magnetic resonance imaging with its excellent soft tissue resolution can help in the further characterization of the nature of the tumor. In this case report, we highlight the role of chemical shift imaging in making a confident preoperative diagnosis of liposarcoma thereby guiding optimal and timely management.

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

    Science.gov (United States)

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

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

  15. Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding.

    Science.gov (United States)

    Andrew, Audra L; Card, Daren C; Ruggiero, Robert P; Schield, Drew R; Adams, Richard H; Pollock, David D; Secor, Stephen M; Castoe, Todd A

    2015-05-01

    Snakes provide a unique and valuable model system for studying the extremes of physiological remodeling because of the ability of some species to rapidly upregulate organ form and function upon feeding. The predominant model species used to study such extreme responses has been the Burmese python because of the extreme nature of postfeeding response in this species. We analyzed the Burmese python intestine across a time series, before, during, and after feeding to understand the patterns and timing of changes in gene expression and their relationship to changes in intestinal form and function upon feeding. Our results indicate that >2,000 genes show significant changes in expression in the small intestine following feeding, including genes involved in intestinal morphology and function (e.g., hydrolases, microvillus proteins, trafficking and transport proteins), as well as genes involved in cell division and apoptosis. Extensive changes in gene expression occur surprisingly rapidly, within the first 6 h of feeding, coincide with changes in intestinal morphology, and effectively return to prefeeding levels within 10 days. Collectively, our results provide an unprecedented portrait of parallel changes in gene expression and intestinal morphology and physiology on a scale that is extreme both in the magnitude of changes, as well as in the incredibly short time frame of these changes, with up- and downregulation of expression and function occurring in the span of 10 days. Our results also identify conserved vertebrate signaling pathways that modulate these responses, which may suggest pathways for therapeutic modulation of intestinal function in humans. Copyright © 2015 the American Physiological Society.

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

    DEFF Research Database (Denmark)

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

    2000-01-01

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

  17. Rapid neutron capture process in supernovae and chemical element formation

    NARCIS (Netherlands)

    Baruah, Rulee; Duorah, Kalpana; Duorah, H. L.

    2009-01-01

    The rapid neutron capture process (r-process) is one of the major nucleosynthesis processes responsible for the synthesis of heavy nuclei beyond iron. Isotopes beyond Fe are most exclusively formed in neutron capture processes and more heavier ones are produced by the r-process. Approximately half

  18. Experimental setup for rapid crystallization using favoured chemical ...

    Indian Academy of Sciences (India)

    Unknown

    tors (3005 type), the output of which drives the d.c. motor. M3. The solution of ... to motor M1 prevents rapid temperature fluctuations and hence ensures very good temperature control. The thermostatic bath is heated with an infrared lamp I at the base of the unit and ... through chains of hydrogen bonds and these polymers.

  19. Experimental setup for rapid crystallization using favoured chemical ...

    Indian Academy of Sciences (India)

    The rapid crystallization of KH2PO4 (KDP) from solution is demonstrated at a rate up to ≈7.5 mm/day along [100] and 22 mm/day along [001] in a crystallizer of 5 l capacity, using accelerated crucible rotation technique (ACRT) and simulated platform geometry for controlling the hydrodynamic conditions. On an experimental ...

  20. Four-bond deuterium isotope effects on the chemical shifts of amide nitrogens in proteins.

    Science.gov (United States)

    Tugarinov, Vitali

    2013-11-01

    An approach towards precision NMR measurements of four-bond deuterium isotope effects on the chemical shifts of backbone amide nitrogen nuclei in proteins is described. Three types of four-bond (15) N deuterium isotope effects are distinguished depending on the site of proton-to-deuterium substitution: (4)ΔN(N(i-1)D), (4)ΔN(N(i+1)D) and (4)ΔN(Cβ,(i-1)D). All the three types of isotope shifts are quantified in the (partially) deuterated protein ubiquitin. The (4)ΔN(N(i+1)D) and (4)ΔN(C(β,i-1)D) effects are by far the largest in magnitude and vary between 16 and 75 ppb and -18 and 46 ppb, respectively. A semi-quantitative correlation between experimental (4)ΔN(N(i+1)D) and (4)ΔN(C(β,i-1)D) values and the distances between nitrogen nuclei and the sites of (1)H-to-D substitution is noted. The largest isotope shifts in both cases correspond to the shortest inter-nuclear distances. Copyright © 2013 John Wiley & Sons, Ltd.

  1. Benefits of photobiological light exposure during rapidly rotating night-shift work

    NARCIS (Netherlands)

    Groot, E.H. de; Knoop, M.

    2007-01-01

    In the Netherlands, 76%o of the working population sometimes or regularly works between midnight and 6 a.m. This percentage is comparable to those of other countries. Two of the most common and harmful problems associated with shift work are reduced quality of sleep and a reduced alertness while at

  2. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    Science.gov (United States)

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-04

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. High spectral specificity of local chemical components characterization with multichannel shift-excitation Raman spectroscopy

    Science.gov (United States)

    Chen, Kun; Wu, Tao; Wei, Haoyun; Wu, Xuejian; Li, Yan

    2015-09-01

    Raman spectroscopy has emerged as a promising tool for its noninvasive and nondestructive characterization of local chemical structures. However, spectrally overlapping components prevent the specific identification of hyperfine molecular information of different substances, because of limitations in the spectral resolving power. The challenge is to find a way of preserving scattered photons and retrieving hidden/buried Raman signatures to take full advantage of its chemical specificity. Here, we demonstrate a multichannel acquisition framework based on shift-excitation and slit-modulation, followed by mathematical post-processing, which enables a significant improvement in the spectral specificity of Raman characterization. The present technique, termed shift-excitation blind super-resolution Raman spectroscopy (SEBSR), uses multiple degraded spectra to beat the dispersion-loss trade-off and facilitate high-resolution applications. It overcomes a fundamental problem that has previously plagued high-resolution Raman spectroscopy: fine spectral resolution requires large dispersion, which is accompanied by extreme optical loss. Applicability is demonstrated by the perfect recovery of fine structure of the C-Cl bending mode as well as the clear discrimination of different polymorphs of mannitol. Due to its enhanced discrimination capability, this method offers a feasible route at encouraging a broader range of applications in analytical chemistry, materials and biomedicine.

  4. WAter Saturation Shift Referencing (WASSR) for chemical exchange saturation transfer experiments

    Science.gov (United States)

    Kim, Mina; Gillen, Joseph; Landman, Bennett. A.; Zhou, Jinyuan; van Zijl, Peter C.M.

    2010-01-01

    Chemical exchange saturation transfer (CEST) is a contrast mechanism exploiting exchange-based magnetization transfer (MT) between solute and water protons. CEST effects compete with direct water saturation and conventional MT processes and generally can only be quantified through an asymmetry analysis of the water saturation spectrum (Z-spectrum) with respect to the water frequency, a process that is exquisitely sensitive to magnetic field inhomogeneities. Here, it is shown that direct water saturation imaging allows measurement of the absolute water frequency in each voxel, allowing proper centering of Z-spectra on a voxel-by-voxel basis independent of spatial B0 field variations. Optimal acquisition parameters for this “water saturation shift referencing” or “WASSR” approach were estimated using Monte Carlo simulations and later confirmed experimentally. The optimal ratio of the WASSR sweep width to the linewidth of the direct saturation curve was found to be 3.3–4.0, requiring a sampling of 16–32 points. The frequency error was smaller than 1 Hz at signal to noise ratios of 40 or higher. The WASSR method was applied to study glycogen, where the chemical shift difference between the hydroxyl (OH) protons and bulk water protons at 3T is so small (0.75–1.25 ppm) that the CEST spectrum is inconclusive without proper referencing. PMID:19358232

  5. Water saturation shift referencing (WASSR) for chemical exchange saturation transfer (CEST) experiments.

    Science.gov (United States)

    Kim, Mina; Gillen, Joseph; Landman, Bennett A; Zhou, Jinyuan; van Zijl, Peter C M

    2009-06-01

    Chemical exchange saturation transfer (CEST) is a contrast mechanism that exploits exchange-based magnetization transfer (MT) between solute and water protons. CEST effects compete with direct water saturation and conventional MT processes, and generally can only be quantified through an asymmetry analysis of the water saturation spectrum (Z-spectrum) with respect to the water frequency, a process that is exquisitely sensitive to magnetic field inhomogeneities. Here it is shown that direct water saturation imaging allows measurement of the absolute water frequency in each voxel, allowing proper centering of Z-spectra on a voxel-by-voxel basis independently of spatial B(0) field variations. Optimal acquisition parameters for this "water saturation shift referencing" (WASSR) approach were estimated using Monte Carlo simulations and later confirmed experimentally. The optimal ratio of the WASSR sweep width to the linewidth of the direct saturation curve was found to be 3.3-4.0, requiring a sampling of 16-32 points. The frequency error was smaller than 1 Hz at signal-to-noise ratios of 40 or higher. The WASSR method was applied to study glycogen, where the chemical shift difference between the hydroxyl (OH) protons and bulk water protons at 3T is so small (0.75-1.25 ppm) that the CEST spectrum is inconclusive without proper referencing.

  6. Rapid shift in thermal resistance between generations through maternal heat exposure

    NARCIS (Netherlands)

    Zizzari, Z.V.; Ellers, J.

    2014-01-01

    Given the current rapid climate change, understanding the mechanisms underlying heat tolerance and its plasticity is an important goal of global change biology. Soil fauna communities are especially vulnerable because of their limited dispersal ability. It is generally recognized that

  7. A Rapid Compression Expansion Machine (RCEM) for studying chemical kinetics: Experimental principle and first applications

    CERN Document Server

    Werler, Marc; Maas, Ulrich

    2016-01-01

    A novel extension of a rapid compression machine (RCM), namely a Rapid Compression Expansion Machine (RCEM), is described and its use for studying chemical kinetics is demonstrated. Like conventional RCMs, the RCEM quickly compresses a fuel/air mixture by pushing a piston into a cylinder; the resulting high temperatures and pressures initiate chemical reactions. In addition, the machine can rapidly expand the compressed gas in a controlled way by pulling the piston outwards again. This freezes chemical activity after a pre-defined reaction duration, and therefore allows a convenient probe sampling and ex-situ gas analysis of stable species. The RCEM therefore is a promising instrument for studying chemical kinetics, including also partially reacted fuel/air mixtures. The setup of the RCEM, its experimental characteristics and its use for studying chemical reactions are outlined in detail. To allow comparisons of RCEM results with predictions of chemical reaction mechanisms, a simple numerical model of the RCE...

  8. Systemic range shift lags among a pollinator species assemblage following rapid climate change

    DEFF Research Database (Denmark)

    Bedford, Felicity E.; Whittaker, Robert J.; Kerr, Jeremy T.

    2012-01-01

    Contemporary climate change is driving widespread geographical range shifts among many species. If species are tracking changing climate successfully, then leading populations should experience similar climatic conditions through time as new populations establish beyond historical range margins. ...... species assemblage in responses to recent climate change. Even among the most mobile species and without anthropogenic barriers to dispersal, these pollinators have been unable to extend their ranges as fast as required to keep pace with climate change....

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

    Science.gov (United States)

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

    2015-01-01

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

  10. 129 Xe chemical shift in human blood and pulmonary blood oxygenation measurement in humans using hyperpolarized 129 Xe NMR.

    Science.gov (United States)

    Norquay, Graham; Leung, General; Stewart, Neil J; Wolber, Jan; Wild, Jim M

    2017-04-01

    To evaluate the dependency of the 129 Xe-red blood cell (RBC) chemical shift on blood oxygenation, and to use this relation for noninvasive measurement of pulmonary blood oxygenation in vivo with hyperpolarized 129 Xe NMR. Hyperpolarized 129 Xe was equilibrated with blood samples of varying oxygenation in vitro, and NMR was performed at 1.5 T and 3 T. Dynamic in vivo NMR during breath hold apnea was performed at 3 T on two healthy volunteers following inhalation of hyperpolarized 129 Xe. The 129 Xe chemical shift in RBCs was found to increase nonlinearly with blood oxygenation at 1.5 T and 3 T. During breath hold apnea, the 129 Xe chemical shift in RBCs exhibited a periodic time modulation and showed a net decrease in chemical shift of ∼1 ppm over a 35 s breath hold, corresponding to a decrease of 7-10 % in RBC oxygenation. The 129 Xe-RBC signal amplitude showed a modulation with the same frequency as the 129 Xe-RBC chemical shift. The feasibility of using the 129 Xe-RBC chemical shift to measure pulmonary blood oxygenation in vivo has been demonstrated. Correlation between 129 Xe-RBC signal and 129 Xe-RBC chemical shift modulations in the lung warrants further investigation, with the aim to better quantify temporal blood oxygenation changes in the cardiopulmonary vascular circuit. Magn Reson Med 77:1399-1408, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

  11. 129Xe chemical shift in human blood and pulmonary blood oxygenation measurement in humans using hyperpolarized 129Xe NMR

    Science.gov (United States)

    Norquay, Graham; Leung, General; Stewart, Neil J.; Wolber, Jan

    2016-01-01

    Purpose To evaluate the dependency of the 129Xe‐red blood cell (RBC) chemical shift on blood oxygenation, and to use this relation for noninvasive measurement of pulmonary blood oxygenation in vivo with hyperpolarized 129Xe NMR. Methods Hyperpolarized 129Xe was equilibrated with blood samples of varying oxygenation in vitro, and NMR was performed at 1.5 T and 3 T. Dynamic in vivo NMR during breath hold apnea was performed at 3 T on two healthy volunteers following inhalation of hyperpolarized 129Xe. Results The 129Xe chemical shift in RBCs was found to increase nonlinearly with blood oxygenation at 1.5 T and 3 T. During breath hold apnea, the 129Xe chemical shift in RBCs exhibited a periodic time modulation and showed a net decrease in chemical shift of ∼1 ppm over a 35 s breath hold, corresponding to a decrease of 7–10 % in RBC oxygenation. The 129Xe‐RBC signal amplitude showed a modulation with the same frequency as the 129Xe‐RBC chemical shift. Conclusion The feasibility of using the 129Xe‐RBC chemical shift to measure pulmonary blood oxygenation in vivo has been demonstrated. Correlation between 129Xe‐RBC signal and 129Xe‐RBC chemical shift modulations in the lung warrants further investigation, with the aim to better quantify temporal blood oxygenation changes in the cardiopulmonary vascular circuit. Magn Reson Med 77:1399–1408, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:27062652

  12. Experimental study of resolution of proton chemical shifts in solids: Combined multiple pulse NMR and magic-angle spinning

    Energy Technology Data Exchange (ETDEWEB)

    Ryan, L.M.; Taylor, R.E.; Paff, A.J.; Gerstein, B.C.

    1980-01-01

    High-resolution nuclear magnetic resonance spectra of protons in rigid, randomly oriented solids have been measured using combined homonuclear dipolar decoupling (via multiple pulse techniques) and attenuation of chemical shift anisotropies (via magic-angle sample spinning). Under those conditions, isotropic proton chemical shifts were recorded for a variety of chemical species, with individual linewidths varying from about 55 to 110 Hz (1--2 ppm). Residual line broadening was due predominately to (i) magnetic-field instability and inhomogeneity, (ii) unresolved proton--proton spin couplings, (iii) chemical shift dispersion, (iv) residual dipolar broadening, and (v) lifetime broadening under the multiple pulse sequences used. The magnitudes of those effects and the current limits of resolution for this experiment in our spectrometer have been investigated. The compounds studied included organic solids (4, 4'-dimethylbenzophenone, 2, 6-dimethylbenzoic acid, and aspirin), polymers (polystyrene and polymethylmethacrylate), and the vitrain portion of a bituminous coal.

  13. Backbone and side chain chemical shift assignments of apolipophorin III from Galleria mellonella.

    Science.gov (United States)

    Crowhurst, Karin A; Horn, James V C; Weers, Paul M M

    2016-04-01

    Apolipophorin III, a 163 residue monomeric protein from the greater wax moth Galleria mellonella (abbreviated as apoLp-IIIGM), has roles in upregulating expression of antimicrobial proteins as well as binding and deforming bacterial membranes. Due to its similarity to vertebrate apolipoproteins there is interest in performing atomic resolution analysis of apoLp-IIIGM as part of an effort to better understand its mechanism of action in innate immunity. In the first step towards structural characterization of apoLp-IIIGM, 99 % of backbone and 88 % of side chain (1)H, (13)C and (15)N chemical shifts were assigned. TALOS+ analysis of the backbone resonances has predicted that the protein is composed of five long helices, which is consistent with the reported structures of apolipophorins from other insect species. The next stage in the characterization of apoLp-III from G. mellonella will be to utilize these resonance assignments in solving the solution structure of this protein.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-03-15

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

  15. Deuterium isotope effect on 13C chemical shifts of tetrabutylammonium salts of Schiff bases amino acids.

    Science.gov (United States)

    Rozwadowski, Z

    2006-09-01

    Deuterium isotope effects on 13C chemical shift of tetrabutylammonium salts of Schiff bases, derivatives of amino acids (glycine, L-alanine, L-phenylalanine, L-valine, L-leucine, L-isoleucine and L-methionine) and various ortho-hydroxyaldehydes in CDCl3 have been measured. The results have shown that the tetrabutylammonium salts of the Schiff bases amino acids, being derivatives of 2-hydroxynaphthaldehyde and 3,5-dibromosalicylaldehyde, exist in the NH-form, while in the derivatives of salicylaldehyde and 5-bromosalicylaldehyde a proton transfer takes place. The interactions between COO- and NH groups stabilize the proton-transferred form through a bifurcated intramolecular hydrogen bond. Copyright (c) 2006 John Wiley & Sons, Ltd.

  16. FMRP regulates an ethanol-dependent shift in GABABR function and expression with rapid antidepressant properties.

    Science.gov (United States)

    Wolfe, Sarah A; Workman, Emily R; Heaney, Chelcie F; Niere, Farr; Namjoshi, Sanjeev; Cacheaux, Luisa P; Farris, Sean P; Drew, Michael R; Zemelman, Boris V; Harris, R Adron; Raab-Graham, Kimberly F

    2016-09-26

    Alcohol promotes lasting neuroadaptive changes that may provide relief from depressive symptoms, often referred to as the self-medication hypothesis. However, the molecular/synaptic pathways that are shared by alcohol and antidepressants are unknown. In the current study, acute exposure to ethanol produced lasting antidepressant and anxiolytic behaviours. To understand the functional basis of these behaviours, we examined a molecular pathway that is activated by rapid antidepressants. Ethanol, like rapid antidepressants, alters γ-aminobutyric acid type B receptor (GABABR) expression and signalling, to increase dendritic calcium. Furthermore, new GABABRs are synthesized in response to ethanol treatment, requiring fragile-X mental retardation protein (FMRP). Ethanol-dependent changes in GABABR expression, dendritic signalling, and antidepressant efficacy are absent in Fmr1-knockout (KO) mice. These findings indicate that FMRP is an important regulator of protein synthesis following alcohol exposure, providing a molecular basis for the antidepressant efficacy of acute ethanol exposure.

  17. Amyotrophic lateral sclerosis: diffusion-tensor and chemical shift MR imaging at 3.0 T.

    Science.gov (United States)

    Wang, Sumei; Poptani, Harish; Woo, John H; Desiderio, Lisa M; Elman, Lauren B; McCluskey, Leo F; Krejza, Jaroslaw; Melhem, Elias R

    2006-06-01

    To prospectively determine whether diffusion-tensor magnetic resonance (MR) imaging in conjunction with two-dimensional chemical shift imaging can assist in identifying upper motor neuron involvement and whether disease severity and duration can be predicted based on imaging parameters in patients with amyotrophic lateral sclerosis (ALS). Institutional review board approval and informed consent were obtained for this HIPAA-compliant study. Fifteen patients with ALS (12 men, three women; mean age, 57.3 years) with clinical evidence of upper motor neuron involvement and 10 healthy control subjects (five men and five women; mean age, 49.4 years) were studied. Fractional anisotropy (FA) and apparent diffusion coefficient (ADC) were measured from the corticospinal tracts at the level of the internal capsule. Average N-acetylaspartate (NAA)/creatine-phosphocreatine (Cr) and NAA/choline-containing compounds (Cho) ratios were calculated from the precentral gyrus. Student t test, multiple linear regression analysis, and Spearman correlation coefficients were employed to quantify relationships between imaging and clinical parameters. Patients with ALS exhibited significantly reduced FA values and NAA/Cr and NAA/Cho ratios compared with values in control subjects (Psides of the brain. ADC was elevated significantly in the affected side (Pside were even stronger predictors of disease duration. Moderate but statistically significant correlation was found between the FA values for the affected side and the ALS Functional Rating Scale Revised (ALSFRS-R) score (r=0.51, P<.05). The NAA/Cr ratio also correlated with both the ALSFRS-R and upper motor neuron scores (r=0.50 and 0.54, respectively; P<.05). Diffusion-tensor and two-dimensional chemical shift MR imaging spectroscopy can be used to identify upper motor neuron involvement and predict disease duration in patients with ALS. Copyright (c) RSNA, 2006.

  18. Carbon and nitrogen isotopes from top predator amino acids reveal rapidly shifting ocean biochemistry in the outer California Current.

    Directory of Open Access Journals (Sweden)

    Rocio I Ruiz-Cooley

    Full Text Available Climatic variation alters biochemical and ecological processes, but it is difficult both to quantify the magnitude of such changes, and to differentiate long-term shifts from inter-annual variability. Here, we simultaneously quantify decade-scale isotopic variability at the lowest and highest trophic positions in the offshore California Current System (CCS by measuring δ15N and δ13C values of amino acids in a top predator, the sperm whale (Physeter macrocephalus. Using a time series of skin tissue samples as a biological archive, isotopic records from individual amino acids (AAs can reveal the proximate factors driving a temporal decline we observed in bulk isotope values (a decline of ≥1 ‰ by decoupling changes in primary producer isotope values from those linked to the trophic position of this toothed whale. A continuous decline in baseline (i.e., primary producer δ15N and δ13C values was observed from 1993 to 2005 (a decrease of ∼4‰ for δ15N source-AAs and 3‰ for δ13C essential-AAs, while the trophic position of whales was variable over time and it did not exhibit directional trends. The baseline δ15N and δ13C shifts suggest rapid ongoing changes in the carbon and nitrogen biogeochemical cycling in the offshore CCS, potentially occurring at faster rates than long-term shifts observed elsewhere in the Pacific. While the mechanisms forcing these biogeochemical shifts remain to be determined, our data suggest possible links to natural climate variability, and also corresponding shifts in surface nutrient availability. Our study demonstrates that isotopic analysis of individual amino acids from a top marine mammal predator can be a powerful new approach to reconstructing temporal variation in both biochemical cycling and trophic structure.

  19. Rapid Detection of Glycogen Synthase Kinase-3 Activity in Mouse Sperm Using Fluorescent Gel Shift Electrophoresis

    OpenAIRE

    Hoseok Choi; Bomi Choi; Ju Tae Seo; Kyung Jin Lee; Myung Chan Gye; Young-Pil Kim

    2016-01-01

    Assaying the glycogen synthase kinase-3 (GSK3) activity in sperm is of great importance because it is closely implicated in sperm motility and male infertility. While a number of studies on GSK3 activity have relied on labor-intensive immunoblotting to identify phosphorylated GSK3, here we report the simple and rapid detection of GSK3 activity in mouse sperm using conventional agarose gel electrophoresis and a fluorescent peptide substrate. When a dye-tethered and prephosphorylated (primed) p...

  20. sup 13 C NMR study of the C60 cluster in the solid state: Molecular motion and carbon chemical shift anisotropy

    Energy Technology Data Exchange (ETDEWEB)

    Yannoni, C.S.; Johnson, R.D.; Meijer, G.; Bethune, D.S.; Salem, J.R. (Almaden Research Center, San Jose, CA (USA))

    1991-01-10

    {sup 13}C NMR spectra of solid buckminsterfullerene, the soccerball-like cluster of 60 carbon atoms, have been obtained at temperatures down to 77 K. The ambient spectrum shows rapid isotropic rotational motion. The motion is sufficiently slow at 77 K that a measurement of the chemical shift tensor of the carbon nucleus can be made. The tensor components (220, 186, 40 ppm) have values that are typical for an aromatic carbon. Spectra at intermediate temperatures suggest the possibility of either growth of a low-temperature phase in which C60 rotation is inhibited or a distribution of rotational correlation times.

  1. Rapid yet accurate measurement of mass diffusion coefficients by phase shifting interferometer

    CERN Document Server

    Guo Zhi Xiong; Komiya, A

    1999-01-01

    The technique of using a phase-shifting interferometer is applied to the study of diffusion in transparent liquid mixtures. A quick method is proposed for determining the diffusion coefficient from the measurements of the location of fringes on a grey level picture. The measurement time is very short (within 100 s) and a very small transient diffusion field can be observed and recorded accurately with a rate of 30 frames per second. The measurement can be completed using less than 0.12 cc of solutions. The influence of gravity on the measurement of the diffusion coefficient is eliminated in the present method. Results on NaCl-water diffusion systems are presented and compared with the reference data. (author)

  2. 50 years anniversary of the discovery of the core level chemical shifts. The early years of photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mårtensson, Nils [Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala (Sweden); Sokolowski, Evelyn [Tvär-Ramsdal 1, 611 99 Tystberga (Sweden); Svensson, Svante, E-mail: Svante.Svensson@fysik.uu.se [Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala (Sweden)

    2014-03-01

    Highlights: • 50 years since the discovery of t the core level chemical shift. • The pioneering years of ESCA. • A critical review of the first core electron chemical shift results. - Abstract: The pioneering years of photoelectron spectroscopy in Uppsala are discussed, especially the work leading to the discovery of the core level chemical shifts. At a very early stage of the project, the pioneering group observed what they described as evidence for chemical shifts in the core level binding energies. However, it can now be seen that the initial observations to a large extent was due to charging of the samples. It is interesting to note that the decisive experiment was realized, not as a result of a systematic study, but was obtained with a large element of serendipity. Only when a chemical binding energy shift was observed between two S2p electron lines in the same molecule, the results were accepted internationally, and the fascinating expansion of modern core level photoelectron spectroscopy could start.

  3. Chemical amplification--cavity attenuated phase shift spectroscopy measurements of atmospheric peroxy radicals.

    Science.gov (United States)

    Wood, Ezra C; Charest, John R

    2014-10-21

    We describe a new instrument for the quantification of atmospheric peroxy radicals (HO2, CH3O2, C2H5O2, etc.) using the chemical amplification method. Peroxy radicals are mixed with high concentrations of NO and CO, causing a chain reaction that produces a measurable increase in NO2 which is quantified by cavity attenuated phase shift (CAPS) spectroscopy, a highly sensitive spectroscopic detection technique. The instrument utilizes two identical reaction chambers, each with a dedicated CAPS NO2 sensor. Similar to all dual-channel chemical amplifiers, one reaction chamber operates in amplification or "ROx" mode and the other in background or "Ox" mode. The peroxy radical mixing ratio is determined by the difference between the two channels' NO2 readings divided by a laboratory-determined chain length. Each reaction chamber alternates between ROx and Ox mode on an anti-synchronized schedule, eliminating the effect of CAPS baseline offsets on the calculated peroxy radical concentrations. The chain length is determined by a new calibration method: peroxyacetyl and methyl peroxy radicals are produced by the photolysis of acetone and quantified as NO2 following reaction with excess NO. We demonstrate the performance of the instrument with results from ambient sampling in Amherst and several diagnostics of its precision. The detection limit while sampling ambient air at a relative humidity (RH) of 40% is 0.6 ppt (1 min average, signal-to-noise ratio =2), with an estimated accuracy of 25% (2σ).

  4. Rapid northward shift of the Indian Monsoon on the Tibetan Plateau at the end of the Little Ice Age

    Science.gov (United States)

    Zhang, Xiaolong; Xu, Baiqing; Günther, Franziska; Witt, Roman; Wang, Mo; Xie, Ying; Zhao, Huabiao; Li, Jiule; Gleixner, Gerd

    2017-09-01

    Variations in the Indian Monsoon (IM) and Westerlies (WS) significantly affect the climate on the Tibetan Plateau (TP) and have widespread ecological and socioeconomic impacts on the whole of Asian society. So far, however, the rate and magnitude of changes in the IM have still remained unclear. Here we report for the first time that the IM rapidly shifted northward at the end of the Little Ice Age (LIA). We used sediment proxies for humidity and moisture sources from the Taro Co Lake, which is located in the transition zone between the WS and IM. Our comprehensive survey of climate records for the TP and its peripheral mountain ranges revealed that the northern boundary of the IM (i.e., the southern boundary of the WS) lay along the southern slope of the Gandise Range ( 29.5°N) in the late LIA. In contrast, it passed quickly over the Gandise Range by at least 1.5° in latitude at the end of the LIA. Our results suggest that this rapid climatic shift was potentially triggered by the counteracting effects of blocking by the TP and its marginal orography, which hindered the northward movement of the IM, and the pulling thermal gradient of the TP.

  5. Wavelength shifting of intra-cavity photons: Adiabatic wavelength tuning in rapidly wavelength-swept lasers.

    Science.gov (United States)

    Jirauschek, Christian; Huber, Robert

    2015-07-01

    We analyze the physics behind the newest generation of rapidly wavelength tunable sources for optical coherence tomography (OCT), retaining a single longitudinal cavity mode during operation without repeated build up of lasing. In this context, we theoretically investigate the currently existing concepts of rapidly wavelength-swept lasers based on tuning of the cavity length or refractive index, leading to an altered optical path length inside the resonator. Specifically, we consider vertical-cavity surface-emitting lasers (VCSELs) with microelectromechanical system (MEMS) mirrors as well as Fourier domain mode-locked (FDML) and Vernier-tuned distributed Bragg reflector (VT-DBR) lasers. Based on heuristic arguments and exact analytical solutions of Maxwell's equations for a fundamental laser resonator model, we show that adiabatic wavelength tuning is achieved, i.e., hopping between cavity modes associated with a repeated build up of lasing is avoided, and the photon number is conserved. As a consequence, no fundamental limit exists for the wavelength tuning speed, in principle enabling wide-range wavelength sweeps at arbitrary tuning speeds with narrow instantaneous linewidth.

  6. Carbon-13 chemical-shift tensors in indigo: A two-dimensional NMR-ROCSA and DFT Study

    Science.gov (United States)

    Holmes, Sean T.; Dybowski, Cecil

    2016-01-01

    The principal components of the 13C NMR chemical-shift tensors for the eight unique carbon sites of crystalline indigo have been measured using the ROCSA pulse sequence. The chemical shifts have been assigned unambiguously to their respective nuclear sites through comparison of the experimental data to the results of density-functional calculations employing a refined X-ray diffraction structure. These measurements expand the database of measured aromatic 13C chemical-shift tensors to the indole ring. Magnetic shielding calculations for hypoxanthine and adenosine are also reported. Comparisons of calculations that include the effect of the crystalline lattice with calculations that model indigo as an isolated molecule give an estimate of the intermolecular contribution to the magnetic shielding. PMID:26344134

  7. Shifting Thresholds: Rapid Evolution of Migratory Life Histories in Steelhead/Rainbow Trout, Oncorhynchus mykiss.

    Science.gov (United States)

    Phillis, Corey C; Moore, Jonathan W; Buoro, Mathieu; Hayes, Sean A; Garza, John Carlos; Pearse, Devon E

    2016-01-01

    Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or declines in productivity and possibly extinction. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the environmentally influenced cue (e.g., size-at-age) or the state (e.g., size threshold) at which an individual switches between alternative tactics. Using a population of steelhead (Oncorhynchus mykiss) introduced above a barrier waterfall in 1910, we evaluate how the conditional strategy to migrate evolves in response to selection against migration. We created 9 families and 917 offspring from 14 parents collected from the above- and below-barrier populations. After 1 year of common garden-rearing above-barrier offspring were 11% smaller and 32% lighter than below-barrier offspring. Using a novel analytical approach, we estimate that the mean size at which above-barrier fish switch between the resident and migrant tactic is 43% larger than below-barrier fish. As a result, above-barrier fish were 26% less likely to express the migratory tactic. Our results demonstrate how rapid and opposing changes in size-at-age and threshold size contribute to the contemporary evolution of a conditional strategy and indicate that migratory barriers may elicit rapid evolution toward the resident life history on timescales relevant for conservation and management of conditionally migratory species. © The American Genetic Association. 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Coastal regime shifts: rapid responses of coastal wetlands to changes in mangrove cover.

    Science.gov (United States)

    Guo, Hongyu; Weaver, Carolyn; Charles, Sean P; Whitt, Ashley; Dastidar, Sayantani; D'Odorico, Paolo; Fuentes, Jose D; Kominoski, John S; Armitage, Anna R; Pennings, Steven C

    2017-03-01

    Global changes are causing broad-scale shifts in vegetation communities worldwide, including coastal habitats where the borders between mangroves and salt marsh are in flux. Coastal habitats provide numerous ecosystem services of high economic value, but the consequences of variation in mangrove cover are poorly known. We experimentally manipulated mangrove cover in large plots to test a set of linked hypotheses regarding the effects of changes in mangrove cover. We found that changes in mangrove cover had strong effects on microclimate, plant community, sediment accretion, soil organic content, and bird abundance within 2 yr. At higher mangrove cover, wind speed declined and light interception by vegetation increased. Air and soil temperatures had hump-shaped relationships with mangrove cover. The cover of salt marsh plants decreased at higher mangrove cover. Wrack cover, the distance that wrack was distributed from the water's edge, and sediment accretion decreased at higher mangrove cover. Soil organic content increased with mangrove cover. Wading bird abundance decreased at higher mangrove cover. Many of these relationships were non-linear, with the greatest effects when mangrove cover varied from zero to intermediate values, and lesser effects when mangrove cover varied from intermediate to high values. Temporal and spatial variation in measured variables often peaked at intermediate mangrove cover, with ecological consequences that are largely unexplored. Because different processes varied in different ways with mangrove cover, the "optimum" cover of mangroves from a societal point of view will depend on which ecosystem services are most desired. © 2016 by the Ecological Society of America.

  9. Unbounded boundaries and shifting baselines: Estuaries and coastal seas in a rapidly changing world

    Science.gov (United States)

    Little, S.; Spencer, K. L.; Schuttelaars, H. M.; Millward, G. E.; Elliott, M.

    2017-11-01

    future modelling studies and; (4) the importance of shifting baselines on ecosystem functioning and the future provision of ecosystem services.

  10. Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy

    Science.gov (United States)

    Hou, Guangjin; Byeon, In-Ja L.; Ahn, Jinwoo; Gronenborn, Angela M.; Polenova, Tatyana

    2012-10-01

    13C and 15N chemical shift (CS) interaction is a sensitive probe of structure and dynamics in a wide variety of biological and inorganic systems, and in the recent years several magic angle spinning NMR approaches have emerged for residue-specific measurements of chemical shift anisotropy (CSA) tensors in uniformly and sparsely enriched proteins. All of the currently existing methods are applicable to slow and moderate magic angle spinning (MAS) regime, i.e., MAS frequencies below 20 kHz. With the advent of fast and ultrafast MAS probes capable of spinning frequencies of 40-100 kHz, and with the superior resolution and sensitivity attained at such high frequencies, development of CSA recoupling techniques working under such conditions is necessary. In this work, we present a family of R-symmetry based pulse sequences for recoupling of 13C/15N CSA interactions that work well in both natural abundance and isotopically enriched systems. We demonstrate that efficient recoupling of either first-rank (σ1) or second-rank (σ2) spatial components of CSA interaction is attained with appropriately chosen γ-encoded RNnv symmetry sequences. The advantage of these γ-encoded RNnv-symmetry based CSA (RNCSA) recoupling schemes is that they are suitable for CSA recoupling under a wide range of MAS frequencies, including fast MAS regime. Comprehensive analysis of the recoupling properties of these RNnv symmetry sequences reveals that the σ1-CSA recoupling symmetry sequences exhibit large scaling factors; however, the partial homonuclear dipolar Hamiltonian components are symmetry allowed, which makes this family of sequences suitable for CSA measurements in systems with weak homonuclear dipolar interactions. On the other hand, the γ-encoded symmetry sequences for σ2-CSA recoupling have smaller scaling factors but they efficiently suppress the homonuclear dipole-dipole interactions. Therefore, the latter family of sequences is applicable for measurements of CSA parameters in

  11. Drought drives rapid shifts in soil biogeochemistry and greenhouse gas emissions in a wet tropical forest

    Science.gov (United States)

    O'Connell, C.; Silver, W. L.; Ruan, L.

    2016-12-01

    Global circulation models suggest that climate change will increase the frequency and severity of drought in the humid tropics (Neelin et al., 2006). There is considerable uncertainty about the effects of drought on biogeochemical cycling in these ecosystems (Chambers et al., 2012), which play a key role in global carbon (C) and nitrogen (N) budgets (Vitousek & Sanford, 1986; Wright, 2005; Le Quéré et al., 2009). We used an automated sensor array to determine the effects of a recent severe drought on soil moisture, oxygen (O2), greenhouse gas emissions, and key nutrients across a wet tropical forest landscape. The onset of drought led to a rapid decline in soil moisture (46% drop in 21 days) and an associated rise in soil aeration. Drying also led to significant declines in inorganic P concentrations, an element commonly limiting to net primary productivity (NPP) in humid tropical forests (Cleveland et al. 2011). Drought increased soil carbon dioxide (CO2) emissions from slopes by 60% (from 3.79 ± 2.92 to 6.06 ± 4.26 µmol m-2 s-1) and valleys by 163% (from 0.57 ± 0.17 to 1.51 ± 0.75 µmol m-2 s-1). Methane (CH4) fluxes declined by 90% in valleys after the drought (from 17.43 ± 29.60 to 1.67 ± 4.09 nmol m-2 s-1) but increased above pre-drought baseline by tenfold and hundredfold in ridges and slopes, respectively, post-drought, offsetting the initial decline in soil CH4 emissions. Soil moisture and soil O2 concentrations were slow to recover after the onset of rains, effectively increasing the length of the drought effect by up to 65%. Results indicate that drought is likely to result in soil C losses and increased soil P limitation, potentially decreasing tropical forest C uptake and storage in the future.

  12. Chemical shift assignments for F-plasmid TraI (381–569)

    Science.gov (United States)

    Wright, Nathan T.; Majumdar, Ananya

    2011-01-01

    TraI, the F plasmid-encoded nickase, is a 1,756 amino acid protein essential for conjugative transfer of F plasmid DNA from one bacterium to another. While crystal structures of N- and C-terminal domains of F TraI have been determined, central domains of the protein are structurally unexplored. These middle domains (between residues 306 and 1,500) are known to both bind single-stranded DNA (ssDNA) and unwind DNA through a highly processive helicase activity. Of this central region, the more C-terminal portion (~900–1500) appears related to helicase RecD of the E. coli RecBCD complex. The more N-terminal portion (306–900), however, shows limited sequence similarity to other proteins. In an attempt to define the structure of well-folded domains of this middle region and discern their function, we have isolated stable regions of TraI following limited proteolysis. One of these regions, TraI (381–569), was identified and a genetic construct encoding it was engineered. The protein was expressed, purified, and the sequence-specific chemical shifts for it were assigned. PMID:20936510

  13. Chemical shift assignments for F-plasmid TraI (381-569).

    Science.gov (United States)

    Wright, Nathan T; Majumdar, Ananya; Schildbach, Joel F

    2011-04-01

    TraI, the F plasmid-encoded nickase, is a 1,756 amino acid protein essential for conjugative transfer of F plasmid DNA from one bacterium to another. While crystal structures of N- and C-terminal domains of F TraI have been determined, central domains of the protein are structurally unexplored. These middle domains (between residues 306 and 1,500) are known to both bind single-stranded DNA (ssDNA) and unwind DNA through a highly processive helicase activity. Of this central region, the more C-terminal portion (~900-1500) appears related to helicase RecD of the E. coli RecBCD complex. The more N-terminal portion (306-900), however, shows limited sequence similarity to other proteins. In an attempt to define the structure of well-folded domains of this middle region and discern their function, we have isolated stable regions of TraI following limited proteolysis. One of these regions, TraI (381-569), was identified and a genetic construct encoding it was engineered. The protein was expressed, purified, and the sequence-specific chemical shifts for it were assigned.

  14. Rapid shifts in Atta cephalotes fungus-garden enzyme activity after a change in fungal substrate (Attini, Formicidae)

    DEFF Research Database (Denmark)

    Kooij, P W; Schiøtt, M; Boomsma, J J

    2011-01-01

    Fungus gardens of the basidiomycete Leucocoprinus gongylophorus sustain large colonies of leaf-cutting ants by degrading the plant material collected by the ants. Recent studies have shown that enzyme activity in these gardens is primarily targeted toward starch, proteins and the pectin matrix...... associated with cell walls, rather than toward structural cell wall components such as cellulose and hemicelluloses. Substrate constituents are also known to be sequentially degraded in different sections of the fungus garden. To test the plasticity in the extracellular expression of fungus-garden enzymes......, we measured the changes in enzyme activity after a controlled shift in fungal substrate offered to six laboratory colonies of Atta cephalotes. An ant diet consisting exclusively of grains of parboiled rice rapidly increased the activity of endo-proteinases and some of the pectinases attacking...

  15. Analysis of the contributions of ring current and electric field effects to the chemical shifts of RNA bases.

    Science.gov (United States)

    Sahakyan, Aleksandr B; Vendruscolo, Michele

    2013-02-21

    Ring current and electric field effects can considerably influence NMR chemical shifts in biomolecules. Understanding such effects is particularly important for the development of accurate mappings between chemical shifts and the structures of nucleic acids. In this work, we first analyzed the Pople and the Haigh-Mallion models in terms of their ability to describe nitrogen base conjugated ring effects. We then created a database (DiBaseRNA) of three-dimensional arrangements of RNA base pairs from X-ray structures, calculated the corresponding chemical shifts via a hybrid density functional theory approach and used the results to parametrize the ring current and electric field effects in RNA bases. Next, we studied the coupling of the electric field and ring current effects for different inter-ring arrangements found in RNA bases using linear model fitting, with joint electric field and ring current, as well as only electric field and only ring current approximations. Taken together, our results provide a characterization of the interdependence of ring current and electric field geometric factors, which is shown to be especially important for the chemical shifts of non-hydrogen atoms in RNA bases.

  16. Influence of ¹H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins.

    Science.gov (United States)

    Lin, Yi-Jan; Kirchner, Donata K; Güntert, Peter

    2012-09-01

    Homodimeric proteins pose a difficulty for NMR structure determination because the degeneracy of the chemical shifts in the two identical monomers implies an ambiguity in all assignments of distance restraints. For homodimeric proteins, residues involved in the interface between two monomers provide essential intermolecular NOEs. The structure determination of homodimeric proteins hence relies strongly on chemical shift assignments of these interface residues. Our paper discusses the influence of the extent of (1)H chemical shift assignments of interface residues on the structure determinations of homodimeric proteins using the CYANA program. The results reveal that successful structure determinations of homodimeric proteins with automated NOE assignment depend on the percentage of assigned interface residues and that a high completeness of around 80-90% of the (1)H chemical shift assignment in the interface is needed for reliable NMR structure determinations of homodimeric proteins for which no experimental distinction between intra- and intermolecular NOEs, e.g. by filtered NOESY experiments, is available. Our results also show that RMSD and target function values are insufficient to judge the quality of homodimeric structures determined using automated NOE assignment. Structure determinations of homodimeric proteins by NMR using conventional NOESY experiments are thus possible but more challenging than for monomeric proteins. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Dixon quantitative chemical shift MRI for bone marrow evaluation in the lumbar spine: a reproducibility study in healthy volunteers

    NARCIS (Netherlands)

    Maas, M.; Akkerman, E. M.; Venema, H. W.; Stoker, J.; den Heeten, G. J.

    2001-01-01

    PURPOSE: The purpose of this work was to explore the reproducibility of fat-fraction measurements using Dixon quantitative chemical shift imaging (QCSI) in the lumbar spine (L3, L4, and L5) of healthy volunteers. METHOD: Sixteen healthy volunteers were examined at 1.5 T two times to obtain a

  18. 20(R- and 20(S-Simarolide Epimers Isolated from Simaba cuneata: Chemical Shifts Assignment of Carbon and Hydrogen Atoms

    Directory of Open Access Journals (Sweden)

    Vieira Ivo José Curcino

    1999-01-01

    Full Text Available The C25-quassinoids 20(R- and 20(S-simarolide were isolated from Simaba cuneata, Simaroubaceae. The structures of these two compounds were characterized by spectral data, including 1D and 2D NMR spectra which were also used for the complete assignment of the carbon and hydrogen atom chemical shifts.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-15

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-01-15

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

  2. Pressure dependence of side chain13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

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

    2017-10-01

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

  3. Rapid chemical and topological ordering in supercooled liquid Cu46Zr54

    Science.gov (United States)

    Wessels, V.; Gangopadhyay, A. K.; Sahu, K. K.; Hyers, R. W.; Canepari, S. M.; Rogers, J. R.; Kramer, M. J.; Goldman, A. I.; Robinson, D.; Lee, J. W.; Morris, J. R.; Kelton, K. F.

    2011-03-01

    Evidence for rapid ordering in a supercooled Cu46Zr54 liquid, obtained from high-energy x-ray diffraction in a containerless processing environment, is presented. Relatively sudden changes were observed in the topological and chemical short-range order near 850 °C, a temperature that is 75 °C below the liquidus temperature and 465 °C above the glass transition temperature. A peak in the specific heat was observed with supercooling, with an onset near 850 °C (the same temperature as the onset of ordering) and a maximum near 700 °C, consistent with the prediction of a molecular-dynamics calculation using embedded atom potentials. The chemical and topological ordering measured here are in agreement with predictions of a rapid development of chemically ordered icosahedral clusters in the supercooled liquid.

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

    Science.gov (United States)

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

    2017-11-30

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Gokalp, Gokhan; Mutlu, Fatma Senturk; Yazici, Zeynep; Yildirim, Nalan [Uludag University Medical Faculty, Department of Radiology, Gorukle, Bursa (Turkey)

    2011-05-15

    To quantitatively evaluate vertebral bone marrow fat content and investigate its association with osteoporosis with chemical-shift magnetic resonance imaging (CS-MRI). Fifty-six female patients (age range 50-65 years) with varying bone mineral densities as documented with dual x-ray absorptiometry (DXA) were prospectively included in the study. According to the DXA results, the patients were grouped as normal bone density, osteopenic, or osteoporotic. In order to calculate fat content, the lumbar region was visualized in the sagittal plane by CS-MRI sequence. ''Region of interest'' (ROI)s were placed within L3 vertebral bodies and air (our reference point) at different time points by different radiologists. Fat content was calculated through ''signal intensity (SI) suppression rate'' and ''SI Index''. The quantitative values were compared statistically with those obtained from DXA examinations. Kruskal-Wallis, and Mann-Whitney U tests were used for comparisons between groups. The reliability of the measurements performed by two radiologists was evaluated with the ''intraclass correlation coefficient''. This study was approved by an institutional review board and all participants provided informed consent to participate in the study. Eighteen subjects with normal bone density (mean T score, 0.39 {+-} 1.3 [standard deviation]), 20 subjects with osteopenia (mean T score, -1.79 {+-} 0.38), and 18 subjects with osteoporosis (mean T score, -3 {+-} 0.5) were determined according to DXA results. The median age was 55.9 (age range 50-64 years) in the normal group, 55.5 (age range 50-64 years) in the osteopenic group, and 55.1 (age range 50-65 years) in the osteoporotic group (p = 0.872). In the CS-MRI examination, the values of ''SI suppression ratio'' and ''SI Index'' (median [min:max]) were calculated by the first and second reader, independently. There

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

    Science.gov (United States)

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

    2017-01-01

    Developmental stuttering is a neuropsychiatric condition of incompletely understood brain origin. Our recent functional magnetic resonance imaging study indicates a possible partial basis of stuttering in circuits enacting self-regulation of motor activity, attention, and emotion. To further characterize the neurophysiology of stuttering through in vivo assay of neurometabolites in suspect brain regions. Proton chemical shift imaging of the brain was performed in a case-control study of children and adults with and without stuttering. Recruitment, assessment, and magnetic resonance imaging were performed in an academic research setting. Ratios of N-acetyl-aspartate plus N-acetyl-aspartyl-glutamate (NAA) to creatine (Cr) and choline compounds (Cho) to Cr in widespread cerebral cortical, white matter, and subcortical regions were analyzed using region of interest and data-driven voxel-based approaches. Forty-seven children and adolescents aged 5 to 17 years (22 with stuttering and 25 without) and 47 adults aged 21 to 51 years (20 with stuttering and 27 without) were recruited between June 2008 and March 2013. The mean (SD) ages of those in the stuttering and control groups were 12.2 (4.2) years and 13.4 (3.2) years, respectively, for the pediatric cohort and 31.4 (7.5) years and 30.5 (9.9) years, respectively, for the adult cohort. Region of interest-based findings included lower group mean NAA:Cr ratio in stuttering than nonstuttering participants in the right inferior frontal cortex (-7.3%; P = .02), inferior frontal white matter (-11.4%; P stuttering sample included higher NAA:Cr and Cho:Cr ratios (regression coefficient, 197.4-275; P stuttering severity (r = 0.40-0.52; P = .001-.02). This spectroscopy study of stuttering demonstrates brainwide neurometabolite alterations, including several regions implicated by other neuroimaging modalities. Prior ascription of a role in stuttering to inferior frontal and superior temporal gyri, caudate, and other

  7. Potential for modal shift by passenger car and motorcycle users towards Bus Rapid Transit (BRT in an Asian developing city

    Directory of Open Access Journals (Sweden)

    Thaned Satiennam

    2016-03-01

    Full Text Available Many developing Asian cities consider a Bus Rapid Transit (BRT system in their public transport planning because of its advantages, offering lower investment cost and flexible implementation over rail systems. The objective of this research is to assess the potential of BRT for attracting travelers from passenger cars and motorcycles. Three different BRT systems were designed for the main corridor passing through Khon Kaen City in Thailand. The study developed modal split models for predicting the choices of passenger car users and motorcycle users. The models were developed based on a Stated Preference (SP survey. It was found that BRT could attract significantly private vehicle users to change mode choice. The proportion of motorcycle users shifting is higher than passenger car users. However, the majority of private vehicle users still prefer their own private vehicles. Both travel time and travel cost affects the mode choice, in which travel time has a highly significant effect on passenger car users' choice of BRT, but travel cost has a highly significant effect on motorcyclists' choice. Some socio-economic factors, including gender, age, driving license holding and residence location also influence the choice of BRT.

  8. Heterochronic shifts in germband movements contribute to the rapid embryonic development of the coffin fly Megaselia scalaris.

    Science.gov (United States)

    Wotton, Karl R

    2014-11-01

    The coffin fly, Megaselia scalaris, is a species of medical and forensic importance and is increasingly being used for the study of genetics. Postmortem interval can be estimated based on the life stage of M. scalaris recovered from corpses, therefore many studies have addressed the duration of each life stage. These studies demonstrate that embryogenesis completes significantly faster in M. scalaris than in the congener Megaselia abdita and faster even than the 24 h needed for Drosophila melanogaster embryogenesis. However, until now it has been unclear if this increased speed is achieved by reducing developmental time across all embryonic stages or by the acceleration of individual stages and processes. Here I use time-lapse imaging to create a staging scheme for M. scalaris embryogenesis. Comparison of stages between D. melanogaster and both Megaselia species reveals that heterochronic shifts, simultaneous morphogenetic movements and compression of individual stages all contribute to the rapid development of M. scalaris. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Rapid and Sensitive Reporter Gene Assays for Detection of Antiandrogenic and Estrogenic Effects of Environmental Chemicals

    DEFF Research Database (Denmark)

    Vinggaard, Anne Marie; Bonefeld-Jørgensen, Eva Cecilie; Larsen, John Christian

    1999-01-01

    Reports on increasing incidences in developmental abnormalities of the human male reproductive tract and the recent identifications of environmental chemicals with antiandrogenic activity necessitate the screening of a larger number of compounds in order to get an overview of potential...... antiandrogenic chemicals present in our environment. Thus, there is a great need for an effectivein vitroscreening method for (anti)androgenic chemicals. We have developed a rapid, sensitive, and reproducible reporter gene assay for detection of antiandrogenic chemicals. Chinese Hamster Ovary cells were......-on laboratory time. This assay is a powerful tool for the efficient and accurate determination and quantification of the effects of antiandrogens on reporter gene transcription. To extend the application of FuGene, the reagent was shown to be superior compared to Lipofectin for transfecting MCF7 human breast...

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

    Indian Academy of Sciences (India)

    Measurements have been carried out at the energy dispersive EXAFS beamline at INDUS-2 Synchrotron Radiation Source at Raja Ramanna Centre for Advanced Technology, Indore. Energy shifts of ∼8–16 eV were observed for Mn K edge in the Mn-compounds while a shift of 13–20 eV was observed for Cr K edge in ...

  11. Non‐invasive Localization of Thymol Accumulation in Carum copticum (Apiaceae) Fruits by Chemical Shift Selective Magnetic Resonance Imaging

    OpenAIRE

    GERSBACH, P. V.; Reddy, N.

    2002-01-01

    Magnetic resonance imaging was used to localize the site of essential oil accumulation in fruit of Carum copticum L. (Apiaceae). A chemical shift method is described that utilized the spectral properties of the aromatic monoterpene thymol, the major component of the essential oil, to image thymol selectively. The presence of essential oil secretory structures in the fruit and an essential oil containing a high proportion of thymol were confirmed with optical microscopy and gas chromatography‐...

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

    Science.gov (United States)

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

    2015-10-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue's averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80% accuracy measured by Matthew correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with >90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Ricardo Infante-Castillo

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-05-15

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

  15. Rapid Prototyping of Chemical Microsensors Based on Molecularly Imprinted Polymers Synthesized by Two-Photon Stereolithography.

    Science.gov (United States)

    Gomez, Laura Piedad Chia; Spangenberg, Arnaud; Ton, Xuan-Anh; Fuchs, Yannick; Bokeloh, Frank; Malval, Jean-Pierre; Tse Sum Bui, Bernadette; Thuau, Damien; Ayela, Cédric; Haupt, Karsten; Soppera, Olivier

    2016-07-01

    Two-photon stereolithography is used for rapid prototyping of submicrometre molecularly imprinted polymer-based 3D structures. The structures are evaluated as chemical sensing elements and their specific recognition properties for target molecules are confirmed. The 3D design capability is exploited and highlighted through the fabrication of an all-organic molecularly imprinted polymeric microelectromechanical sensor. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics.

    Science.gov (United States)

    Straka, Michal; Lantto, Perttu; Vaara, Juha

    2008-03-27

    We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized

  17. Rapid detection of chemical hazards (toxins, dioxins, and PCBs) in seafood.

    Science.gov (United States)

    Arvanitoyannis, Ioannis S; Kotsanopoulos, Konstantinos V; Papadopoulou, Anna

    2014-01-01

    Among the various hazards occurring in fish and seafood chemical hazards and in particular toxins (ciguatera, scombroid fish poisoning, paralytic shellfish poisoning, neurotoxic (brevetoxic) shellfish poisoning, puffer fish poisoning, diarrhetic shellfish poisoning) have an important place in food poisoning cases. On the other hand, some of the chemical hazards are often due to the pollution of the environment (heavy metals, dioxins, polychlorinated biphenyls, and halogenated aromatic hydrocarbons) and their detection is neither rapid nor facile. As a result there was a great need for developing new rapid and effective methods toward the chemical hazards determination mainly because of their high toxicity. The aim of this review is to provide the information about the new up-to-date detection techniques (Immunological, Chemical and Biochemical, and Molecular assays) in conjunction with detection limits. The latter is made possible by means of inclusion of seven comprehensive and, in most case cases, very extended tables. A reference is also made on the risk characterization of toxins as regards their importance to food contamination or poisoning.

  18. Development of a New Decision Tree to Rapidly Screen Chemical Estrogenic Activities of Xenopus laevis.

    Science.gov (United States)

    Wang, Ting; Li, Weiying; Zheng, Xiaofeng; Lin, Zhifen; Kong, Deyang

    2014-02-01

    During the last past decades, there is an increasing number of studies about estrogenic activities of the environmental pollutants on amphibians and many determination methods have been proposed. However, these determination methods are time-consuming and expensive, and a rapid and simple method to screen and test the chemicals for estrogenic activities to amphibians is therefore imperative. Herein is proposed a new decision tree formulated not only with physicochemical parameters but also a biological parameter that was successfully used to screen estrogenic activities of the chemicals on amphibians. The biological parameter, CDOCKER interaction energy (Ebinding ) between chemicals and the target proteins was calculated based on the method of molecular docking, and it was used to revise the decision tree formulated by Hong only with physicochemical parameters for screening estrogenic activity of chemicals in rat. According to the correlation between Ebinding of rat and Xenopus laevis, a new decision tree for estrogenic activities in Xenopus laevis is finally proposed. Then it was validated by using the randomly 8 chemicals which can be frequently exposed to Xenopus laevis, and the agreement between the results from the new decision tree and the ones from experiments is generally satisfactory. Consequently, the new decision tree can be used to screen the estrogenic activities of the chemicals, and combinational use of the Ebinding and classical physicochemical parameters can greatly improves Hong's decision tree. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Rapid and sensitive reporter gene assays for detection of antiandrogenic and estrogenic effects of environmental chemicals

    DEFF Research Database (Denmark)

    Vinggaard, Anne; Jørgensen, E.C.B.; Larsen, John Christian

    1999-01-01

    antiandrogenic chemicals present in our environment. Thus, there is a great need for an effective in vitro screening method for (anti)androgenic chemicals. We have developed a rapid, sensitive, and reproducible reporter gene assay for detection of antiandrogenic chemicals. Chinese Hamster Ovary cells were...... induction of luciferase activity. The classical antiandrogenic compounds hydroxy-flutamide, bicalutamide, spironolactone, and cyproterone acetate together with the pesticide(metabolite)s, vinclozolin, p,p'-DDE, and procymidone all potently inhibited the response to 0.1 nM R1881, Compared to the traditional...... cancer cells with an estrogen response element-luciferase vector. Thus, FuGene may prove to be valuable in diverse reporter gene assays involving transient transfections for screening of potential endocrine disrupters for (anti)androgenic and (anti)estrogenic properties....

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

    Indian Academy of Sciences (India)

    Administrator

    ion has been investigated by X-ray absorption spectro- scopy (XAS) measurements with synchrotron radiation on few uranium compounds, viz. UF4, U3O8, ammonium diuranate and uranyl nitrate hexahydrate. A relationship between the energy shift and effective charges on U atom in the compounds has been found out. 2.

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

    Indian Academy of Sciences (India)

    ; effective charge. 1. Introduction. It is well known that the X-ray absorption edge of a metal atom changes from its elemental state when it takes part in the formation of a compound. Generally, the absorption edge shifts to higher energy as the ...

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

    Directory of Open Access Journals (Sweden)

    Phoebe Dreux Chappell

    2013-09-01

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

  3. Rapid Shifts in Soil and Forest Floor Microbial Communities with Changes in Vegetation during Secondary Tropical Forest Succession

    Science.gov (United States)

    Smith, A.; Marin-Spiotta, E.; Balser, T. C.

    2012-12-01

    anaerobic gram-negative bacteria (c19:0) in the wet season, which suggests the presence of anaerobic microsites in these very clayey Oxisols. Enzymatic activity did not differ with succession but was highest in the dry season. We expect this may be due to decreased turnover of enzymes with low soil moisture. Interannual sampling has revealed a very rapid microbial response to changes in aboveground cover. Within a year following woody biomass encroachment, we detected a shift in the soil microbial community from a pasture-associated community to an early secondary forest community in one of our replicate pasture sites. This very rapid response in the belowground microbial community structure to changes in vegetation has not been strongly documented in the literature. This data supports a direct link between aboveground and belowground biotic community structures and highlights the importance of long-term repeated sampling of microbial communities in dynamic ecosystems. Our findings have implications for predicting rapid ecological responses to land-cover change.

  4. Quantum mechanical calculations of conformationally relevant 1H and 13C NMR chemical shifts of N-, O-, and S-substituted calixarene systems.

    Science.gov (United States)

    Bifulco, Giuseppe; Riccio, Raffaele; Gaeta, Carmine; Neri, Placido

    2007-01-01

    QM GIAO calculations of (13)C and (1)H chemical shift values of the ArCH(2)Ar group in N-, O-, and S-substituted calixarene systems were performed with a hybrid DFT functional MPW1PW91 and 6-31G(d,p) basis set. A good reproduction of experimental data was obtained for some representative calixarenes and for a series of simplified calixarene models. This allowed the derivation of chemical shift surfaces versus phi and chi dihedral angles. The applicability of chemical shift surfaces in the study of calixarene conformational features is illustrated.

  5. Rapid Cerebral Hemodynamic Modulation during Set Shifting: Evidence of Time-Locked Associations with Cognitive Control in Females

    Science.gov (United States)

    Schuepbach, Daniel; Huizinga, Mariette; Duschek, Stefan; Grimm, Simone; Boeker, Heinz; Hell, Daniel

    2009-01-01

    Set shifting provokes specific alterations of cerebral hemodynamics in basal cerebral arteries. However, no gender differences have been reported. In the following functional transcranial Doppler study, we introduced cerebral hemodynamic modulation to the aspects of set shifting during Wisconsin Card Sorting Test (WCST). Twenty-one subjects…

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

    Science.gov (United States)

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

    2016-06-01

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

  7. Proteomics indicators of the rapidly shifting physiology from whole mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae, adults during early host colonization.

    Directory of Open Access Journals (Sweden)

    Caitlin Pitt

    Full Text Available We developed proteome profiles for host colonizing mountain pine beetle adults, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae. Adult insects were fed in pairs on fresh host lodgepole pine, Pinus contorta Dougl. ex Loud, phloem tissue. The proteomes of fed individuals were monitored using iTRAQ and compared to those of starved beetles, revealing 757 and 739 expressed proteins in females and males, respectively, for which quantitative information was obtained. Overall functional category distributions were similar for males and females, with the majority of proteins falling under carbohydrate metabolism (glycolysis, gluconeogenesis, citric acid cycle, structure (cuticle, muscle, cytoskeleton, and protein and amino acid metabolism. Females had 23 proteins with levels that changed significantly with feeding (p<0.05, FDR<0.20, including chaperones and enzymes required for vitellogenesis. In males, levels of 29 proteins changed significantly with feeding (p<0.05, FDR<0.20, including chaperones as well as motor proteins. Only two proteins, both chaperones, exhibited a significant change in both females and males with feeding. Proteins with differential accumulation patterns in females exhibited higher fold changes with feeding than did those in males. This difference may be due to major and rapid physiological changes occurring in females upon finding a host tree during the physiological shift from dispersal to reproduction. The significant accumulation of chaperone proteins, a cytochrome P450, and a glutathione S-transferase, indicate secondary metabolite-induced stress physiology related to chemical detoxification during early host colonization. The females' activation of vitellogenin only after encountering a host indicates deliberate partitioning of resources and a balancing of the needs of dispersal and reproduction.

  8. 129Xe chemical shift in human blood and pulmonary blood oxygenation measurement in humans using hyperpolarized 129Xe NMR

    OpenAIRE

    Norquay, G.; Leung, G; Stewart, N J; Wolber, J.; Wild, J.M.

    2016-01-01

    Purpose To evaluate the dependency of the 129Xe?red blood cell (RBC) chemical shift on blood oxygenation, and to use this relation for noninvasive measurement of pulmonary blood oxygenation in vivo with hyperpolarized 129Xe NMR. Methods Hyperpolarized 129Xe was equilibrated with blood samples of varying oxygenation in vitro, and NMR was performed at 1.5 T and 3 T. Dynamic in vivo NMR during breath hold apnea was performed at 3 T on two healthy volunteers following inhalation of hyperpolarized...

  9. Beyond DP4: an Improved Probability for the Stereochemical Assignment of Isomeric Compounds using Quantum Chemical Calculations of NMR Shifts.

    Science.gov (United States)

    Grimblat, Nicolás; Zanardi, María M; Sarotti, Ariel M

    2015-12-18

    The DP4 probability is one of the most sophisticated and popular approaches for the stereochemical assignment of organic molecules using GIAO NMR chemical shift calculations when only one set of experimental data is available. In order to improve the performance of the method, we have developed a modified probability (DP4+), whose main differences from the original DP4 are the inclusion of unscaled data and the use of higher levels of theory for the NMR calculation procedure. With these modifications, a significant improvement in the overall performance was achieved, providing accurate and confident results in establishing the stereochemistry of 48 challenging isomeric compounds.

  10. Phase resetting of the mammalian circadian clock relies on a rapid shift of a small population of pacemaker neurons.

    Directory of Open Access Journals (Sweden)

    Jos H T Rohling

    Full Text Available The circadian pacemaker of the suprachiasmatic nuclei (SCN contains a major pacemaker for 24 h rhythms that is synchronized to the external light-dark cycle. In response to a shift in the external cycle, neurons of the SCN resynchronize with different pace. We performed electrical activity recordings of the SCN of rats in vitro following a 6 hour delay of the light-dark cycle and observed a bimodal electrical activity pattern with a shifted and an unshifted component. The shifted component was relatively narrow as compared to the unshifted component (2.2 h and 5.7 h, respectively. Curve fitting and simulations predicted that less than 30% of the neurons contribute to the shifted component and that their phase distribution is small. This prediction was confirmed by electrophysiological recordings of neuronal subpopulations. Only 25% of the neurons exhibited an immediate shift in the phase of the electrical activity rhythms, and the phases of the shifted subpopulations appeared significantly more synchronized as compared to the phases of the unshifted subpopulations (p<0.05. We also performed electrical activity recordings of the SCN following a 9 hour advance of the light-dark cycle. The phase advances induced a large desynchrony among the neurons, but consistent with the delays, only 19% of the neurons peaked at the mid of the new light phase. The data suggest that resetting of the central circadian pacemaker to both delays and advances is brought about by an initial shift of a relatively small group of neurons that becomes highly synchronized following a shift in the external cycle. The high degree of synchronization of the shifted neurons may add to the ability of this group to reset the pacemaker. The large desynchronization observed following advances may contribute to the relative difficulty of the circadian system to respond to advanced light cycles.

  11. COMPUTATIONAL INVESTIGATION ON THE STRUCTURE AND NMR CHEMICAL SHIFTS OF ENDO-CONE [CS2(p-METHYLCALIX[4]ARENE] COMPLEX

    Directory of Open Access Journals (Sweden)

    Hanggara Sudrajat

    2010-06-01

    Full Text Available The structure and NMR chemical shifts of endo-cone [CS2(p-methylcalix[4]arene] complex have been computationally investigated using BIO+ force fields, semi-empirical (PM3 and ab initio (RHF/6-311G++(d,p calculations. The first comparison of ab initio NMR chemical shift calculations for a calix[4]arene inclusion complex with solid-state 13C NMR chemical shifts based on the 1:1 complex of p-methylcalix[4]arenes with carbon disulfide in endo-cone complexation mode has been reported. The results showed that ab initio (RHF/6-311G++(d,p NMR calculations of the host-guest [CS2(p-methylcalix[4]arene] complex are in good agreement with experimental solid-state NMR data.    Keywords: computational investigation, structure, NMR chemical shifts, [CS2(p-methylcalix[4]arene].

  12. 15N Chemical Shifts in Energetic Materials: CP/MAS and ab Initio Studies of Aminonitropyridines, Aminonitropyrimidines, and Their N-Oxides

    Directory of Open Access Journals (Sweden)

    Julio C. Facelli

    2002-08-01

    Full Text Available Abstract: Solid state 15N NMR chemical shift measurements have been performed on a series of nitro- and amino-substituted nitrogen-containing heterocycles that are of interest as potential new insensitive explosives. Due to low solubilities, many of these compounds are not amenable to study by solution state methods. Theoretical calculations of 15N chemical shift parameters have been performed on the structures of interest and are reported herein. The calculated and experimental values are in good agreement. The use of a model that includes intermolecular effects and allows the proton positions of the nearest neighbors to be optimized leads to the best agreement between calculated and experimental values. The theoretical models accurately predict the effects of nitro and amino substituents on ringnitrogen chemical shifts, explaining a seeming reversal in trend that is noted in the pyridine and pyridine-1-oxide chemical shifts of the highly substituted compounds.

  13. Modeling the chemical shift of lanthanide 4f electron binding energies

    NARCIS (Netherlands)

    Dorenbos, P.

    2012-01-01

    Lanthanides in compounds can adopt the tetravalent [Xe]4fn?1 (like Ce4+, Pr4+, Tb4+), the trivalent [Xe]4fn (all lanthanides), or the divalent [Xe]4f n+1 configuration (like Eu2+, Yb2+, Sm2+, Tm2+). The 4f-electron binding energy depends on the charge Q of the lanthanide ion and its chemical

  14. Rapid Electrochemical Detection and Identification of Microbiological and Chemical Contaminants for Manned Spaceflight Project

    Science.gov (United States)

    Pierson, Duane; Botkin, Douglas; Gazda, Daniel

    2014-01-01

    Microbial control in the spacecraft environment is a daunting task, especially in the presence of human crew members. Currently, assessing the potential crew health risk associated with a microbial contamination event requires return of representative environmental samples that are analyzed in a ground-based laboratory. It is therefore not currently possible to quickly identify microbes during spaceflight. This project addresses the unmet need for spaceflight-compatible microbial identification technology. The electrochemical detection and identification platform is expected to provide a sensitive, specific, and rapid sample-to-answer capability for in-flight microbial monitoring that can distinguish between related microorganisms (pathogens and non-pathogens) as well as chemical contaminants. This will dramatically enhance our ability to monitor the spacecraft environment and the health risk to the crew. Further, the project is expected to eliminate the need for sample return while significantly reducing crew time required for detection of multiple targets. Initial work will focus on the optimization of bacterial detection and identification. The platform is designed to release nucleic acids (DNA and RNA) from microorganisms without the use of harmful chemicals. Bacterial DNA or RNA is captured by bacteria-specific probe molecules that are bound to a microelectrode, and that capture event can generate a small change in the electrical current (Lam, et al. 2012. Anal. Chem. 84(1): 21-5.). This current is measured, and a determination is made whether a given microbe is present in the sample analyzed. Chemical detection can be accomplished by directly applying a sample to the microelectrode and measuring the resulting current change. This rapid microbial and chemical detection device is designed to be a low-cost, low-power platform anticipated to be operated independently of an external power source, characteristics optimal for manned spaceflight and areas where power

  15. Using chemical shifts to generate structural ensembles for intrinsically disordered proteins with converged distributions of secondary structure.

    Science.gov (United States)

    Ytreberg, F Marty; Borcherds, Wade; Wu, Hongwei; Daughdrill, Gary W

    2015-01-01

    A short segment of the disordered p53 transactivation domain (p53TAD) forms an amphipathic helix when bound to the E3 ubiquitin ligase, MDM2. In the unbound p53TAD, this short segment has transient helical secondary structure. Using a method that combines broad sampling of conformational space with re-weighting, it is shown that it is possible to generate multiple, independent structural ensembles that have highly similar secondary structure distributions for both p53TAD and a P27A mutant. Fractional amounts of transient helical secondary structure were found at the MDM2 binding site that are very similar to estimates based directly on experimental observations. Structures were identified in these ensembles containing segments that are highly similar to short p53 peptides bound to MDM2, even though the ensembles were re-weighted using unbound experimental data. Ensembles were generated using chemical shift data (alpha carbon only, or in combination with other chemical shifts) and cross-validated by predicting residual dipolar couplings. We think this ensemble generator could be used to predict the bound state structure of protein interaction sites in IDPs if there are detectable amounts of matching transient secondary structure in the unbound state.

  16. Calculation of fluorine chemical shift tensors for the interpretation of oriented (19)F-NMR spectra of gramicidin A in membranes.

    Science.gov (United States)

    Sternberg, Ulrich; Klipfel, Marco; Grage, Stephan L; Witter, Raiker; Ulrich, Anne S

    2009-08-28

    A semi-empirical method for the prediction of chemical shifts, based on bond polarization theory, has recently been introduced for (13)C. Here, we extended this approach to calculate the (19)F chemical shift tensors of fluorine bound to aromatic rings and in aliphatic CF(3) groups. For the necessary parametrization, ab initio chemical shift calculations were performed at the MP2 level for a set of fluorinated molecules including tryptophan. The bond polarization parameters obtained were used to calculate the (19)F chemical shift tensors for several crystalline molecules, and to reference the calculated values on a chemical shift scale relative to CFCl(3). As a first biophysical application, we examined the distribution of conformations of a (19)F-labeled tryptophan side chain in the membrane-bound ion channel peptide, gramicidin A. The fluorine chemical shift tensors were calculated from snapshots of a molecular dynamics simulation employing the (19)F-parametrized bond polarization theory. In this MD simulation, published (2)H quadrupolar and (15)N-(1)H dipolar couplings of the indole ring were used as orientational constraints to determine the conformational distribution of the 5F-Trp(13) side chain. These conformations were then used to interpret the spectra of (19)F-labeled gramicidin A in fluid and gel phase lipid bilayers.

  17. Alloy composition dependence of formation of porous Ni prepared by rapid solidification and chemical dealloying

    Energy Technology Data Exchange (ETDEWEB)

    Qi Zhen [Key Laboratory of Liquid Structure and Heredity of Materials, Shandong University, Jingshi Road 73, Jinan 250061 (China); Zhang Zhonghua [Key Laboratory of Liquid Structure and Heredity of Materials, Shandong University, Jingshi Road 73, Jinan 250061 (China)], E-mail: zh_zhang@sdu.edu.cn; Jia Haoling [Key Laboratory of Liquid Structure and Heredity of Materials, Shandong University, Jingshi Road 73, Jinan 250061 (China); Qu Yingjie [Shandong Labor Occupational Technology College, Jingshi Road 388, Jinan 250022 (China); Liu Guodong; Bian Xiufang [Key Laboratory of Liquid Structure and Heredity of Materials, Shandong University, Jingshi Road 73, Jinan 250061 (China)

    2009-03-20

    In this paper, the effect of alloy composition on the formation of porous Ni catalysts prepared by chemical dealloying of rapidly solidified Al-Ni alloys has been investigated using X-ray diffraction (XRD), scanning electron microscopy (SEM) with energy dispersive X-ray (EDX) analysis and N{sub 2} adsorption experiments. The experimental results show that rapid solidification and alloy composition have a significant effect on the phase constituent and microstructure of Al-Ni alloys. The melt spun Al-20 at.% Ni alloy consists of {alpha}-Al, NiAl{sub 3} and Ni{sub 2}Al{sub 3}, while the melt spun Al-25 and 31.5 at.% Ni alloys comprise NiAl{sub 3} and Ni{sub 2}Al{sub 3}. Moreover, the formation and microstructure of the porous Ni catalysts are dependent upon the composition of the melt spun Al-Ni alloys. The morphology and size of Ni particles in the Ni catalysts inherit from those of grains in the melt spun Al-Ni alloys. Rapid solidification can extend the alloy composition of Al-Ni alloys suitable for preparation of the Ni catalysts, and obviously accelerate the dealloying process of the Al-Ni alloys.

  18. Observation of Optical Chemical Shift by Precision Nuclear Spin Optical Rotation Measurements and Calculations.

    Science.gov (United States)

    Shi, Junhui; Ikäläinen, Suvi; Vaara, Juha; Romalis, Michael V

    2013-02-07

    Nuclear spin optical rotation (NSOR) is a recently developed technique for detection of nuclear magnetic resonance via rotation of light polarization, instead of the usual long-range magnetic fields. NSOR signals depend on hyperfine interactions with virtual optical excitations, giving new information about the nuclear chemical environment. We use a multipass optical cell to perform the first precision measurements of NSOR signals for a range of organic liquids and find clear distinction between proton signals for different compounds, in agreement with our earlier theoretical predictions. Detailed first-principles quantum mechanical NSOR calculations are found to be in agreement with the measurements.

  19. Observation of optical chemical shift by precision nuclear spin optical rotation measurements and calculations

    CERN Document Server

    Shi, Junhui; Vaara, Juha; Romalis, Michael V

    2012-01-01

    Nuclear spin optical rotation (NSOR) is a recently developed technique for detection of nuclear magnetic resonance via rotation of light polarization, instead of the usual long-range magnetic fields. NSOR signals depend on hyperfine interactions with virtual optical excitations, giving new information about the nuclear chemical environment. We use a multi-pass optical cell to perform first precision measurements of NSOR signals for a range of organic liquids and find clear distinction between proton signals for different compounds, in agreement with our earlier predictions. Detailed first principles quantum-mechanical NSOR calculations are found to be in good agreement with the measurements.

  20. Rapid upslope shifts in New Guinean birds illustrate strong distributional responses of tropical montane species to global warming

    Science.gov (United States)

    Freeman, Benjamin G.; Class Freeman, Alexandra M.

    2014-01-01

    Temperate-zone species have responded to warming temperatures by shifting their distributions poleward and upslope. Thermal tolerance data suggests that tropical species may respond to warming temperatures even more strongly than temperate-zone species, but this prediction has yet to be tested. We addressed this data gap by conducting resurveys to measure distributional responses to temperature increases in the elevational limits of the avifaunas of two geographically and faunally independent New Guinean mountains, Mt. Karimui and Karkar Island, 47 and 44 y after they were originally surveyed. Although species richness is roughly five times greater on mainland Mt. Karimui than oceanic Karkar Island, distributional shifts at both sites were similar: upslope shifts averaged 113 m (Mt. Karimui) and 152 m (Karkar Island) for upper limits and 95 m (Mt. Karimui) and 123 m (Karkar Island) for lower limits. We incorporated these results into a metaanalysis to compare distributional responses of tropical species with those of temperate-zone species, finding that average upslope shifts in tropical montane species match local temperature increases significantly more closely than in temperate-zone montane species. That tropical species appear to be strong responders has global conservation implications and provides empirical support to hitherto untested models that predict widespread extinctions in upper-elevation tropical endemics with small ranges. PMID:24550460

  1. Lower-Income Countries That Face The Most Rapid Shift In Noncommunicable Disease Burden Are Also The Least Prepared.

    Science.gov (United States)

    Bollyky, Thomas J; Templin, Tara; Cohen, Matthew; Dieleman, Joseph L

    2017-11-01

    Demographic and epidemiological changes are shifting the disease burden from communicable to noncommunicable diseases in lower-income countries. Within a generation, the share of disease burden attributed to noncommunicable diseases in some poor countries will exceed 80 percent, rivaling that of rich countries, but this burden is likely to affect much younger people in poorer countries. The health systems of lower-income countries are unprepared for this change. We examined the shift to noncommunicable diseases and estimated preparedness for the shift by ranking 172 nations using a health system capacity index for noncommunicable disease. We project that the countries with the greatest increases in the share of disease burden attributable to noncommunicable disease over the next twenty-five years will also be the least prepared for the change, as they ranked low on our capacity index and are expected to have the smallest increases in national health spending. National governments and donors must invest more in preparing the health systems of lower-income countries for the dramatic shift to noncommunicable diseases and in reducing modifiable noncommunicable disease risks.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-15

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

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

    Science.gov (United States)

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

    2017-05-01

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

  4. Non‐invasive Localization of Thymol Accumulation in Carum copticum (Apiaceae) Fruits by Chemical Shift Selective Magnetic Resonance Imaging

    Science.gov (United States)

    GERSBACH, P. V.; REDDY, N.

    2002-01-01

    Magnetic resonance imaging was used to localize the site of essential oil accumulation in fruit of Carum copticum L. (Apiaceae). A chemical shift method is described that utilized the spectral properties of the aromatic monoterpene thymol, the major component of the essential oil, to image thymol selectively. The presence of essential oil secretory structures in the fruit and an essential oil containing a high proportion of thymol were confirmed with optical microscopy and gas chromatography‐mass spectrometry, respectively. Selective imaging of whole C. copticum fruits showed that thymol accumulation was localized to the secretory structures (canals) situated in the fruit wall. The technique was considered non‐invasive as the seeds used in the imaging experiments remained intact and viable. PMID:12197523

  5. Shifting chemical equilibria in flow--efficient decarbonylation driven by annular flow regimes.

    Science.gov (United States)

    Gutmann, Bernhard; Elsner, Petteri; Glasnov, Toma; Roberge, Dominique M; Kappe, C Oliver

    2014-10-20

    To efficiently drive chemical reactions, it is often necessary to influence an equilibrium by removing one or more components from the reaction space. Such manipulation is straightforward in open systems, for example, by distillation of a volatile product from the reaction mixture. Herein we describe a unique high-temperature/high-pressure gas/liquid continuous-flow process for the rhodium-catalyzed decarbonylation of aldehydes. The carbon monoxide released during the reaction is carried with a stream of an inert gas through the center of the tubing, whereas the liquid feed travels as an annular film along the wall of the channel. As a consequence, carbon monoxide is effectively vaporized from the liquid phase into the gas phase and stripped from the reaction mixture, thus driving the equilibrium to the product and preventing poisoning of the catalyst. This approach enables the catalytic decarbonylation of a variety of aldehydes with unprecedented efficiency with a standard coil-based flow device. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment

    Energy Technology Data Exchange (ETDEWEB)

    Tremblay, Marie-Laurence; Banks, Aaron W.; Rainey, Jan K., E-mail: jan.rainey@dal.c [Dalhousie University, Department of Biochemistry and Molecular Biology (Canada)

    2010-04-15

    Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift ({Delta}{delta}) values, measured as the difference between experimental and random coil chemical shifts (RCCS). Most published random coil data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane proteins. Two new RCCS sets are presented here, determined in dimethyl sulfoxide (DMSO) and chloroform:methanol:water (4:4:1 by volume) at 298 K. A web-based program, CS-CHEMeleon, has been implemented to determine the accuracy of secondary structure assessment by calculating and comparing {Delta}{delta} values for various RCCS datasets. Using CS-CHEMeleon, {Delta}{delta} predicted versus experimentally determined secondary structures were compared for large datasets of membrane and non-membrane proteins as a function of RCCS dataset, {Delta}{delta} threshold, nucleus, localized parameter averaging and secondary structure type. Optimized {Delta}{delta} thresholds are presented both for published and for the DMSO and chloroform:methanol:water derived RCCS tables. Despite obvious RCCS variations between datasets, prediction of secondary structure was consistently similar. Strikingly, predictive accuracy seems to be most dependent upon the type of secondary structure, with helices being the most accurately predicted by {Delta}{delta} values using five different RCCS tables. We suggest caution when using {Delta}{delta}-based restraints in structure calculations as the underlying dataset may be biased. Comparative assessment of multiple RCCS datasets should be performed, and resulting {Delta}{delta}-based restraints weighted appropriately relative to other experimental restraints.

  7. A portable photoelectrochemical probe for rapid determination of chemical oxygen demand in wastewaters.

    Science.gov (United States)

    Zhang, Shanqing; Li, Lihong; Zhao, Huijun

    2009-10-15

    A photoelectrochemical probe for rapid determination of chemical oxygen demand (COD) is developed using a nanostructured mixed-phase TiO2 photoanode, namely PeCOD probe. A UV-LED light source and a USB mircroelectrochemical station are powered and controlled by a laptop computer, which makes the probe portable for onsite COD analyses. The photoelectrochemical measurement of COD was optimized in terms of light intensity, applied bias, and pH. Under the optimized conditions, the net steady state currents originated from the oxidation of organic compounds were found to be directly proportional to COD concentrations. A practical detection limit of 0.2 ppm COD and a linear range of 0-120 ppm COD were achieved. The analytical method using the portable PeCOD probe has the advantages of being rapid, low cost, robust, user-friendly, and environmental friendly. It has been successfully applied to determine the COD values of the synthetic samples consisting of potassium hydrogen phthalate, D-glucose, glutamic acid, glutaric acid, succinic acid, and malonic acid, and real samples from various industries, such as bakery, oil and grease manufacturer, poultry, hotel, fine food factory, and fresh food producer, commercial bread manufacturer. Excellent agreement between the proposed method and the conventional COD method (dichromate) was achieved.

  8. Learning to rapidly re-contact the lost plume in chemical plume tracing.

    Science.gov (United States)

    Cao, Meng-Li; Meng, Qing-Hao; Wang, Jia-Ying; Luo, Bing; Jing, Ya-Qi; Ma, Shu-Gen

    2015-03-27

    Maintaining contact between the robot and plume is significant in chemical plume tracing (CPT). In the time immediately following the loss of chemical detection during the process of CPT, Track-Out activities bias the robot heading relative to the upwind direction, expecting to rapidly re-contact the plume. To determine the bias angle used in the Track-Out activity, we propose an online instance-based reinforcement learning method, namely virtual trail following (VTF). In VTF, action-value is generalized from recently stored instances of successful Track-Out activities. We also propose a collaborative VTF (cVTF) method, in which multiple robots store their own instances, and learn from the stored instances, in the same database. The proposed VTF and cVTF methods are compared with biased upwind surge (BUS) method, in which all Track-Out activities utilize an offline optimized universal bias angle, in an indoor environment with three different airflow fields. With respect to our experimental conditions, VTF and cVTF show stronger adaptability to different airflow environments than BUS, and furthermore, cVTF yields higher success rates and time-efficiencies than VTF.

  9. Learning to Rapidly Re-Contact the Lost Plume in Chemical Plume Tracing

    Directory of Open Access Journals (Sweden)

    Meng-Li Cao

    2015-03-01

    Full Text Available Maintaining contact between the robot and plume is significant in chemical plume tracing (CPT. In the time immediately following the loss of chemical detection during the process of CPT, Track-Out activities bias the robot heading relative to the upwind direction, expecting to rapidly re-contact the plume. To determine the bias angle used in the Track-Out activity, we propose an online instance-based reinforcement learning method, namely virtual trail following (VTF. In VTF, action-value is generalized from recently stored instances of successful Track-Out activities. We also propose a collaborative VTF (cVTF method, in which multiple robots store their own instances, and learn from the stored instances, in the same database. The proposed VTF and cVTF methods are compared with biased upwind surge (BUS method, in which all Track-Out activities utilize an offline optimized universal bias angle, in an indoor environment with three different airflow fields. With respect to our experimental conditions, VTF and cVTF show stronger adaptability to different airflow environments than BUS, and furthermore, cVTF yields higher success rates and time-efficiencies than VTF.

  10. Learning to Rapidly Re-Contact the Lost Plume in Chemical Plume Tracing

    Science.gov (United States)

    Cao, Meng-Li; Meng, Qing-Hao; Wang, Jia-Ying; Luo, Bing; Jing, Ya-Qi; Ma, Shu-Gen

    2015-01-01

    Maintaining contact between the robot and plume is significant in chemical plume tracing (CPT). In the time immediately following the loss of chemical detection during the process of CPT, Track-Out activities bias the robot heading relative to the upwind direction, expecting to rapidly re-contact the plume. To determine the bias angle used in the Track-Out activity, we propose an online instance-based reinforcement learning method, namely virtual trail following (VTF). In VTF, action-value is generalized from recently stored instances of successful Track-Out activities. We also propose a collaborative VTF (cVTF) method, in which multiple robots store their own instances, and learn from the stored instances, in the same database. The proposed VTF and cVTF methods are compared with biased upwind surge (BUS) method, in which all Track-Out activities utilize an offline optimized universal bias angle, in an indoor environment with three different airflow fields. With respect to our experimental conditions, VTF and cVTF show stronger adaptability to different airflow environments than BUS, and furthermore, cVTF yields higher success rates and time-efficiencies than VTF. PMID:25825974

  11. A role for prostaglandins in rapid cycling suggested by episode-specific gene expression shifts in peripheral blood mononuclear cells

    DEFF Research Database (Denmark)

    Gurvich, Artem; Begemann, Martin; Dahm, Liane

    2014-01-01

    OBJECTIVES: Over 12% of patients with bipolar disorder exhibit rapid cycling. The underlying biological mechanisms of this extreme form of bipolar disease are still unknown. This study aimed at replicating and extending findings of our previously published case report, where an involvement of pro...

  12. Predictions of the fluorine NMR chemical shifts of perfluorinated carboxylic acids, CnF(2n+1)COOH (n = 6-8).

    Science.gov (United States)

    Liu, Zizhong; Goddard, John D

    2009-12-17

    Perfluorinated carboxylic acids (PFCAs) are a class of persistent environmental pollutants. Commercially available PFCAs are mixtures of linear and branched isomers, possibly with impurities. Different isomers have different physical and chemical properties and toxicities. However, little is known about the properties and the finer details of the structures of the individual branched isomers. Full geometry optimizations for the linear n-alkane (C(6)-C(27)) PFCAs indicated that all have helical structures. The helical angle increases slightly with increasing chain length, from 16.3 degrees in C(6)F(13)COOH to 17.0 degrees in C(27)F(55)COOH. This study predicts (19)F NMR parameters for 69 linear and branched isomers of the perfluoro carboxylic acids C(6)F(13)COOH, C(7)F(15)COOH, and C(8)F(17)COOH. B3LYP-GIAO/6-31++G(d,p)//B3LYP/6-31G(d,p) was used for the NMR calculations with analysis of the chemical shifts by the natural bond orbital method. The predictions of the (19)F chemical shifts revealed the differences among the CF(3), CF(2), and CF groups. In general, the absolute values for the chemical shifts for the CF(3) group are smaller than 90 ppm, for the CF larger than 160 ppm, and for the CF(2) between 110 and 130 ppm. The chemical shifts of the branched isomers are smaller in magnitude than the linear ones. The decrease is correlated with the steric hindrance of the CF(3) groups, the more hindered the CF(3), the greater the decrease in the (19)F chemical shifts. The predicted (19)F chemical shifts are similar to those for analogous perfluoro compounds with other terminal functional groups such as -SO(3)H or -SO(3)NH(2)CH(2)CH(3).

  13. Predictions of the Fluorine NMR Chemical Shifts of Perfluorinated Carboxylic Acids, CnF2n+1COOH (n = 6-8)

    Science.gov (United States)

    Liu, Zizhong; Goddard, John D.

    2009-10-01

    Perfluorinated carboxylic acids (PFCAs) are a class of persistent environmental pollutants. Commercially available PFCAs are mixtures of linear and branched isomers, possibly with impurities. Different isomers have different physical and chemical properties and toxicities. However, little is known about the properties and the finer details of the structures of the individual branched isomers. Full geometry optimizations for the linear n-alkane (C6-C27) PFCAs indicated that all have helical structures. The helical angle increases slightly with increasing chain length, from 16.3° in C6F13COOH to 17.0° in C27F55COOH. This study predicts 19F NMR parameters for 69 linear and branched isomers of the perfluoro carboxylic acids C6F13COOH, C7F15COOH, and C8F17COOH. B3LYP-GIAO/6-31++G(d,p)//B3LYP/6-31G(d,p) was used for the NMR calculations with analysis of the chemical shifts by the natural bond orbital method. The predictions of the 19F chemical shifts revealed the differences among the CF3, CF2, and CF groups. In general, the absolute values for the chemical shifts for the CF3 group are smaller than 90 ppm, for the CF larger than 160 ppm, and for the CF2 between 110 and 130 ppm. The chemical shifts of the branched isomers are smaller in magnitude than the linear ones. The decrease is correlated with the steric hindrance of the CF3 groups, the more hindered the CF3, the greater the decrease in the 19F chemical shifts. The predicted 19F chemical shifts are similar to those for analogous perfluoro compounds with other terminal functional groups such as -SO3H or -SO3NH2CH2CH3.

  14. Shifts in Mortality During a Hot Weather Event in Vancouver, British Columbia: Rapid Assessment With Case-Only Analysis

    Science.gov (United States)

    Henderson, Sarah B.; Pollock, Sue L.

    2012-01-01

    Objectives. We assessed shifts in patterns of mortality during a hot weather event in greater Vancouver, British Columbia. Methods. We used a case-only analysis to compare characteristics of individuals who died during the hottest week of 2009 with those who died (1) during earlier summer weeks in 2009 and (2) during the same calendar weeks in the summers of 2001 through 2008. Results. Compared with the 8 previous weeks of 2009, odds of mortality during the summer’s hottest week were highest in the 65 to 74 years age category, compared with the 85 years and older category (odds ratio [OR] = 1.47; 95% confidence interval [CI] = 1.06, 2.03). The number of deaths at home increased over deaths in hospitals or institutions (OR = 1.43; 95% CI = 1.10, 1.86). Densely populated administrative health areas were more affected. Conclusions. A shift toward deaths at home suggests that in-home–based protective measures should be part of planning for hot weather events in greater Vancouver. Targeting should be considered for those aged 65 to 74 years. The case-only approach is quick and easy to apply and can provide useful information about localized, time-limited events. PMID:23078510

  15. Inverted cucurbit[n]urils: density functional investigations on the electronic structure, electrostatic potential, and NMR chemical shifts.

    Science.gov (United States)

    Pinjari, Rahul V; Gejji, Shridhar P

    2009-02-19

    Inverted cucurbit[n]uril (i(x)CB[n], x = 1, 2; n = 6-8), the enantiomers of cucurbit[n]uril (CB[n]) comprising one or more inverted glycouril units, show distinct selectivity in recognition toward the guest by the virtue of shape and dimensions of its cavity. The iCB[n] (x = 1 and n = 6, 7) are isolated as intermediates during the synthesis of CB[n]. In this work, density functional theory using the hybrid B3LYP functional has been employed to derive the electronic structure and the NMR chemical shifts in the i(x)CB[n] hosts. The present calculations have shown that the inversion of the glycouril unit of CB[6] and CB[7] engenders a destabilization by 4.2 and 5.7 kJ mol(-1), respectively, and, as opposed to this, the iCB[8] is favored by 18.6 kJ mol(-1) over the corresponding CB[8] host. Likewise, i2CB[7] possessing two inverted glycourils are highly destabilized over CB[7]. A large separation of the inverted glycouril units reduces the repulsion between methine protons inside the cavity, rendering the 1,4-i2CB[n] (n = 7 or 8) to be of lowest energy. Stabilization energies from the self-consistent reaction field (SCRF) theory are calculated with water, ethanol, and tetrahydrofuran (THF) as solvents. Unlike in gas phase and other solvents, the stabilization hierarchy iCB[6] portals. The electron-rich region within the cavity explains the large affinity of CB[n] toward the electron deficient guests. The electronic distribution and shape and size of the cavity thus derived provide insights for the inclusion of guests of different shapes in a variety of i(x)CB[n] hosts. NMR chemical shifts have shown that the methylene protons near the inverted glycouril and the methine protons those are directing toward the cavity yield distinct signals, consistent with those observed in experiments. The protons within the cavity are less affected by solvation.

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

    Science.gov (United States)

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

    2013-06-11

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

  17. Characterization of a rapid climate shift at the MIS 8/7 transition in central Spain (Valdocarros II, Autonomous Region of Madrid) by means of the herpetological assemblages

    Science.gov (United States)

    Blain, Hugues-Alexandre; Panera, Joaquin; Uribelarrea, David; Rubio-Jara, Susana; Pérez-González, Alfredo

    2012-07-01

    Climate instability with high-amplitude and rapid shifts during the Middle Pleistocene is well known from pollen records and deep-ocean sediment cores. Although poorly correlatable with such long climate/environment records, the successive fossil amphibian and reptile assemblages from the Middle Pleistocene site of Valdocarros II (Autonomous Region of Madrid, central Spain) provide a unique opportunity to characterize the climatic and environmental features of such rapid (certainly less than 1000 years) shifts from cold to warm conditions in a terrestrial sequence. As the amphibians and reptiles do not differ at species level from the extant herpetofauna of the Iberian Peninsula, they can contribute to the reconstruction of the landscape and climate. In this paper, the mutual climatic range and habitat weighting methods are applied to the herpetofaunistic assemblages in order to estimate quantitative data. The difference in mean annual temperature between "cold" and "warm" periods is estimated at 3.2 °C, with a greater increase in temperature during winter (+3 °C) than during summer (+1 °C). During "cold" periods the climate was more Oceanic (although preserving some dryness during the summers), whereas during "warm" periods the climate became Mediterranean (with mild winters and a long period of dryness in the summer and early autumn). Though higher during cold periods, the continentality (or atmospheric temperature range) remained roughly similar, in accordance with the geographical location of the site in the centre of the Iberian Peninsula. A greater amount of open landscape occurred during "cold" periods, whereas during "warm" periods the wooded areas expanded from 20% to 40% of the landscape surface. Such climatic/environmental changes, together with the numeric datings of the site, suggest that this shift may correspond to the transition from MIS 8 to MIS 7, also called Termination III.

  18. Rapid thermal chemical vapor deposition growth of nanometer-thin SiC on silicon

    Energy Technology Data Exchange (ETDEWEB)

    Steckl, A.J.; Li, J.P. (Univ. of Cincinnati, OH (United States))

    1992-08-28

    Rapid thermal chemical vapor deposition growth of [beta]-SiC ultrathin films on Si (100) was achieved using the carbonization reaction of the silicon substrate with C[sub 3]H[sub 8] gas. Growth rates of 0.5-2 nm s[sup -1] have been achieved at 1100-1300degC using C[sub 3]H[sub 8] flow rates of 7-9 standard cm[sup 3] min[sup -1]. X-ray and electron diffraction indicate single-crystal growth. Therefore nanometer-scale SiC films can be grown by controlling the reaction time to a few seconds. The activation energy at atmospheric pressure is 3.12 eV. The growth rate was found to decrease significantly at higher C[sub 3]H[sub 8] flow rates, leading to films of constant thickness beyond a certain critical reaction time. Using this regime of self-limiting growth, SiC films of 3-5 nm have been grown with relatively little sensitivity to the growth time. (orig.).

  19. Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-05-15

    Statistical analysis reveals that the set of differences between the secondary shifts of the {alpha}- and {beta}-carbons for residues i of a protein ({delta}{delta}{sup 13}C{sup {alpha}}{sub i}- {delta}{delta}{sup 13}C{sup {beta}}{sub i}) provides the means to detect and correct referencing errors for {sup 1}H and {sup 13}C nuclei within a given dataset. Linear analysis of chemical shifts (LACS) can be used to detect referencing errors and to recalibrate the {sup 1}H and {sup 13}C chemical shift scales if needed. The analysis requires only that the signals be identified with distinct residue types (intra-residue spin systems). LACS allows errors in calibration to be detected and corrected in advance of sequence-specific assignments and secondary structure determinations. Signals that do not fit the linear model (outliers) deserve scrutiny since they could represent errors in identifying signals with a particular residue, or interesting features such as a cis-peptide bond. LACS provides the basis for the automated detection of such features and for testing reassignment hypotheses. Early detection and correction of errors in referencing and spin system identifications can improve the speed and accuracy of chemical shift assignments and secondary structure determinations. We have used LACS to create a database of offset-corrected chemical shifts corresponding to nearly 1800 BMRB entries: 300 with and 1500 without corresponding three-dimensional (3D) structures. This database can serve as a resource for future analysis of the effects of amino acid sequence and protein secondary and tertiary structure on NMR chemical shifts.

  20. Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications.

    Science.gov (United States)

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

    2005-05-01

    Statistical analysis reveals that the set of differences between the secondary shifts of the alpha- and beta-carbons for residues i of a protein (Deltadelta13C(alpha)i - Deltadelta13C(beta)i) provides the means to detect and correct referencing errors for 1H and 13C nuclei within a given dataset. In a correctly referenced protein dataset, linear regression plots of Deltadelta13C(alpha)i, Deltadelta13C(beta)i, or Deltadelta1H(alpha)i vs. (Deltadelta13C(alpha)i - Deltadelta13C(beta)i) pass through the origin from two directions, the helix-to-coil and strand-to-coil directions. Thus, linear analysis of chemical shifts (LACS) can be used to detect referencing errors and to recalibrate the 1H and 13C chemical shift scales if needed. The analysis requires only that the signals be identified with distinct residue types (intra-residue spin systems). LACS allows errors in calibration to be detected and corrected in advance of sequence-specific assignments and secondary structure determinations. Signals that do not fit the linear model (outliers) deserve scrutiny since they could represent errors in identifying signals with a particular residue, or interesting features such as a cis-peptide bond. LACS provides the basis for the automated detection of such features and for testing reassignment hypotheses. Early detection and correction of errors in referencing and spin system identifications can improve the speed and accuracy of chemical shift assignments and secondary structure determinations. We have used LACS to create a database of offset-corrected chemical shifts corresponding to nearly 1800 BMRB entries: 300 with and 1500 without corresponding three-dimensional (3D) structures. This database can serve as a resource for future analysis of the effects of amino acid sequence and protein secondary and tertiary structure on NMR chemical shifts.

  1. Mapping phosphorylation rate of fluoro-deoxy-glucose in rat brain by 19F chemical shift imaging

    Science.gov (United States)

    Coman, Daniel; Sanganahalli, Basavaraju G.; Cheng, David; McCarthy, Timothy; Rothman, Douglas L.; Hyder, Fahmeed

    2014-01-01

    19F magnetic resonance spectroscopy (MRS) studies of 2-fluoro-2-deoxy-D-glucose (FDG) and 2-fluoro-2-deoxy-D-glucose-6-phosphate (FDG-6P) can be used for directly assessing total glucose metabolism in vivo. To date, 19F MRS measurements of FDG phosphorylation in the brain have either been achieved ex vivo from extracted tissue or in vivo by unusually long acquisition times. Electrophysiological and functional magnetic resonance imaging (fMRI) measurements indicate that FDG doses up to 500mg/kg can be tolerated with minimal side effects on cerebral physiology and evoked fMRI-BOLD responses to forepaw stimulation. In halothane-anesthetized rats, we report localized in vivo detection and separation of FDG and FDG-6P MRS signals with 19F 2D chemical shift imaging (CSI) at 11.7T. A metabolic model based on reversible transport between plasma and brain tissue, which included a non-saturable plasma to tissue component, was used to calculate spatial distribution of FDG and FDG-6P concentrations in rat brain. In addition, spatial distribution of rate constants and metabolic fluxes of FDG to FDG-6P conversion were estimated. Mapping the rate of FDG to FDG-6P conversion by 19F CSI provides an MR methodology that could impact other in vivo applications such as characterization of tumor pathophysiology. PMID:24581725

  2. A multidimensional approach to the analysis of chemical shift titration experiments in the frame of a multiple reaction scheme.

    Science.gov (United States)

    D'Aléo, Anthony; Dumont, Elise; Maury, Olivier; Giraud, Nicolas

    2013-10-01

    We present a method for fitting curves acquired by chemical shift titration experiments, in the frame of a three-step complexation mechanism. To that end, we have implemented a fitting procedure, based on a nonlinear least squares fitting method, that determines the best fitting curve using a "coarse grid search" approach and provides distributions for the different parameters of the complexation model that are compatible with the experimental precision. The resulting analysis protocol is first described and validated on a theoretical data set. We show its ability to converge to the true parameter values of the simulated reaction scheme and to evaluate complexation constants together with multidimensional uncertainties. Then, we apply this protocol to the study of the supramolecular interactions, in aqueous solution, between a lanthanide complex and three different model molecules, using NMR titration experiments. We show that within the uncertainty that can be evaluated from the parameter distributions generated during our analysis, the affinities between the lanthanide derivative and each model molecule can be discriminated, and we propose values for the corresponding thermodynamic constants. Copyright © 2013 John Wiley & Sons, Ltd.

  3. Centerband-only analysis of rotor-unsynchronized spin echo for measurement of lipid (31) P chemical shift anisotropy.

    Science.gov (United States)

    Umegawa, Yuichi; Yamaguchi, Toshiyuki; Murata, Michio; Matsuoka, Shigeru

    2015-07-01

    Structural diversity and molecular flexibility of phospholipids are essential for biological membranes to play key roles in numerous cellular processes. Uncovering the behavior of individual lipids in membrane dynamics is crucial for understanding the molecular mechanisms underlying biological functions of cell membranes. In this paper, we introduce a simple method to investigate dynamics of lipid molecules in multi-component systems by measuring the (31) P chemical shift anisotropy (CSA) under magic angle spinning (MAS) conditions. For achieving both signal separation and CSA determination, we utilized a centerband-only analysis of rotor-unsynchronized spin echo (COARSE). This analysis is based on the curve fitting of periodic modulation of centerband intensity along the interpulse delay time in rotor-unsynchronized spin-echo experiments. The utility of COARSE was examined by using phospholipid vesicles, a three-component lipid raft model system, and archaeal purple membranes. We found that the apparent advantages of this method are high resolution and high sensitivity given by the moderate MAS speed and the one-dimensional acquisition with short spin-echo delays. COARSE provides an alternative method for CSA measurement that is effective in the investigation of lipid polymorphologies. Copyright © 2015 John Wiley & Sons, Ltd.

  4. T1-corrected fat quantification using chemical shift-based water/fat separation: application to skeletal muscle

    Science.gov (United States)

    Karampinos, Dimitrios C.; Yu, Huzanzhou; Shimakawa, Ann; Link, Thomas M.; Majumdar, Sharmila

    2011-01-01

    Chemical shift based water/fat separation, like iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL), has been proposed for quantifying intermuscular adipose tissue (IMAT). An important confounding factor in IDEAL-based IMAT quantification is the large difference in T1 between muscle and fat, which can cause significant overestimation in the fat fraction. This T1 bias effect is usually reduced by employing small flip angles. T1-correction can be performed by employing at least two different flip angles and fitting for T1 of water and fat. In the present work, a novel approach for the water/fat separation problem in a dual flip angle experiment is introduced and a new approach for the selection of the two flip angles, labeled as the unequal small flip angle approach, is developed, aiming to improve the noise efficiency of the T1-correction step relative to existing approaches. It is shown that the use of flip angles, selected such the muscle water signal is assumed to be T1-independent for the first flip angle and the fat signal is assumed to be T1-independent for the second flip angle, has superior noise performance to the use of equal small flip angles (no T1 estimation required) and the use of large flip angles (T1 estimation required). PMID:21452279

  5. A Fast Variant of 1H Spectroscopic U-FLARE Imaging Using Adjusted Chemical Shift Phase Encoding

    Science.gov (United States)

    Ebel, Andreas; Dreher, Wolfgang; Leibfritz, Dieter

    2000-02-01

    So far, fast spectroscopic imaging (SI) using the U-FLARE sequence has provided metabolic maps indirectly via Fourier transformation (FT) along the chemical shift (CS) dimension and subsequent peak integration. However, a large number of CS encoding steps Nω is needed to cover the spectral bandwidth and to achieve sufficient spectral resolution for peak integration even if the number of resonance lines is small compared to Nω and even if only metabolic images are of interest and not the spectra in each voxel. Other reconstruction algorithms require extensive prior knowledge, starting values, and/or model functions. An adjusted CS phase encoding scheme (APE) can be used to overcome these drawbacks. It incorporates prior knowledge only about the resonance frequencies present in the sample. Thus, Nω can be reduced by a factor of 4 for many 1H in vivo studies while no spectra have to be reconstructed, and no additional user interaction, prior knowledge, starting values, or model function are required. Phantom measurements and in vivo experiments on rat brain have been performed at 4.7 T to test the feasibility of the method for proton SI.

  6. Improvement of water saturation shift referencing by sequence and analysis optimization to enhance chemical exchange saturation transfer imaging.

    Science.gov (United States)

    Müller-Lutz, Anja; Matuschke, Felix; Schleich, Christoph; Wickrath, Frithjof; Boos, Johannes; Schmitt, Benjamin; Wittsack, Hans-Jörg

    2016-07-01

    To optimize B0-field inhomogeneity correction for chemical exchange saturation transfer (CEST) imaging by investigating different water saturation shift referencing (WASSR) Z-spectrum shapes and different frequency correction techniques. WASSR Z-spectra were simulated for different B1-fields and pulse durations (PD). Two parameter settings were used for further simulations and experiments (WASSR1: B1=0.1 μT, PD=50ms; WASSR2: B1=0.3 μT, PD=40ms). Four frequency correction techniques were investigated: 1) MinW: Minimum of the spline-interpolated WASSR-spectrum; 2) MSCF: maximum symmetry center frequency algorithm; 3) PMSCF: further development of MSCF algorithm; 4) BFit: fit with Bloch equations. Performance of frequency correction was assessed with Monte-Carlo simulations and in-vivo MR examinations in the brain and intervertebral disks. Different shapes of WASSR-Z-spectra were obtained by changing B1 and PD including spectra with one (1-Peak) or two (2-Peak) minima. WASSR1 resulted in 1-Peak WASSR-spectrum, whereas WASSR2 resulted in 2-Peak WASSR-spectrum. Both Monte-Carlo simulations and in-vivo MR examinations revealed highest accuracy of field-inhomogeneity correction with WASSR1 combined with PMSCF or BFit. Using a WASSR sequence, which results in a Z-spectrum with a single absorption peak, in combination with advanced postprocessing algorithms enables improved B0-field inhomogeneity correction for CEST imaging. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Making our data impactful: Working with researchers to meet diverse data needs in a rapidly shifting technological world.

    Science.gov (United States)

    Laney, C. M.

    2016-12-01

    Making data easily accessible and actionable is critical in our drive to understand ecological drivers and responses in our rapidly changing world. The National Ecological Observatory Network (NEON), operated by Battelle and sponsored by the National Science Foundation, is a continental-scale, long-term observation facility built specifically to meet such needs. By the end of construction at the end of 2017, NEON will be generating and synthesizing data from in situ instruments, field sampling, and airborne platforms covering 81 field sites across the U.S. A challenge of such observatories is not only to generate, quality-control, and synthesize enormous and high-resolution datasets, but to provide it freely to researchers in formats that are easy to understand and integrate with other datasets. Here, we present how NEON is preparing publication-ready data for ready reuse by a broad range of practitioners through numerous mechanisms: 1) developing a robust and intuitive data portal and public API, 2) collaborating with numerous partners to support and enrich standards to assure interoperability and reproducibility, and 3) providing training materials covering the key concepts and tools researchers may need to fully leverage NEON data. In addition, we will solicit feedback on NEON's current, in-design, and proposed data services and portal features in order to best serve the diverse research interests of a AGU's scientific community.

  8. Materials characterization of rapid thermal chemical vapor deposition of titanium disilicide

    Science.gov (United States)

    Gladden-Green, Dannellia Banay

    Technological advancements of novel processes and materials involving refractory metal silicides for ultra large scale integration is of paramount importance to the semiconductor industry. Scaling of devices to meet the demands for increased packing density and speed requires such novel processes and materials. Rapid thermal chemical vapor deposition (RTCVD) of titanium disilicide (TiSisb2) was investigated in an effort to meet some of the challenges of ultra large scale integration (ULSI) technology. Selective RTCVD of TiSisb2 offers an optimal technological vehicle for achieving contacts to ultra-shallow junctions. Of all of the metal silicides, TiSisb2 has the lowest resistivity and meets the microelectronics demands for a thermally stable contact. The research results presented in this dissertation explores the mechanisms of selective RTCVD of TiSisb2 in terms of thermodynamic trends and kinetic driving forces for nucleation and growth. The present research addresses the qualitative and quantitative parameters that affect the controlling mechanisms for nucleation and therefore the results provide significant data and theoretical insights into a state-of-the-art process. Just as the fundamental building block in understanding the kinetic constraints of a process lie in the realm of thermodynamic exploration, understanding the complex processes involved in RTCVD TiSisb2 begin with characterization of the mechanisms governing thin film nucleation. In this work, the early stages of growth are investigated as they offer insight into how process parameters are optimized to render desired silicide film properties. Equilibrium simulations have been used to model the CVD reaction with very good trend indicating accuracy. Empirical investigations of CVD TiSisb2 took place in a low-pressure rapid-thermal environment using the SiHsb4 + TiClsb4 gas system on silicon (100) substrates. Secondary ion mass spectroscopy (SIMS) has been used to qualify the benefits of vacuum and

  9. Microwave-assisted chemical insertion: a rapid technique for screening cathodes for Mg-ion batteries

    Energy Technology Data Exchange (ETDEWEB)

    Kaveevivitchai, Watchareeya; Huq, Ashfia; Manthiram, Arumugam

    2016-12-19

    We report an ultrafast microwave-assisted solvothermal method for chemical insertion of Mg2+ ions into host materials using magnesium acetate [Mg(CH3COO)2] as a metal-ion source and diethylene glycol (DEG) as a reducing agent. For instance, up to 3 Mg ions per formula unit of a microporous host framework Mo2.5+yVO9+z could be inserted in as little as 30 min at 170–195 °C in air. This process is superior to the traditional method which involves the use of organometallic reagents, such as di-n-butylmagnesium [(C4H9)2Mg] and magnesium bis(2,6-di-tert-butylphenoxide) [Mg-(O-2,6-But2C6H3)2], and requires an inert atmosphere with extremely long reaction times. Considering the lack of robust electrolytes for Mg-ion batteries, this facile approach can be readily used as a rapid screening technique to identify potential Mg-ion electrode hosts without the necessity of fabricating electrodes and assembling electrochemical cells. Due to the mild reaction conditions, the overall structure and morphology of the Mg-ion inserted products are maintained and the compounds can be used successfully as a cathode in Mg-ion batteries. The combined synchrotron X-ray and neutron diffraction Rietveld analysis reveals the structure of the Mg-inserted compounds and gives an insight into the interactions between the Mg ions and the open-tunnel host framework.

  10. Fully adiabatic 31P 2D-CSI with reduced chemical shift displacement error at 7 T--GOIA-1D-ISIS/2D-CSI.

    Science.gov (United States)

    Chmelík, M; Kukurová, I Just; Gruber, S; Krššák, M; Valkovič, L; Trattnig, S; Bogner, W

    2013-05-01

    A fully adiabatic phosphorus (31P) two-dimensional (2D) chemical shift spectroscopic imaging sequence with reduced chemical shift displacement error for 7 T, based on 1D-image-selected in vivo spectroscopy, combined with 2D-chemical shift spectroscopic imaging selection, was developed. Slice-selective excitation was achieved by a spatially selective broadband GOIA-W(16,4) inversion pulse with an interleaved subtraction scheme before nonselective adiabatic excitation, and followed by 2D phase encoding. The use of GOIA-W(16,4) pulses (bandwidth 4.3-21.6 kHz for 10-50 mm slices) reduced the chemical shift displacement error in the slice direction ∼1.5-7.7 fold, compared to conventional 2D-chemical shift spectroscopic imaging with Sinc3 selective pulses (2.8 kHz). This reduction was experimentally demonstrated with measurements of an MR spectroscopy localization phantom and with experimental evaluation of pulse profiles. In vivo experiments in clinically acceptable measurement times were demonstrated in the calf muscle (nominal voxel volume, 5.65 ml in 6 min 53 s), brain (10 ml, 6 min 32 s), and liver (8.33 ml, 8 min 14 s) of healthy volunteers at 7 T. High reproducibility was found in the calf muscle at 7 T. In combination with adiabatic excitation, this sequence is insensitive to the B1 inhomogeneities associated with surface coils. This sequence, which is termed GOIA-1D-ISIS/2D-CSI (goISICS), has the potential to be applied in both clinical research and in the clinical routine. Copyright © 2012 Wiley Periodicals, Inc.

  11. Broad target chemical screening approach used as tool for rapid assessment of groundwater quality

    NARCIS (Netherlands)

    ter Laak, T.L.; Puijker, L.M.; van Leerdam, J.A.; Raat, K.J.; Kolkman, A.; de Voogt, P.; van Wezel, A.P.

    2012-01-01

    The chemical water quality is often assessed by screening for a limited set of target chemicals. This ‘conventional’ target analysis approach inevitably misses chemicals present in the samples. In this study a ‘broad’ target screening approach for water quality assessment using high resolution and

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-12-15

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

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

    Science.gov (United States)

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

    2009-01-01

    Temperature and pH are two of the most important physiological parameters and are believed to be tightly regulated because they are intricately related to energy metabolism in living organisms. Temperature and/or pH data in mammalian brain are scarce, however, mainly due to lack of precise and non-invasive methods. At 11.7T, we demonstrate that a thulium-based macrocyclic complex infused through the blood stream can be used to obtain temperature and pH maps of rat brain in vivo by 1H chemical shift imaging (CSI) of the sensor itself in conjunction with a multi-parametric model that depends on several proton resonances of the sensor. Accuracies of temperature and pH determination with the thulium sensor – which has a predominantly extracellular presence – depend on stable signals during the course of the CSI experiment as well as redundancy for temperature and pH sensitivities contained within the observed signals. The thulium-based method compared well with other methods for temperature (1H magnetic resonance spectroscopy (MRS) of N-acetyl aspartate and water; copper-constantan thermocouple wire) and pH (31P MRS of inorganic phosphate and phosphocreatine) assessment, as established by in vitro and in vivo studies. In vitro studies in phantoms with two compartments of differing pH values observed under different ambient temperature conditions generated precise temperature and pH distribution maps. In vivo studies in α-chloralose anesthetized and renal-ligated rats revealed temperature (33–34 °C) and pH (7.3–7.4) distributions in the cerebral cortex which are in agreement with observations by other methods. These results demonstrate that the thulium sensor can be used to measure temperature and pH distributions in rat brain in vivo simultaneously and accurately with 1H CSI. PMID:19130468

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

    Energy Technology Data Exchange (ETDEWEB)

    Kueker, W.; Mehnert, F.; Mader, I.; Naegele, T. [Department of Neuroradiology, University of Tuebingen Medical School, Hoppe-Seyler-Str. 3, 72076, Tuebingen (Germany); Ruff, J. [Siemens Medical Solutions, Erlangen (Germany); Gaertner, S. [Department of Neurology, University of Tuebingen Medical School, Tuebingen (Germany)

    2004-06-01

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

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

    KAUST Repository

    Jang, Richard

    2011-01-01

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

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

    Science.gov (United States)

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

    2010-12-01

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

  17. Proton-detected 3D (15)N/(1)H/(1)H isotropic/anisotropic/isotropic chemical shift correlation solid-state NMR at 70kHz MAS.

    Science.gov (United States)

    Pandey, Manoj Kumar; Yarava, Jayasubba Reddy; Zhang, Rongchun; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2016-01-01

    Chemical shift anisotropy (CSA) tensors offer a wealth of information for structural and dynamics studies of a variety of chemical and biological systems. In particular, CSA of amide protons can provide piercing insights into hydrogen-bonding interactions that vary with the backbone conformation of a protein and dynamics. However, the narrow span of amide proton resonances makes it very difficult to measure (1)H CSAs of proteins even by using the recently proposed 2D (1)H/(1)H anisotropic/isotropic chemical shift (CSA/CS) correlation technique. Such difficulties due to overlapping proton resonances can in general be overcome by utilizing the broad span of isotropic chemical shifts of low-gamma nuclei like (15)N. In this context, we demonstrate a proton-detected 3D (15)N/(1)H/(1)H CS/CSA/CS correlation experiment at fast MAS frequency (70kHz) to measure (1)H CSA values of unresolved amide protons of N-acetyl-(15)N-l-valyl-(15)N-l-leucine (NAVL). Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Measurement of SDS Micelle-Peptide Association Using (1)H NMR Chemical Shift Analysis and Pulsed-Field Gradient NMR Spectroscopy.

    Science.gov (United States)

    Orfi, L; Lin, M; Larive, C K

    1998-04-01

    The binding of two simple tripeptides, glycyl-histidyl-glycine (GHG) and phenylalanyl-histidyl-phenylalanine (FHF) with SDS micelles was examined using (1)H NMR chemical shift analysis and self-diffusion coefficients measured with pulsed-field gradient NMR spectroscopy. The presence of GHG or FHF did not appear to significantly affect the critical micelle concentration (cmc) or the average size of the SDS micelles formed. The chemical shifts of several of the GHG resonances change as a function of SDS concentration, indicating an interaction between the peptide and the micelles. In addition, the concentration-dependent decrease observed for the GHG diffusion coefficients suggests association of the peptide with SDS micelles. The free and micelle-associated GHG are in fast exchange on both the (1)H chemical shift and diffusion time scales. The equilibrium constant for the binding of GHG to SDS micelles was determined from the analysis of the concentration dependence of the histidine C2 and C4 resonances to be 17 ± 5 and 24 ± 6 M(-)(1), respectively. The precision of the equilibrium constants obtained by analysis of the chemical shift data is limited by the small chemical shift changes observed. Analysis of the concentration dependence of the diffusion coefficients produced an equilibrium constant of 17 ± 1 M(-)(1). The more hydrophobic peptide, FHF is strongly associated with the SDS micelles. Because the fraction of free FHF is small in these solutions, it was not possible to determine a formation constant for the interaction of FHF with the SDS micelles by analysis of either the (1)H chemical shift or diffusion coefficient data. The cmc of SDS in 0.10 M Na(2)C(2)O(4) buffer was determined to be 5.4 ± 0.1 mM by analysis of the SDS diffusion coefficients in the absence of the peptides. The SDS cmc could also be extracted from the GHG and FHF diffusion coefficients measured as a function of the SDS concentration. The cmc determined from the GHG diffusion data, 5

  19. Solvent-induced chemical shifts of methoxyl nuclear resonance signals in chalcones by benzene and trifluoroacetic acid

    Science.gov (United States)

    Khurana, Shashi K.; Krishnamoorthy, V.; Parmar, Virinder S.

    The 1H NMR spectra of eight different methoxylated chalcones have separately been recorded, (1) in deuterated chloroform; (2) in a mixture (1:1) of deuterated chloroform and benzene; and (3) in a mixture of deuterated chloroform, benzene and trifluoroacetic acid (2:2:1) and the benzene induced and TFA induced shift values have been assigned to different methoxyl groups. These shift values can serve as a guide in determining the structures of natural or new chalcones. The steric, electronic and conformational factors are discussed to explain the shift values.

  20. Optofluidic refractive-index sensors employing bent waveguide structures for low-cost, rapid chemical and biomedical sensing.

    Science.gov (United States)

    Liu, I-Chen; Chen, Pin-Chuan; Chau, Lai-Kwan; Chang, Guo-En

    2018-01-08

    We propose and develop an intensity-detection-based refractive-index (RI) sensor for low-cost, rapid RI sensing. The sensor is composed of a polymer bent ridge waveguide (BRWG) structure on a low-cost glass substrate and is integrated with a microfluidic channel. Different-RI solutions flowing through the BRWG sensing region induce output optical power variations caused by optical bend losses, enabling simple and real-time RI detection. Additionally, the sensors are fabricated using rapid and cost-effective vacuum-less processes, attaining the low cost and high throughput required for mass production. A good RI solution of 5.31 10-4 × RIU-1 is achieved from the RI experiments. This study demonstrates mass-producible and compact RI sensors for rapid and sensitive chemical analysis and biomedical sensing.

  1. The protein amide ¹H(N) chemical shift temperature coefficient reflects thermal expansion of the N-H···O=C hydrogen bond.

    Science.gov (United States)

    Hong, Jingbo; Jing, Qingqing; Yao, Lishan

    2013-01-01

    The protein amide (1)H(N) chemical shift temperature coefficient can be determined with high accuracy by recording spectra at different temperatures, but the physical mechanism responsible for this temperature dependence is not well understood. In this work, we find that this coefficient strongly correlates with the temperature coefficient of the through-hydrogen-bond coupling, (3h)J(NC'), based on NMR measurements of protein GB3. Parallel tempering molecular dynamics simulation suggests that the hydrogen bond distance variation at different temperatures/replicas is largely responsible for the (1)H(N) chemical shift temperature dependence, from which an empirical equation is proposed to predict the hydrogen bond thermal expansion coefficient, revealing responses of individual hydrogen bonds to temperature changes. Different expansion patterns have been observed for various networks formed by β strands.

  2. Rapid Electrochemical Detection and Identification of Microbiological and Chemical Contaminants for Manned Spaceflight Project

    Data.gov (United States)

    National Aeronautics and Space Administration — A great deal of effort has gone into the development of point-of-use methods to meet the challenge of rapid bacterial identification for both environmental...

  3. Chemical Probes of Rapid Estrogen Signaling in Breast Cancer Treatment and Chemoprevention

    National Research Council Canada - National Science Library

    Weatherman, Rose V

    2007-01-01

    .... Over the course of the project, we synthesized and tested approximately 15 new estrogen receptor modulators, some with novel activity in terms of both classic transcriptional and rapid response modulation...

  4. pH Dependent Spin State Population and 19F NMR Chemical Shift via Remote Ligand Protonation in an Iron(II) Complex (Postprint)

    Science.gov (United States)

    2017-12-11

    rare, and compounds that exhibit such behavior are unsuitable for most biological sensing applications due to pKa values far from biological pH12 or...advantages over the more commonly employed 1H MRS, most notably the absence of endogenous fluorine in living systems.14 Furthermore, the chemical...Indeed, diamagnetic 19F MRS pH probes with pKa values near 7 have been developed for in vivo applications , where a variation in 19F chemical shift of

  5. Design of a hyperpolarized (15)N NMR probe that induces a large chemical-shift change upon binding of calcium ions.

    Science.gov (United States)

    Hata, Ryunosuke; Nonaka, Hiroshi; Takakusagi, Yoichi; Ichikawa, Kazuhiro; Sando, Shinsuke

    2015-08-07

    Ca(2+) is a fundamental metal ion for physiological functioning. Therefore, molecular probes for Ca(2+) analysis are required. Recently, a hyperpolarized NMR probe has emerged as a promising tool. Here, we report a new design of a hyperpolarized NMR probe for Ca(2+), which showed a large chemical shift change upon binding to Ca(2+) and was applied for Ca(2+) sensing in a hyperpolarized state.

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

    DEFF Research Database (Denmark)

    Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek

    2016-01-01

    Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for non-relativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton and xenon dimers and free atoms. Relativistic correcti......Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for non-relativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton and xenon dimers and free atoms. Relativistic...... shieldings and chemical shifts are combined with non-relativistic CCSD(T) calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr and the AQZP basis set for Xe. For the dimers also zero-point vibrational corrections obtained at the CCSD......(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, zero-point vibrational and relativistic corrections for the shieldings and chemical shifts is analyzed....

  7. NMR and computational studies of the configurational properties of spirodioxyselenuranes. Are dynamic exchange processes or temperature-dependent chemical shifts involved?

    Science.gov (United States)

    Press, David J; McNeil, Nicole M R; Rauk, Arvi; Back, Thomas G

    2012-10-19

    Spirodioxyselenurane 4a and several substituted analogs revealed unexpected (1)H NMR behavior. The diastereotopic methylene hydrogens of 4a appeared as an AB quartet at low temperature that coalesced to a singlet upon warming to 267 K, suggesting a dynamic exchange process with a relatively low activation energy. However, DFT computational investigations indicated high activation energies for exchange via inversion through the selenium center and for various pseudorotation processes. Moreover, the NMR behavior was unaffected by the presence of water or acid catalysts, thereby ruling out reversible Se-O or benzylic C-O cleavage as possible stereomutation pathways. Remarkably, when 4a was heated beyond 342 K, the singlet was transformed into a new AB quartet. Further computations indicated that a temperature dependence of the chemical shifts of the diastereotopic protons results in convergence upon heating, followed by crossover and divergence at still higher temperatures. The NMR behavior is therefore not due to dynamic exchange processes, but rather to temperature dependence of the chemical shifts of the diastereotopic hydrogens, which are coincidentally equivalent at intermediate temperatures. These results suggest the general need for caution in ascribing the coalescence of variable-temperature NMR signals of diastereotopic protons to dynamic exchange processes that could instead be due to temperature-dependent chemical shifts and highlight the importance of corroborating postulated exchange processes through additional computations or experiments wherever possible.

  8. Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids.

    Science.gov (United States)

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

    2011-12-01

    Unravelling the complex correlation between chemical shifts of (13) C (α), (13) C (β), (13) C', (1) H (α), (15) N, (1) H ( N ) atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous empirical correlation scores which relate chemical shifts of (13) C (α), (13) C (β), (13) C', (1) H (α), (15) N, (1) H ( N ) atoms to secondary structures resulted in progresses toward assigning secondary structures of proteins. However, the physical-mathematical framework for these was elusive partly due to both the limited and orthogonal exploration of higher-dimensional chemical shifts of hetero-nucleus and the lack of physical-mathematical understanding underlying those correlation scores. Here we present a simple multi-dimensional hetero-nuclear chemical shift score function (MDHN-CSSF) which captures systematically the salient feature of such complex correlations without any references to a random coil state of proteins. We uncover the symmetry-breaking vector and its reliability order not only for distinguishing different secondary structures of proteins but also for capturing the delicate sensitivity interplayed among chemical shifts of (13) C (α), (13) C (β), (13) C', (1) H (α), (15) N, (1) H ( N ) atoms simultaneously, which then provides a straightforward framework toward assigning secondary structures of proteins. MDHN-CSSF could correctly assign secondary structures of training (validating) proteins with the favourable (comparable) Q3 scores in comparison with those from the previous correlation scores. MDHN-CSSF provides a simple and robust strategy for the systematic assignment of secondary structures of proteins and would facilitate the de novo determination of three-dimensional structures

  9. [3,3]-Sigmatropic shifts of N-allylhydrazones: quantum chemical comparison of concerted and radical cation pathways.

    Science.gov (United States)

    Siebert, Matthew R; Tantillo, Dean J

    2008-08-07

    N-Allylhydrazones are reported to undergo an elaborate [3,3]-sigmatropic shift/N2 extrusion sequence. Both concerted and radical cation pathways for the [3,3]-sigmatropic shift of several N-allylhydrazones were investigated using B3LYP/6-31+G(d,p) calculations. It was discovered that, assuming facile formation of the N-allylhydrazone radical cation, the rearrangement takes place through a series of low barrier steps energetically preferred to the concerted alternative available to neutral N-allylhydrazones. Subsequent N2 extrusions forming corresponding homoallyl radicals were found to be extremely facile.

  10. [Rapid detection of four antipertensive chemicals adulterated in traditional Chinese medicine for hypertension using TLC-SERS].

    Science.gov (United States)

    Zhu, Qing-Xia; Cao, Yong-Bing; Cao, Ying-Ying; Lu, Feng

    2014-04-01

    A novel facile method for on-site detection of antipertensive chemicals (e. g. nicardipine hydrochloride, doxazosin mesylate, propranolol hydrochloride, and hydrochlorothiazide) adulterated in traditional Chinese medicine for hypertension using thin layer chromatography (TLC) combined with surface enhanced Raman spectroscopy (SERS) was reported in the present paper. Analytes and pharmaceutical matrices was separated by TLC, then SERS method was used to complete qualitative identification of trace substances on TLC plate. By optimizing colloidal silver concentration and developing solvent, as well as exploring the optimal limits of detection (LOD), the initially established TLC-SERS method was used to detect real hypertension Chinese pharmaceuticals. The results showed that this method had good specificity for the four chemicals and high sensitivity with a limit of detection as lower as to 0.005 microg. Finally, two of the ten antipertensive drugs were detected to be adulterated with chemicals. This simple and fast method can realize rapid detection of chemicals illegally for doping in antipertensive Chinese pharmaceuticals, and would have good prospects in on-site detection of chemicals for doping in Chinese pharmaceuticals.

  11. Rapid continuous chemical methods for studies of nuclei far from stability

    CERN Document Server

    Trautmann, N; Eriksen, D; Gaggeler, H; Greulich, N; Hickmann, U; Kaffrell, N; Skarnemark, G; Stender, E; Zendel, M

    1981-01-01

    Fast continuous separation methods accomplished by combining a gas-jet recoil-transport system with a variety of chemical systems are described. Procedures for the isolation of individual elements from fission product mixtures with the multistage solvent extraction facility SISAK are presented. Thermochromatography in connection with a gas-jet has been studied as a technique for on-line separation of volatile fission halides. Based on chemical reactions in a gas-jet system itself separation procedures for tellurium, selenium and germanium from fission products have been worked out. All the continuous chemical methods can be performed within a few seconds. The application of such procedures to the investigation of nuclides far from the line of beta -stability is illustrated by a few examples. (16 refs).

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

    Energy Technology Data Exchange (ETDEWEB)

    Wu Zhengrong; Delaglio, Frank [National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Chemical Physics (United States); Tjandra, Nico [National Heart, Lung and Blood Institute, National Cancer Institute, National Institutes of Health, Laboratory of Biophysical Chemistry (United States); Zhurkin, Victor B. [National Cancer Institute, National Institutes of Health, Laboratory of Experimental and Computational Biology (United States); Bax, Ad [National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Chemical Physics (United States)

    2003-08-15

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

  13. Developing, Applying, and Evaluating Models for Rapid Screening of Chemical Exposures

    DEFF Research Database (Denmark)

    Arnot, J.; Shin, H.; Ernstoff, Alexi

    2015-01-01

    provides an introduction to underlying principles of some models used for exposure- and risk-based HTS for chemical prioritization for human health, including tools used in the ExpoDat project (USEtox, RAIDAR, CalTox) and other initiatives (SHEDS-HT). Case study examples of HTS include(i) model...

  14. Rapid Production of a Porous Cellulose Acetate Membrane for Water Filtration Using Readily Available Chemicals

    Science.gov (United States)

    Kaiser, Adrian; Stark, Wendelin J.; Grass, Robert N.

    2017-01-01

    A chemistry laboratory experiment using everyday items and readily available chemicals is described to introduce advanced high school students and undergraduate college students to porous polymer membranes. In a three-step manufacturing process, a membrane is produced at room temperature. The filtration principle of the membrane is then…

  15. Towards an integrated biosensor array for simultaneous and rapid multi-analysis of endocrine disrupting chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Scognamiglio, Viviana, E-mail: viviana.scognamiglio@mlib.ic.cnr.it [IC-CNR Istituto di Cristallografia, AdR1 Dipartimento Agroalimentare - Via Salaria Km 29.3 00015, Rome (Italy); Pezzotti, Italo; Pezzotti, Gianni; Cano, Juan; Manfredonia, Ivano [Biosensor S.r.l. - Via degli Olmetti 44 00060 Formello, Rome (Italy); Buonasera, Katia [IC-CNR Istituto di Cristallografia, AdR1 Dipartimento Agroalimentare - Via Salaria Km 29.3 00015, Rome (Italy); Arduini, Fabiana; Moscone, Danila; Palleschi, Giuseppe [Universita di Roma Tor Vergata, Dipartimento di Scienze e Tecnologie Chimiche - Via della Ricerca Scientifica 00133, Rome (Italy); Giardi, Maria Teresa [IC-CNR Istituto di Cristallografia, AdR1 Dipartimento Agroalimentare - Via Salaria Km 29.3 00015, Rome (Italy)

    2012-11-02

    Highlights: Black-Right-Pointing-Pointer A multitask biosensor for the detection of endocrine disrupting chemicals is proposed. Black-Right-Pointing-Pointer The sensing system employ an array of biological recognition elements. Black-Right-Pointing-Pointer Amperometric and optical transduction methods are provided in an integrated biosensor together with flow control systems. Black-Right-Pointing-Pointer The biosensing device results in an integrated, automatic and portable system for environmental and agrifood application. - Abstract: In this paper we propose the construction and application of a portable multi-purpose biosensor array for the simultaneous detection of a wide range of endocrine disruptor chemicals (EDCs), based on the recognition operated by various enzymes and microorganisms. The developed biosensor combines both electrochemical and optical transduction systems, in order to increase the number of chemical species which can be monitored. Considering to the maximum residue level (MRL) of contaminants established by the European Commission, the biosensor system was able to detect most of the chemicals analysed with very high sensitivity. In particular, atrazine and diuron were detected with a limit of detection of 0.5 nM, with an RSD% less than 5%; paraoxon and chlorpyrifos were revealed with a detection of 5 {mu}M and 4.5 {mu}M, respectively, with an RSD% less than 6%; catechol and bisphenol A were identified with a limit of detection of 1 {mu}M and 35 {mu}M respectively, with an RSD% less than 5%.

  16. Rapid Species-level Identification of Salvias by Chemometric Processing of Ambient Ionisation Mass Spectrometry-derived Chemical Profiles.

    Science.gov (United States)

    Giffen, Justine E; Lesiak, Ashton D; Dane, A John; Cody, Robert B; Musah, Rabi A

    2017-01-01

    The Salvia genus contains numerous economically important plants that have horticultural, culinary and nutraceutical uses. They are often similar in appearance, making species determination difficult. Species identification of dried Salvia products is also challenging since distinguishing plant morphological features are no longer present. The development of a simple high-throughput method of analysis of fresh and dried Salvia leaves that would permit rapid species-level identification and detection of diagnostic biomarkers. Plant leaves were analysed in their native form by DART-MS without the need for any sample preparation steps. This furnished chemical fingerprints characteristic of each species. In the same experiment, in-source collision-induced dissociation was used to identify biomarkers. Biomarker presence was also independently confirmed by GC-MS. Chemometric processing of DART-MS profiles was performed by kernel discriminant analysis (KDA) and soft independent modelling of class analogy (SIMCA) to classify the fingerprints according to species. The approach was successful despite the occurrence of diurnal cycle and plant-age related chemical profile variations within species. In a single rapid experiment, the presence of essential oil biomarkers such as 3-carene, α-pinene, β-pinene, β-thujone, β-caryophyllene, camphor and borneol could be confirmed. The method was applied to rapid identification and differentiation of Salvia apiana, S. dominica, S. elegans, S. officinalis, S. farinacea and S. patens. Species-level identification of Salvia plant material could be accomplished by chemometric processing of DART-HRMS-derived chemical profiles of both fresh and dried Salvia material. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  17. Effects of Irritant Chemicals on Aedes aegypti Resting Behavior: Is There a Simple Shift to Untreated “Safe Sites”?

    Science.gov (United States)

    Manda, Hortance; Arce, Luana M.; Foggie, Tarra; Shah, Pankhil; Grieco, John P.; Achee, Nicole L.

    2011-01-01

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

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

    Science.gov (United States)

    Manda, Hortance; Arce, Luana M; Foggie, Tarra; Shah, Pankhil; Grieco, John P; Achee, Nicole L

    2011-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Hortance Manda

    2011-07-01

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

  20. Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

    Science.gov (United States)

    Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

    2017-03-07

    The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

  1. Hydrogen Atomic Positions of O–H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with 1H-NMR Chemical Shifts and X-ray Diffraction Methods

    Directory of Open Access Journals (Sweden)

    Michael G. Siskos

    2017-03-01

    Full Text Available The exact knowledge of hydrogen atomic positions of O–H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i density functional theory (DFT calculations after a structure has been determined by X-ray from single crystals or from powders; (ii 1H-NMR chemical shifts as constraints in DFT calculations, and (iii use of root-mean-square deviation between experimentally determined and DFT calculated 1H-NMR chemical shifts considering the great sensitivity of 1H-NMR shielding to hydrogen bonding properties.

  2. A rapidly deployable chemical sensing network for the real-time monitoring of toxic airborne contaminant releases in urban environments

    Science.gov (United States)

    Lepley, Jason J.; Lloyd, David R.

    2010-04-01

    We present findings of the DYCE project, which addresses the needs of military and blue light responders in providing a rapid, reliable on-scene analysis of the dispersion of toxic airborne contaminants following their malicious or accidental release into a rural, urban or industrial environment. We describe the development of a small network of ad-hoc deployable chemical and meteorological sensors capable of identifying and locating the source of the contaminant release, as well as monitoring and estimating the dispersion characteristics of the plume. We further present deployment planning methodologies to optimize the data gathering mission given a constrained asset base.

  3. Rapid yeast DNA extraction by boiling and freeze-thawing without using chemical reagents and DNA purification

    Directory of Open Access Journals (Sweden)

    Gildo Almeida da Silva

    2012-04-01

    Full Text Available The purpose of this work was to study a rapid yeast DNA extraction by boiling and freeze-thawing processes without using chemical reagents or any purification procedures, to obtain a high grade PCR-product. A specific DNA fragment of the 18S region of Dekkera bruxellensis and Saccharomyces cerevisiae was chosen. The described boiling and freeze-thawing protocols generated the PCR-grade product preparations and could be used to process many samples. The amplification of the fragments could be observed after 30 and 35 cycles. These processes of extraction without using any kind of chemical reagents, especial water, and purification procedures proved to be efficient, reproducible, simple, fast, and inexpensive.

  4. An improved technique for the rapid chemical characterisation of bacterial terpene cyclases.

    Science.gov (United States)

    Dickschat, Jeroen S; Pahirulzaman, Khomaizon A K; Rabe, Patrick; Klapschinski, Tim A

    2014-04-14

    A derivative of the pET28c(+) expression vector was constructed. It contains a yeast replication system (2μ origin of replication) and a yeast selectable marker (URA3), and can be used for gene cloning in yeast by efficient homologous recombination, and for heterologous expression in E. coli. The vector was used for the expression and chemical characterisation of three bacterial terpene cyclases. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. A rapid chemical method for lysing Arabidopsis cells for protein analysis

    OpenAIRE

    Takano Tetsuo; Liu Shenkui; Tsugama Daisuke

    2011-01-01

    Abstract Background Protein extraction is a frequent procedure in biological research. For preparation of plant cell extracts, plant materials usually have to be ground and homogenized to physically break the robust cell wall, but this step is laborious and time-consuming when a large number of samples are handled at once. Results We developed a chemical method for lysing Arabidopsis cells without grinding. In this method, plants are boiled for just 10 minutes in a solution containing a Ca2+ ...

  6. Rapid and highly efficient growth of graphene on copper by chemical vapor deposition of ethanol

    Energy Technology Data Exchange (ETDEWEB)

    Lisi, Nicola, E-mail: nicola.lisi@enea.it [ENEA, Materials Technology Unit, Surface Technology Laboratory, Casaccia Research Centre, Via Anguillarese 301, 00123 Rome (Italy); Buonocore, Francesco; Dikonimos, Theodoros; Leoni, Enrico [ENEA, Materials Technology Unit, Surface Technology Laboratory, Casaccia Research Centre, Via Anguillarese 301, 00123 Rome (Italy); Faggio, Giuliana; Messina, Giacomo [Dipartimento di Ingegneria dell' Informazione, delle Infrastrutture e dell' Energia Sostenibile (DIIES), Università “Mediterranea” di Reggio Calabria, 89122 Reggio Calabria (Italy); Morandi, Vittorio; Ortolani, Luca [CNR-IMM Bologna, Via Gobetti 101, 40129 Bologna (Italy); Capasso, Andrea [ENEA, Materials Technology Unit, Surface Technology Laboratory, Casaccia Research Centre, Via Anguillarese 301, 00123 Rome (Italy)

    2014-11-28

    The growth of graphene by chemical vapor deposition on metal foils is a promising technique to deliver large-area films with high electron mobility. Nowadays, the chemical vapor deposition of hydrocarbons on copper is the most investigated synthesis method, although many other carbon precursors and metal substrates are used too. Among these, ethanol is a safe and inexpensive precursor that seems to offer favorable synthesis kinetics. We explored the growth of graphene on copper from ethanol, focusing on processes of short duration (up to one min). We investigated the produced films by electron microscopy, Raman and X-ray photoemission spectroscopy. A graphene film with high crystalline quality was found to cover the entire copper catalyst substrate in just 20 s, making ethanol appear as a more efficient carbon feedstock than methane and other commonly used precursors. - Highlights: • Graphene films were grown by fast chemical vapor deposition of ethanol on copper. • High-temperature/short-time growth produced highly crystalline graphene. • The copper substrate was entirely covered by a graphene film in just 20 s. • Addition of H{sub 2} had a negligible effect on the crystalline quality.

  7. Theoretical study on conformation dynamics of three-station molecular shuttle in different environments and its influence on NMR chemical shifts and binding interactions.

    Science.gov (United States)

    Liu, Pingying; Li, Wei; Liu, Li; Wang, Leyong; Ma, Jing

    2014-10-02

    Microscopic information on conformational flexibility and macrocycle-thread binding interactions is helpful in rational design of novel multistation molecular shuttles with interesting topology and functions. Molecular dynamics (MD) was applied to simulate conformational changes of thread and macrocycle of a three-station molecular shuttle in different chemical environments (vacuum, CD3CN-CDCl3 solution, and crystal). In contrast with the highly distorted thread conformation in the gas phase and nonpolar CDCl3 solution, the solvated thread in CD3CN-CDCl3 (1:1) mix solvents exhibited a relatively rigid structure. Experimental observations of preferential binding at the protonated dibenzylammonium group (station I) were rationalized by quantum chemical calculations of macrocycle-thread binding energies at three different stations. The orthogonality of site-specific binding interactions at three different stations was also revealed by the nearly constant binding energy obtained at each specific recognition center with the replacement of different neighboring groups and terminal stoppers on the thread. Conformational flexibility has little effect on NMR signals of binding sites, but for some protons that are close to the solvent molecules in the first solvent shell, their chemical shifts are sensitive to the local electrostatic environment caused by nearby solvents. In crystal, π stacking induced evident upfield shifts of NMR signals in comparison with the isolated monomer.

  8. ZnO nanorod arrays prepared by chemical bath deposition combined with rapid thermal annealing: structural, photoluminescence and field emission characteristics

    Science.gov (United States)

    Chen, Hung-Wei; Yang, Hsi-Wen; He, Hsin-Min; Lee, Yi-Mu

    2016-01-01

    ZnO nanorod arrays were prepared by low temperature chemical bath deposition (CBD) combined with rapid thermal annealing (RTA) under different ambient conditions. The structure and morphology of the synthesized ZnO have been characterized by field-emission scanning electron microscopy (FESEM) and x-ray diffraction (XRD). The obtained ZnO samples are highly crystalline with a hexagonal wurtzite phase and also display well-aligned array structure. A pronounced effect on increased nanorod length was found for the RTA-treated ZnO as compared to the as-grown ZnO. Analysis of XRD indicates that the (0 0 2) feature peak of the as-grown ZnO was shifted towards a lower angle as compared to the peaks of RTA-treated ZnO samples due to the reduction of tensile strain along the c-axis by RTA. Photoluminescence (PL) studies reveal that the ZnO nanorod arrays receiving RTA in an O2 environment have the sharpest UV emission band and greatest intensity ratio of near band-edge emission (NBE) to deep level emission (DLE). Additionally, the effects of RTA on the field emission properties were evaluated. The results demonstrate that RTA an O2 environment can lower the turn-on field and improve the field enhancement factor. The stability of the field emission current was also tested for 4 h.

  9. Solid state 13C NMR of unlabeled phosphatidylcholine bilayers: spectral assignments and measurement of carbon-phosphorus dipolar couplings and 13C chemical shift anisotropies.

    Science.gov (United States)

    Sanders, C R

    1993-01-01

    The direct measurement of 13C chemical shift anisotropies (CSA) and 31P-13C dipolar splitting in random dispersions of unlabeled L alpha-phase phosphatidylcholine (PC) has traditionally been difficult because of extreme spectral boradening due to anisotropy. In this study, mixtures of dimyristoyl phosphatidylcholine (DMPC) with three different detergents known to promote the magnetic orientation of DMPC were employed to eliminate the powder-pattern nature of signals without totally averaging out spectral anisotropy. The detergents utilized were CHAPSO, Triton X-100, and dihexanoylphosphatidylcholine (DHPC). Using such mixtures, many of the individual 13C resonances from DMPC were resolved and a number of 13C-31P dipolar couplings were evident. In addition, differing line widths were observed for the components of some dipolar doublets, suggestive of dipolar/chemical shift anisotropy (CSA) relaxation interference effects. Oriented sample resonance assignments were made by varying the CHAPSO or DHPC to DMPC ratio to systematically scale overall bilayer order towards the isotropic limit. In this manner, peaks could be identified based upon extrapolation to their isotropic positions, for which assignments have previously been made (Lee, C.W.B., and R.G. Griffin. 1989. Biophys. J. 55:355-358; Forbes, J., J. Bowers, X. Shan, L. Moran, E. Oldfield, and M.A. Moscarello. 1988. J. Chem. Soc., Faraday, Trans. 1 84:3821-3849). It was observed that the plots of CSA or dipolar coupling versus overall bilayer order obtained from DHPC and CHAPSO titrations were linear. Estimates of the intrinsic dipolar couplings and chemical shift anisotropies for pure DMPC bilayers were made by extrapolating shifts and couplings from the detergent titrations to zero detergent. Both detergent titrations led to similar "intrinsic" CSAs and dipolar couplings. Results extracted from an oriented Triton-DMPC mixture also led to similar estimates for the detergent-free DMPC shifts and couplings. The

  10. Rapid stress system drives chemical transfer of fear from sender to receiver.

    Directory of Open Access Journals (Sweden)

    Jasper H B de Groot

    Full Text Available Humans can register another person's fear not only with their eyes and ears, but also with their nose. Previous research has demonstrated that exposure to body odors from fearful individuals elicited implicit fear in others. The odor of fearful individuals appears to have a distinctive signature that can be produced relatively rapidly, driven by a physiological mechanism that has remained unexplored in earlier research. The apocrine sweat glands in the armpit that are responsible for chemosignal production contain receptors for adrenalin. We therefore expected that the release of adrenalin through activation of the rapid stress response system (i.e., the sympathetic-adrenal medullary system is what drives the release of fear sweat, as opposed to activation of the slower stress response system (i.e., hypothalamus-pituitary-adrenal axis. To test this assumption, sweat was sampled while eight participants prepared for a speech. Participants had higher heart rates and produced more armpit sweat in the fast stress condition, compared to baseline and the slow stress condition. Importantly, exposure to sweat from participants in the fast stress condition induced in receivers (N = 31 a simulacrum of the state of the sender, evidenced by the emergence of a fearful facial expression (facial electromyography and vigilant behavior (i.e., faster classification of emotional facial expressions.

  11. Chemically synthesized PbS Nano particulate thin films for a rapid NO2 gas sensor

    Directory of Open Access Journals (Sweden)

    Burungale Vishal V.

    2016-03-01

    Full Text Available Rapid NO2 gas sensor has been developed based on PbS nanoparticulate thin films synthesized by Successive Ionic Layer Adsorption and Reaction (SILAR method at different precursor concentrations. The structural and morphological properties were investigated by means of X-ray diffraction and field emission scanning electron microscope. NO2 gas sensing properties of PbS thin films deposited at different concentrations were tested. PbS film with 0.25 M precursor concentration showed the highest sensitivity. In order to optimize the operating temperature, the sensitivity of the sensor to 50 ppm NO2 gas was measured at different operating temperatures, from 50 to 200 °C. The gas sensitivity increased with an increase in operating temperature and achieved the maximum value at 150 °C, followed by a decrease in sensitivity with further increase of the operating temperature. The sensitivity was about 35 % for 50 ppm NO2 at 150 °C with rapid response time of 6 s. T90 and T10 recovery time was 97 s at this gas concentration.

  12. Quantitative analysis of lipid droplet fusion: inefficient steady state fusion but rapid stimulation by chemical fusogens.

    Directory of Open Access Journals (Sweden)

    Samantha Murphy

    Full Text Available Lipid droplets (LDs are dynamic cytoplasmic organelles containing neutral lipids and bounded by a phospholipid monolayer. Previous studies have suggested that LDs can undergo constitutive homotypic fusion, a process linked to the inhibitory effects of fatty acids on glucose transporter trafficking. Using strict quantitative criteria for LD fusion together with refined light microscopic methods and real-time analysis, we now show that LDs in diverse cell types show low constitutive fusogenic activity under normal growth conditions. To investigate the possible modulation of LD fusion, we screened for agents that can trigger fusion. A number of pharmacological agents caused homotypic fusion of lipid droplets in a variety of cell types. This provided a novel cell system to study rapid regulated fusion between homotypic phospholipid monolayers. LD fusion involved an initial step in which the two adjacent membranes became continuous (<10 s, followed by the slower merging (100 s of the neutral lipid cores to produce a single spherical LD. These fusion events were accompanied by changes to the LD surface organization. Measurements of LDs undergoing homotypic fusion showed that fused LDs maintained their initial volume, with a corresponding decrease in surface area suggesting rapid removal of membrane from the fused LD. This study provides estimates for the level of constitutive LD fusion in cells and questions the role of LD fusion in vivo. In addition, it highlights the extent of LD restructuring which occurs when homotypic LD fusion is triggered in a variety of cell types.

  13. Quantitative analysis of lipid droplet fusion: inefficient steady state fusion but rapid stimulation by chemical fusogens.

    Science.gov (United States)

    Murphy, Samantha; Martin, Sally; Parton, Robert G

    2010-12-23

    Lipid droplets (LDs) are dynamic cytoplasmic organelles containing neutral lipids and bounded by a phospholipid monolayer. Previous studies have suggested that LDs can undergo constitutive homotypic fusion, a process linked to the inhibitory effects of fatty acids on glucose transporter trafficking. Using strict quantitative criteria for LD fusion together with refined light microscopic methods and real-time analysis, we now show that LDs in diverse cell types show low constitutive fusogenic activity under normal growth conditions. To investigate the possible modulation of LD fusion, we screened for agents that can trigger fusion. A number of pharmacological agents caused homotypic fusion of lipid droplets in a variety of cell types. This provided a novel cell system to study rapid regulated fusion between homotypic phospholipid monolayers. LD fusion involved an initial step in which the two adjacent membranes became continuous (lipid cores to produce a single spherical LD. These fusion events were accompanied by changes to the LD surface organization. Measurements of LDs undergoing homotypic fusion showed that fused LDs maintained their initial volume, with a corresponding decrease in surface area suggesting rapid removal of membrane from the fused LD. This study provides estimates for the level of constitutive LD fusion in cells and questions the role of LD fusion in vivo. In addition, it highlights the extent of LD restructuring which occurs when homotypic LD fusion is triggered in a variety of cell types.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-15

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

  15. 1H NMR spectra. Part 30(+): 1H chemical shifts in amides and the magnetic anisotropy, electric field and steric effects of the amide group.

    Science.gov (United States)

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

    2013-03-01

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

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

    Science.gov (United States)

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

    2015-07-01

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

  17. Chemical Screening Method for the Rapid Identification of Microbial Sources of Marine Invertebrate-Associated Metabolites

    Directory of Open Access Journals (Sweden)

    Russell G. Kerr

    2011-03-01

    Full Text Available Marine invertebrates have proven to be a rich source of secondary metabolites. The growing recognition that marine microorganisms associated with invertebrate hosts are involved in the biosynthesis of secondary metabolites offers new alternatives for the discovery and development of marine natural products. However, the discovery of microorganisms producing secondary metabolites previously attributed to an invertebrate host poses a significant challenge. This study describes an efficient chemical screening method utilizing a 96-well plate-based bacterial cultivation strategy to identify and isolate microbial producers of marine invertebrate-associated metabolites.

  18. Rapid identification and quantitative analysis of chemical constituents of Gentiana veitchiorum by UHPLC-PDA-QTOF-MS

    Directory of Open Access Journals (Sweden)

    Shan Li

    Full Text Available ABSTRACT Gentiana veitchiorum Hemsl., Gentianaceae, a traditional Tibetan medicine, was used for the treatment of liver jaundice with damp-heat pathogen, as well as for headache and chronic pharyngitis. A rapid ultra-performance liquid chromatography, photodiode array detector, quadrupole time-of-flight mass spectrometry method was developed for the fast and accurate identification and quantification of the chemical constituents of G. veitchiorum. In fact, eighteen compounds were detected and identified on the basis of their mass spectra, fragment characteristics and comparison with published data. Especially, the MS fragmentation pathways of iridoid glycosides and flavone C-glycosides were illustrated. Five compounds among them were quantified by UHPLC-PDA, including swertiamarin, gentiopicroside, sweroside, isoorientin, and isovitexin. The proposed method was then validated based on the analyses of linearity, accuracy, precision, and recovery. The overall recoveries for the five analytes ranged from 96.54% to 100.81%, with RSD from 1.05% to 1.82%. In addition, ten batches of G. veitchiorum from different areas were also analyzed. The developed method was rapid and reliable for both identification and quantification of the chemical constituents of G. veitchiorum, especially for simultaneous qualitative and quantitative analysis of iridoid glycosides and flavone C-glycosides.

  19. Other compounds isolated from Simira glaziovii and the {sup 1}H and {sup 13}C NMR chemical shift assignments of new 1-epi-castanopsol

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Marcelo F. de; Vieira, Ivo J. Curcino [Universidade Federal Rural do Rio de Janeiro, Seropedica, RJ (Brazil). Dept. de Quimica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Centro de Ciencias Tecnologicas. Lab. de Ciencias Quimicas; Carvalho, Mario G. de, E-mail: mgeraldo@ufrrj.br [Universidade Federal do Rio de Janeiro (NPPN/UFRJ), RJ (Brazil). Centro de Ciencias da Saude. Nucleo de Pesquisa em Produtos Naturais

    2012-07-01

    A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D {sup 1}H, {sup 13}C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of {sup 1}H and {sup 13}C NMR chemical shift assignments. (author)

  20. Effectiveness of different chemical agents in rapid decontamination of gutta-percha cones

    Directory of Open Access Journals (Sweden)

    Cardoso Celso Luíz

    2000-01-01

    Full Text Available The effectiveness of seven disinfectant compounds used in dentistry for a rapid decontamination of 32 gutta-percha cones adhered with Staphylococcus aureus, Enterococcus faecalis, Escherichia coli strains or Bacillus subtilis spores was compared. Cones were treated with 2% glutaraldehyde, 1% sodium hypochlorite, 70% ethyl alcohol, 1% and 0.3% iodine alcohol, 2% chlorhexidine, 6% hydrogen peroxide, and 10% polyvinylpyrrolidone-iodine, for 1, 5, 10, and 15 minutes. After treatment, each cone was transferred to thioglycollate broth and incubated at 37ºC for 7 days. The products were bactericidal after 1 to 5 minutes and, with exception of ethyl alcohol and iodine-alcohol, sporicidal after 1 to 15 minutes of exposure. Results suggest that chlorhexidine, sodium hypochlorite, polyvinylpyrrolidone-iodine, hydrogen peroxide, and glutaraldehyde were the most effective products in the decontamination of gutta-percha cones.

  1. The evolution of structural and chemical heterogeneity during rapid solidification at gas atomization

    Science.gov (United States)

    Golod, V. M.; Sufiiarov, V. Sh

    2017-04-01

    Gas atomization is a high-performance process for manufacturing superfine metal powders. Formation of the powder particles takes place primarily through the fragmentation of alloy melt flow with high-pressure inert gas, which leads to the formation of non-uniform sized micron-scale particles and subsequent their rapid solidification due to heat exchange with gas environment. The article presents results of computer modeling of crystallization process, simulation and experimental studies of the cellular-dendrite structure formation and microsegregation in different size particles. It presents results of adaptation of the approach for local nonequilibrium solidification to conditions of crystallization at gas atomization, detected border values of the particle size at which it is possible a manifestation of diffusionless crystallization.

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

    DEFF Research Database (Denmark)

    Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof

    2013-01-01

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

  3. The Sign of Nuclear Magnetic Resonance Chemical Shift Difference as a Determinant of the Origin of Binding Selectivity: Elucidation of the Position Dependence of Phosphorylation in Ligands Binding to Scribble PDZ1.

    Science.gov (United States)

    Sundell, Gustav N; Vögeli, Beat; Ivarsson, Ylva; Chi, Celestine N

    2018-01-09

    The use of nuclear magnetic resonance chemical shift perturbation to monitor changes taking place around the binding site of a ligand-protein interaction is a routine and widely applied methodology in the field of protein biochemistry. Shifts are often acquired by titrating various concentrations of ligand to a fixed concentration of the receptor and may serve the purpose, among others, of determining affinity constants, locating binding surfaces, or differentiating between binding mechanisms. Shifts are quantified by the so-called combined chemical shift difference. Although the directionality of shift changes is often used for detailed analysis of specific cases, the approach has not been adapted in standard chemical shift monitoring. This is surprising as it would not require additional effort. Here, we demonstrate the importance of the sign of the chemical shift difference induced by ligand-protein interaction. We analyze the sign of the 15N/1H shift changes of the PDZ1 domain of Scribble upon interaction with two pairs of phosphorylated and unphosphorylated peptides. We find that detailed differences in the molecular basis of this PDZ-ligand interaction can be obtained from our analysis to which the classical method of combined chemical shift perturbation analysis is insensitive. In addition, we find a correlation between affinity and millisecond motions. Application of the methodology to Cyclophilin a, a cis-trans isomerase, reveals molecular details of peptide recognition. We consider our directionality vector chemical shift analysis as a method of choice when distinguishing the molecular origin of binding specificities of a class of similar ligands, which is often done in drug discovery.

  4. Time-domain quanification of amplitude, chemical shift, apparent relaxation time T2, and phase by wavelet-transform analysis. Application to biomedical magnetic resonance spectroscopy.

    Science.gov (United States)

    Serrai, H; Senhadji, L; de Certaines, J D; Coatrieux, J L

    1997-01-01

    The wavelet-transform method is used to quantify the magnetic resonance spectroscopy (MRS) parameters: chemical shift, apparent relaxation time T2, resonance amplitude, and phase. Wavelet transformation is a time-frequency representation which separates each component from the FID, then successively quantifies it and subtracts it from the raw signal. Two iterative procedures have been developed. They have been combined with a nonlinear regression analysis method and tested on both simulated and real sets of biomedical MRS data selected with respect to the main problems usually encountered in quantifying biomedical MRS, specifically "chemical noise," resulting from overlapping resonances, and baseline distortion. The results indicate that the wavelet-transform method can provide efficient and accurate quantification of MRS data.

  5. 13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

    DEFF Research Database (Denmark)

    Nyrop Albers, Christian; Hansen, Poul Erik

    2010-01-01

    Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical...

  6. A tree-based method for the rapid screening of chemical fingerprints

    Directory of Open Access Journals (Sweden)

    Pedersen Christian NS

    2010-01-01

    Full Text Available Abstract Background The fingerprint of a molecule is a bitstring based on its structure, constructed such that structurally similar molecules will have similar fingerprints. Molecular fingerprints can be used in an initial phase of drug development for identifying novel drug candidates by screening large databases for molecules with fingerprints similar to a query fingerprint. Results In this paper, we present a method which efficiently finds all fingerprints in a database with Tanimoto coefficient to the query fingerprint above a user defined threshold. The method is based on two novel data structures for rapid screening of large databases: the kD grid and the Multibit tree. The kD grid is based on splitting the fingerprints into k shorter bitstrings and utilising these to compute bounds on the similarity of the complete bitstrings. The Multibit tree uses hierarchical clustering and similarity within each cluster to compute similar bounds. We have implemented our method and tested it on a large real-world data set. Our experiments show that our method yields approximately a three-fold speed-up over previous methods. Conclusions Using the novel kD grid and Multibit tree significantly reduce the time needed for searching databases of fingerprints. This will allow researchers to (1 perform more searches than previously possible and (2 to easily search large databases.

  7. Proof of ion-pair structures in ammonium-based protic ionic liquids using combined NMR and DFT/PCM-based chemical shift calculations.

    Science.gov (United States)

    Lozynski, M; Pernak, J; Gdaniec, Z; Gorska, B; Béguin, F

    2017-09-20

    The self-assembly of triethylammonium bis(trifluoromethylsulfonyl)imide, i.e. [(C 2 H 5 ) 3 NH][TFSI], in chloroform and aqueous solutions has been investigated using 1 H NMR spectroscopy and computational (DFT/PCM prediction) methods. We have examined a number of ion pairs formed between the [(C 2 H 5 ) 3 NH] + cation with different conformations of alkyl substituents as well as various dispositions of the multi-site [TFSI] - anion. Based on the agreement between the calculated (DFT) and observed 1 H NMR chemical shifts, [(C 2 H 5 ) 3 NH][TFSI] in chloroform formed lipophilic complexes with effective N + -HN or N + -HO hydrogen bonding, whereas hydrophilic complexes with C α -HO and C α -HF hydrogen bonding are found in aqueous solutions. This study provides a new insight into the self-aggregation of ammonium PILs incorporating the widely used [TFSI] - anion and demonstrates the importance of solvent effects on chemical shifts. The simulations with explicit and implicit dielectric continuum solvents are found to be the most realistic method, yielding a representative ensemble of structures.

  8. Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori

    Energy Technology Data Exchange (ETDEWEB)

    Gardiennet, Carole [Université de Lorraine, CNRS, CRM2, UMR 7036 (France); Wiegand, Thomas [ETH Zurich, Physical Chemistry (Switzerland); Bazin, Alexandre [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Cadalbert, Riccardo [ETH Zurich, Physical Chemistry (Switzerland); Kunert, Britta; Lacabanne, Denis [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Gutsche, Irina [Université Grenoble Alpes, Institut de Biologie Structurale (IBS), CNRS, IBS, CEA, IBS (France); Terradot, Laurent, E-mail: l.terradot@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France)

    2016-03-15

    We here investigate the interactions between the DnaB helicase and the C-terminal domain of the corresponding DnaG primase of Helicobacter pylori using solid-state NMR. The difficult crystallization of this 387 kDa complex, where the two proteins interact in a six to three ratio, is circumvented by simple co-sedimentation of the two proteins directly into the MAS-NMR rotor. While the amount of information that can be extracted from such a large protein is still limited, we can assign a number of amino-acid residues experiencing significant chemical-shift perturbations upon helicase-primase complex formation. The location of these residues is used as a guide to model the interaction interface between the two proteins in the complex. Chemical-shift perturbations also reveal changes at the interaction interfaces of the hexameric HpDnaB assembly on HpDnaG binding. A structural model of the complex that explains the experimental findings is obtained.

  9. UPLC-QTOF-MS with chemical profiling approach for rapidly evaluating chemical consistency between traditional and dispensing granule decoctions of Tao-Hong-Si-Wu decoction

    Directory of Open Access Journals (Sweden)

    Shang Erxin

    2012-11-01

    Full Text Available Abstract Background In the present study, chemical consistency between traditional and dispensing granule decoctions of Tao-Hong-Si-Wu decoction was rapidly evaluated by UPLC-QTOF-MS coupled with the MarkerLynx software. Two different kinds of decoctions, namely traditional decoction: water extract of mixed six constituent herbs of Tao-Hong-Si-Wu decoction, and dispensing granules decoction: mixed water extract of each individual herbs of Tao-Hong-Si-Wu decoction, were prepared. Results Chemical difference was found between traditional and dispensing granule decoctions, and albiflorin, paeoniflorin, gallic acid, amygdalin, and hydroxysafflor yellow A were identified as the significantly changed components during decocting Tao-Hong-Si-Wu decoction. All the peaks of mass spectrum from Tao-Hong-Si-Wu decoction and each herb were extracted and integration by using QuanLynx™. And the optimized data was used for linear regression analysis. The contribution of each herb in Tao-Hong-Si-Wu decoction, and the optimal compatibility proportion of dispensing granule decoction were derived from the linear regression equation. Conclusions The optimal dosage proportionality of Tao-Hong-Si-Wu dispensing granule decoction was obtained as 2.5:0.2:1:0.5:0.6:0.1 (DG : CX : BS : SD : TR : HH, which guided better clinic application of Tao-Hong-Si-Wu decoction as dispensing granule decoctions usage, and it also provided some experimental data to reveal the compatibility rule of the relative TCM formulae.

  10. A Rapid Deposition of Fluorine Doped Zinc Oxide Using the Atmospheric Pressure Chemical Vapour Deposition Method

    Science.gov (United States)

    Najafi, Navid; Rozati, S. M.

    2018-03-01

    Fluorine-doped zinc oxide (FZO) (ZnO:F) thin films were manufactured by atmospheric pressure chemical vapor deposition (APCVD) on glass substrates using zinc acetate dihydrate [C4H6O4Zn·2H2O, ZnAc] and ammonium fluoride (NH4F) as the source of fluorine with deposition duration of only 120 s for each sample. The effects of different amounts of fluorine as the dopant on the structural, electrical and optical properties of FZO thin films were investigated. The results show a polycrystalline structure at higher temperatures compared to amorphous structure at lower temperatures. The x-ray diffraction patterns of the polycrystalline films were identified as a hexagonal wurtzite structure of zinc oxide (ZnO) with the (002) preferred orientation. Also, the sheet resistance decreased from 17.8 MΩ/□ to 28.9 KΩ/□ for temperatures 325°C to 450°C, respectively. In order to further decrease the sheet resistance of the undoped ZnO thin films, fluorine was added using NH4F as the precursor, and again a drastic change in sheet resistance of only 17.7 Ω/□ was obtained. Based on the field emission scanning electron microscopy images, the fluorine concentration in CVD source is an important factor affecting the grain size and modifies electrical parameters. Ultraviolet-visible measurements revealed reduction of transparency of the layers with increasing fluorine as the dopant.

  11. A Rapid Deposition of Fluorine Doped Zinc Oxide Using the Atmospheric Pressure Chemical Vapour Deposition Method

    Science.gov (United States)

    Najafi, Navid; Rozati, S. M.

    2017-12-01

    Fluorine-doped zinc oxide (FZO) (ZnO:F) thin films were manufactured by atmospheric pressure chemical vapor deposition (APCVD) on glass substrates using zinc acetate dihydrate [C4H6O4Zn·2H2O, ZnAc] and ammonium fluoride (NH4F) as the source of fluorine with deposition duration of only 120 s for each sample. The effects of different amounts of fluorine as the dopant on the structural, electrical and optical properties of FZO thin films were investigated. The results show a polycrystalline structure at higher temperatures compared to amorphous structure at lower temperatures. The x-ray diffraction patterns of the polycrystalline films were identified as a hexagonal wurtzite structure of zinc oxide (ZnO) with the (002) preferred orientation. Also, the sheet resistance decreased from 17.8 MΩ/□ to 28.9 KΩ/□ for temperatures 325°C to 450°C, respectively. In order to further decrease the sheet resistance of the undoped ZnO thin films, fluorine was added using NH4F as the precursor, and again a drastic change in sheet resistance of only 17.7 Ω/□ was obtained. Based on the field emission scanning electron microscopy images, the fluorine concentration in CVD source is an important factor affecting the grain size and modifies electrical parameters. Ultraviolet-visible measurements revealed reduction of transparency of the layers with increasing fluorine as the dopant.

  12. Rapid determination of the chemical oxygen demand of water using a thermal biosensor.

    Science.gov (United States)

    Yao, Na; Wang, Jinqi; Zhou, Yikai

    2014-06-06

    In this paper we describe a thermal biosensor with a flow injection analysis system for the determination of the chemical oxygen demand (COD) of water samples. Glucose solutions of different concentrations and actual water samples were tested, and their COD values were determined by measuring the heat generated when the samples passed through a column containing periodic acid. The biosensor exhibited a large linear range (5 to 3000 mg/L) and a low detection limit (1.84 mg/L). It could tolerate the presence of chloride ions in concentrations of 0.015 M without requiring a masking agent. The sensor was successfully used for detecting the COD values of actual samples. The COD values of water samples from various sources were correlated with those obtained by the standard dichromate method; the linear regression coefficient was found to be 0.996. The sensor is environmentally friendly, economical, and highly stable, and exhibits good reproducibility and accuracy. In addition, its response time is short, and there is no danger of hazardous emissions or external contamination. Finally, the samples to be tested do not have to be pretreated. These results suggest that the biosensor is suitable for the continuous monitoring of the COD values of actual wastewater samples.

  13. Thermal and chemical diffusion in the rapid solidification of binary alloys

    Science.gov (United States)

    Conti

    2000-01-01

    Solidification of binary alloys is characterized by the necessity to reject away from the advancing front two conserved quantities: the latent heat released at the solid-liquid interface and the solute atoms that cannot be accommodated in the solid phase. As thermal diffusion is much faster than chemical diffusion, the latter is generally assumed to be the rate limiting mechanism for the process, and the problem is addressed through the isothermal approximation. In the present paper we use the phase-field model to study the planar growth of a solid germ, nucleated in its undercooled melt. We focus on the effects of a noninstantaneous thermal relaxation. The steady growth predicted at large supersaturation in the isothermal limit is prevented. Depending on the value of the Lewis number the growth rate is limited by either mass or heat diffusion; in the latter case we observe a sharp transition between two different regimes, in which originates a nonmonotonic time dependence of the interface temperature. The effects of this transition reflect in the composition of the solidified alloy.

  14. Rapid screening of N-oxides of chemical warfare agents degradation products by ESI-tandem mass spectrometry.

    Science.gov (United States)

    Sridhar, L; Karthikraj, R; Lakshmi, V V S; Raju, N Prasada; Prabhakar, S

    2014-08-01

    Rapid detection and identification of chemical warfare agents and related precursors/degradation products in various environmental matrices is of paramount importance for verification of standards set by the chemical weapons convention (CWC). Nitrogen mustards, N,N-dialkylaminoethyl-2-chlorides, N,N-dialkylaminoethanols, N-alkyldiethanolamines, and triethanolamine, which are listed CWC scheduled chemicals, are prone to undergo N-oxidation in environmental matrices or during decontamination process. Thus, screening of the oxidized products of these compounds is also an important task in the verification process because the presence of these products reveals alleged use of nitrogen mustards or precursors of VX compounds. The N-oxides of aminoethanols and aminoethylchlorides easily produce [M + H](+) ions under electrospray ionization conditions, and their collision-induced dissociation spectra include a specific neutral loss of 48 u (OH + CH2OH) and 66 u (OH + CH2Cl), respectively. Based on this specific fragmentation, a rapid screening method was developed for screening of the N-oxides by applying neutral loss scan technique. The method was validated and the applicability of the method was demonstrated by analyzing positive and negative samples. The method was useful in the detection of N-oxides of aminoethanols and aminoethylchlorides in environmental matrices at trace levels (LOD, up to 500 ppb), even in the presence of complex masking agents, without the use of time-consuming sample preparation methods and chromatographic steps. This method is advantageous for the off-site verification program and also for participation in official proficiency tests conducted by the Organization for the Prohibition of Chemical Weapons (OPCW), the Netherlands. The structure of N-oxides can be confirmed by the MS/MS experiments on the detected peaks. A liquid chromatography-mass spectrometry (LC-MS) method was developed for the separation of isomeric N-oxides of aminoethanols and

  15. Rapid monitoring of mercury in air from an organic chemical factory in China using a portable mercury analyzer.

    Science.gov (United States)

    Yasutake, Akira; Cheng, Jin Ping; Kiyono, Masako; Uraguchi, Shimpei; Liu, Xiaojie; Miura, Kyoko; Yasuda, Yoshiaki; Mashyanov, Nikolay

    2011-01-01

    A chemical factory, using a production technology of acetaldehyde with mercury catalysis, was located southeast of Qingzhen City in Guizhou Province, China. Previous research showed heavy mercury pollution through an extensive downstream area. A current investigation of the mercury distribution in ambient air, soils, and plants suggests that mobile mercury species in soils created elevated mercury concentrations in ambient air and vegetation. Mercury concentrations of up to 600 ng/m(3) in air over the contaminated area provided evidence of the mercury transformation to volatile Hg(0). Mercury analysis of soil and plant samples demonstrated that the mercury concentrations in soil with vaporized and plant-absorbable forms were higher in the southern area, which was closer to the factory. Our results suggest that air monitoring using a portable mercury analyzer can be a convenient and useful method for the rapid detection and mapping of mercury pollution in advanced field surveys.

  16. Rapid Monitoring of Mercury in Air from an Organic Chemical Factory in China Using a Portable Mercury Analyzer

    Directory of Open Access Journals (Sweden)

    Akira Yasutake

    2011-01-01

    Full Text Available A chemical factory, using a production technology of acetaldehyde with mercury catalysis, was located southeast of Qingzhen City in Guizhou Province, China. Previous research showed heavy mercury pollution through an extensive downstream area. A current investigation of the mercury distribution in ambient air, soils, and plants suggests that mobile mercury species in soils created elevated mercury concentrations in ambient air and vegetation. Mercury concentrations of up to 600 ng/m3 in air over the contaminated area provided evidence of the mercury transformation to volatile Hg(0. Mercury analysis of soil and plant samples demonstrated that the mercury concentrations in soil with vaporized and plant-absorbable forms were higher in the southern area, which was closer to the factory. Our results suggest that air monitoring using a portable mercury analyzer can be a convenient and useful method for the rapid detection and mapping of mercury pollution in advanced field surveys.

  17. Combination of Cooling Curve and Micro-Chemical Phase Analysis of Rapidly Quenched Magnesium AM60B Alloy

    Science.gov (United States)

    Marchwica, P. C.; Gesing, A. J.; Sokolowski, J. H.; Blawert, C.; Jekl, J.; Berkmortel, R.

    Macro test samples of magnesium alloy AM60B were melted and quenched at maximum instantaneous cooling rates ranging from -5°C/s to -500°C/s and the resultant cooling curves were analyzed. Characteristic reactions on these curves corresponding to formation of individual phases were identified with the aid of literature data as well as metallographic and micro-chemical analysis. The results indicate that these phases, their size and location in the micro structure, their chemistry and their relative proportions all change in response to the increase in the cooling rate. These rapid cooling rates are typical of real industrial solidification processes such as die casting. These findings can be used to improve future computer models of casting solidification processes for magnesium and for other alloys.

  18. Rapid characterization of chemical compounds in liquid and solid states using thermal desorption electrospray ionization mass spectrometry.

    Science.gov (United States)

    Huang, Min-Zong; Zhou, Chi-Chang; Liu, De-Lin; Jhang, Siou-Sian; Cheng, Sy-Chyi; Shiea, Jentaie

    2013-10-01

    Rapid characterization of thermally stable chemical compounds in solid or liquid states is achieved through thermal desorption electrospray ionization mass spectrometry (TD-ESI/MS). A feature of this technique is that sampling, desorption, ionization, and mass spectrometric detection are four separate events with respect to time and location. A metal probe was used to sample analytes in their solid or liquid states. The probe was then inserted in a preheated oven to thermally desorb the analytes on the probe. The desorbed analytes were carried by a nitrogen gas stream into an ESI plume, where analyte ions were formed via interactions with charged solvent species generated in the ESI plume. The analyte ions were subsequently detected by a mass analyzer attached to the TD-ESI source. Quantification of acetaminophen in aqueous solutions using TD-ESI/MS was also performed in which a linear response for acetaminophen was obtained between 25 and 500 ppb (R(2) = 0.9978). The standard deviation for a reproducibility test for ten liquid samples was 9.6%. Since sample preparation for TD-ESI/MS is unnecessary, a typical analysis can be completed in less than 10 s. Analytes such as the active ingredients in over-the-counter drugs were rapidly characterized regardless of the different physical properties of said drugs, which included liquid eye drops, viscous cold syrup solution, ointment cream, and a drug tablet. This approach was also used to detect trace chemical compounds in illicit drugs and explosives, in which samples were obtained from the surfaces of a cell phone, piece of luggage made from hard plastic, business card, and wooden desk.

  19. Rapidly developed squamous cell carcinoma after laser therapy used to treat chemical burn wound: a case report.

    Science.gov (United States)

    Cho, Hyung-Rok; Kwon, Soon-Sung; Chung, Seum; Kie, Jeong-Hae

    2015-02-07

    In chronic wounds, especially burn scars, malignant tumors can arise. However, it is rare for a subacute burn injury to change to a malignant lesion within one month. Moreover, a case of squamous cell carcinoma arising from HeNe laser therapy after a chemical burn has never been reported. In this report, we examine a rare case of squamous cell carcinoma arising from HeNe laser therapy after a chemical burn. Because pathologic investigations were made from the first operation, both early detection of the squamous cell carcinoma and consideration of the HeNe laser therapy as a risk factor for the skin cancer were possible. The cancer was completely removed and reconstruction of the defect was successfully achieved in a timely manner. Although there has as yet been no reported case of squamous cell carcinoma induced by laser therapy, it is important for clinicians to recognize both the possibility of laser-induced cancer and the rapid change of cancer, so they can provide appropriate and timely treatment.

  20. Rapid chemical decontamination of infectious CJD and scrapie particles parallels treatments known to disrupt microbes and biofilms

    Science.gov (United States)

    Botsios, Sotirios; Tittman, Sarah; Manuelidis, Laura

    2015-01-01

    Neurodegenerative human CJD and sheep scrapie are diseases caused by several different transmissible encephalopathy (TSE) agents. These infectious agents provoke innate immune responses in the brain, including late-onset abnormal prion protein (PrP-res) amyloid. Agent particles that lack detectable PrP sequences by deep proteomic analysis are highly infectious. Yet these agents, and their unusual resistance to denaturation, are often evaluated by PrP amyloid disruption. To reexamine the intrinsic resistance of TSE agents to denaturation, a paradigm for less resistant viruses and microbes, we developed a rapid and reproducible high yield agent isolation procedure from cultured cells that minimized PrP amyloid and other cellular proteins. Monotypic neuronal GT1 cells infected with the FU-CJD or 22L scrapie agents do not have complex brain changes that can camouflage infectious particles and prevent their disruption, and there are only 2 reports on infectious titers of any human CJD strain treated with chemical denaturants. Infectious titers of both CJD and scrapie were reduced by >4 logs with Thiourea-urea, a treatment not previously tested. A mere 5 min exposure to 4M GdnHCl at 22°C reduced infectivity by >5 logs. Infectious 22L particles were significantly more sensitive to denaturation than FU-CJD particles. A protocol using sonication with these chemical treatments may effectively decontaminate complicated instruments, such as duodenoscopes that harbor additional virulent microbes and biofilms associated with recent iatrogenic infections. PMID:26556670

  1. Chemical potential shift and gap-state formation in SrTiO{sub 3−δ} revealed by photoemission spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Pal, Prabir, E-mail: palp@nplindia.org; Kumar, Pramod; Aswin, V.; Dogra, Anjana; Joshi, Amish G. [CSIR-National Physical Laboratory, Dr. K. S. Krishnan Road, New Delhi 110012 (India)

    2014-08-07

    In this study, we report on investigations of the electronic structure of SrTiO{sub 3} annealed at temperature ranging between 550 and 840 °C in an ultrahigh vacuum. Annealing induced oxygen vacancies (O{sub vac}) impart considerable changes in the electronic structure of SrTiO{sub 3}. Using core-level photoemission spectroscopy, we have studied the chemical potential shift (Δμ) as a function of annealing temperature. The result shows that the chemical potential monotonously increases with electron doping in SrTiO{sub 3−δ}. The monotonous increase of the chemical potential rules out the existence of electronic phase separation in the sample. Using valence band photoemission, we have demonstrated the formation of a low density of states at the near Fermi level electronic spectrum of SrTiO{sub 3−δ}. The gap-states were observed by spectral weight transfer over a large energy scale of the stoichiometric band gap of SrTiO{sub 3} system leading finally to an insulator-metal transition. We have interpreted our results from the point of structural distortions induced by oxygen vacancies.

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

    Energy Technology Data Exchange (ETDEWEB)

    Herbst, Christian

    2010-04-27

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

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

    DEFF Research Database (Denmark)

    Steinmann, Casper; Bratholm, Lars Andersen; Olsen, Jógvan Magnus Haugaard

    2017-01-01

    Full-protein nuclear magnetic resonance (NMR) shielding constants based on ab initio calculations are desirable, because they can assist in elucidating protein structures from NMR experiments. In this work, we present NMR shielding constants computed using a new automated fragmentation (J. Phys....... Chem. B 2009, 113, 10380–10388) approach in the framework of polarizable embedding density functional theory. We extend our previous work to give both basis set recommendations and comment on how large the quantum mechanical region should be to successfully compute 13C NMR shielding constants...... that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we...

  4. Characterization of adrenal lesions using chemical shift MRI: comparison between 1.5 Tesla and two echo time pair selection at 3.0 Tesla MRI.

    Science.gov (United States)

    Nakamura, Shinichi; Namimoto, Tomohiro; Morita, Kosuke; Utsunomiya, Daisuke; Oda, Seitaro; Nakaura, Takeshi; Hirai, Toshinori; Yamashita, Yasuyuki

    2012-01-01

    To compare chemical shift MRI obtained at 1.5 Tesla (T) and two pairs of echo time (TE) in-phase and opposed-phase 3.0T MRI to assess their usefulness for the differentiation between adrenal adenomas and non-adenomas. We evaluated 91 adrenal masses (75 adenomas, 16 non-adenomas) in 85 patients. The MR imaging parameters were: T1-dual-gradient-echo(GRE) [echo times (TEs) = 1.1/2.3 ms (first-echo-pair) or 3.5/4.6 ms (second-echo-pair)] at 3.0T, and T1-dual-GRE (TEs = 2.4/4.8 ms) at 1.5T. Scans were quantitatively assessed for the signal intensity (SI) index, calculated as [(SIin-phase-SIopposed-phase)/(SIin-phase)] × 100(%). To test for differences between adenomas and non-adenomas, we performed quantitative analysis and analysis of variance. For all images, the SI index differed significantly between adenomas and non-adenomas. The sensitivity /specificity of SI index at the first-echo-pair of 3.0T was 100%/ 100%, that of 95.6%/ 100% at the second-echo-pair of 3.0T, and 91.7%/ 88.9% at 1.5T, respectively. At intra-individual comparisons, the SI indices obtained with the second-echo-pair at 3.0T were significantly lower than on the first-echo-pair at 3.0T and 1.5T. Chemical shift MRI at 3.0T provides more accurate differentiation between adenomas and non-adenomas than at 1.5T. The SI index of the first-echo-pair at 3.0T is the most reliable evaluation method for differentiating adrenal adenomas from non-adenomas. Copyright © 2011 Wiley Periodicals, Inc.

  5. Chemical shift MR imaging in the lumbar vertebra: the effect of field strength, scanner vendors and flip angles in repeatability of signal intensity index measurement.

    Science.gov (United States)

    Xiao, Zebin; Li, Jian; Li, Chengqi; Zhang, Yuyang; She, Dejun; Cao, Dairong

    2016-11-25

    To evaluate the reproducibility of signal intensity index (SII) measurements with MRI systems from different vendors and with different field strengths, and to test the effectiveness of flip angle. Thirty-two healthy volunteers (mean age 35.3 ± 9.3 years) were enrolled in this ethics committee-approved study. Chemical shift MR imaging was performed on 1.5- and 3.0-T MR systems from three vendors. Two independent observers measured SII values in five lumbar segments. Inter- and intraobserver agreement was assessed using the interclass correlation coefficients (ICCs). Differences of mean SII values between different field strengths and MR vendors as well as flip angles were compared by using repeated-measures analysis of variance. Differences of mean SII values between different flip angles were also compared by using paired-sample t test. Inter- and intra-observer correlation coefficients showed good agreement (all ICC > 0.75) when measuring SII values at different MR systems (ICCs ranging from 0.896 to 0.983) and flip angles (ICCs ranging from 0.824 to 0.983). There were no significant differences in mean SII values measured by different MR vendors with different field strengths (all p > 0.05 ranging from 0.337 to 0.824). The differences in the mean SII between the four different flip angles were statistically significant (all p measurement using chemical shift MR imaging may be comparable between different MR systems. Also high flip angles showed better stability to quantitate lumbar fat content.

  6. ¹H, ¹⁵N, and ¹³C backbone chemical shift assignment of titin domains A59-A60 and A60 alone.

    Science.gov (United States)

    Czajlik, András; Thompson, Gary S; Khan, Ghulam N; Kalverda, Arnout P; Homans, Steve W; Trinick, John

    2014-10-01

    The giant protein titin is the third most abundant protein of vertebrate striated muscle. The titin molecule is >1 μm long and spans half the sarcomere, from the Z-disk to the M-line, and has important roles in sarcomere assembly, elasticity and intracellular signaling. In the A-band of the sarcomere titin is attached to the thick filaments and mainly consists immunoglobulin-like and fibronectin type III-like domains. These are mostly arranged in long-range patterns or 'super-repeats'. The large super-repeats each contain 11 domains and are repeated 11 times, thus forming nearly half the titin molecule. Through interactions with myosin and C-protein, they are involved in thick filament assembly. The importance of titin in muscle assembly is highlighted by the effect of mutations in the A-band portion, which are the commonest cause of dilated cardiomyopathy, affecting ~1 in 250 (Herman et al. in N Engl J Med 366:619-628, 2012). Here we report backbone (15)N, (13)C and (1)H chemical shift and (13)Cβ assignments for the A59-A60 domain tandem from the titin A59-A69 large super-repeat, completed using triple resonance NMR. Since, some regions of the backbone remained unassigned in A60 domain of the complete A59-A60 tandem, a construct containing a single A60 domain, A60sd, was also studied using the same methods. Considerably improved assignment coverage was achieved using A60sd due to its lower mass and improved molecular tumbling rate; these assignments also allowed the analysis of inter-domain interactions using chemical shift mapping against A59-A60.

  7. Shifts in soil chemical properties and bacterial communities responding to biotransformed dry olive residue used as organic amendment.

    Science.gov (United States)

    Siles, José A; Cajthaml, Tomas; Hernández, Paola; Pérez-Mendoza, Daniel; García-Romera, Inmaculada; Sampedro, Inmaculada

    2015-07-01

    Dry olive residue (DOR) is a waste product derived from olive oil extraction and has been proposed as an organic amendment. However, it has been demonstrated that a pre-treatment, such as its transformation by saprophytic fungi, is required before DOR soil application. A greenhouse experiment was designed where 0 and 50 g kg(-1) of raw DOR (DOR), Coriolopsis floccosa-transformed DOR (CORDOR) and Fusarium oxysporum-transformed DOR (FUSDOR) were added to soil. Analyses of the soil chemical properties as well as the structure and relative abundance of bacterial and actinobacterial communities were conducted after 0, 30 and 60 days following amendment. The different amendments produced a slight decrease in soil pH and significant increases in carbon fractions, C/N ratios, phenols and K, with these increases being more significant after DOR application. Quantitative PCR assays of the 16S rRNA gene and PLFA analyses showed that all amendments favoured bacterial growth at 30 and 60 days, although actinobacterial proliferation was more evident after CORDOR and FUSDOR application at 60 days. Bacterial and actinobacterial DGGE multivariate analyses showed that the amendments produced structural changes in both communities, especially after 60 days of amendment. PLFA data analysis identified changes in soil microbial communities according to the amendment considered, with FUSDOR and CORDOR being less disruptive than DOR. Finally, integrated analysis of all data monitored in the present study enabled us to conclude that the greatest impact on soil properties was caused by DOR at 30 days and that soil showed some degree of resilience after this time.

  8. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database.

    Science.gov (United States)

    Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L; Markley, John L; Akutsu, Hideo; Fujiwara, Toshimichi

    2012-08-01

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including (1)H, (13)C and (15)N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001-2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

  9. QM AND AB INITIO INVESTIGATION ON THE HYDROGEN BONDING, NMR CHEMICAL SHIFTS AND SOLVENT EFFECTS ON THE DPPE

    Directory of Open Access Journals (Sweden)

    M. Monajjemi

    2010-06-01

    Full Text Available The hydrogen bonding effects that were produced from interaction of membrane lipid dipalmitoylphosphatidyl-ethanolamine (DPPE with 1-5 water molecules, has been theoretically  investigated through the quantum mechanical calculations at the Hartree-Fock level of theory and the 3-21G, 6-31G and 6-31G* basis sets with the computational package of Gaussian 98. According to the obtained results of the structural optimization of the isolated DPPE in the gas phase, we can see the evidences of interactions in the head group of this macromolecule (from the molecular point of view we have a proton transfer from the ammonium group to the phosphate oxygen of zwitterionic form. As we know that the hydrogen bonding of DPPE with water molecules which have surrounded its head group plays an important role in the permeability of DPPE. So, in order to understand the microscopic physico-chemical nature of this subject we have analyzed bond and torsion angles of DPPE before and after added water molecules.  In this paper we have theoretically studied the complexes DPPE with water molecules which have surrounded its head group. As mentioned before, this theoretically study has been done through Hartree-Fock level of theory by using simple basis sets. Theoretical data shows that the interaction of head group of DPPE with water molecules causes some changes in the geometry of DPPE which were explained by the contribution of zwitterionic form of DPPE macromolecule, and finally hydrated DPPE becomes stable complex. Comparison between theoretical and experimental geometry data of DPPE macromolecule shows that the calculation at the HF/3-21 level of theory produces results which they are in better agreement with the experimental data. Moreover the hydrogen bonding effects on the NMR shielding tensor of selected atoms in the hydrated complexes of DPPE were reported. The ";Gauge Including Atomic Orbitals"; (GIAO approaches within the SCF-Hartree-Fock approximation have

  10. Rapid, Efficient and Versatile Strategies for Functionally Sophisticated Polymers and Nanoparticles: Degradable Polyphosphoesters and Anisotropic Distribution of Chemical Functionalities

    Science.gov (United States)

    Zhang, Shiyi

    conjugate by densely attaching the polyphosphoester block with azide-functionalized Paclitaxel by azide-alkyne Huisgen cycloaddition. This Paclitaxel drug conjugate provides a powerful platform for combinational cancer therapy and bioimaging due to its ultra-high Paclitaxel loading (> 65 wt%), high water solubility (>6.2 mg/mL for PTX) and easy functionalization. Another polyphosphoester-based nanoparticle system has been developed by a programmable process for the rapid and facile preparation of a family of nanoparticles with different surface charges and functionalities. The non-ionic, anionic, cationic and zwitterionic nanoparticles with hydrodynamic diameters between 13 nm to 21 nm and great size uniformity could be rapidly prepared from small molecules in 6 h or 2 days. The anionic and zwitterionic nanoparticles were designed to load silver ions to treat pulmonary infections, while the cationic nanoparticles are being applied to regulate lung injuries by serving as a degradable iNOS inhibitor conjugates. In addition, a direct synthesis of acid-labile polyphosphoramidate by organobase-catalyzed ring-opening polymerization and an improved two-step preparation of polyphosphoester ionomer by acid-assisted cleavage of phosphoramidate bonds on polyphosphoramidate were developed. Polyphosphoramidate and polyphosphoester ionomers may be applied to many applications, due to their unique chemical and physical properties.

  11. Rapid identification of regulated organic chemical compounds in toys using ambient ionization and a miniature mass spectrometry system.

    Science.gov (United States)

    Guo, Xiangyu; Bai, Hua; Lv, Yueguang; Xi, Guangcheng; Li, Junfang; Ma, Xiaoxiao; Ren, Yue; Ouyang, Zheng; Ma, Qiang

    2018-04-01

    Rapid, on-site analysis was achieved through significantly simplified operation procedures for a wide variety of toy samples (crayon, temporary tattoo sticker, finger paint, modeling clay, and bubble solution) using a miniature mass spectrometry system with ambient ionization capability. The labor-intensive analytical protocols involving sample workup and chemical separation, traditionally required for MS-based analysis, were replaced by direct sampling analysis using ambient ionization methods. A Mini β ion trap miniature mass spectrometer was coupled with versatile ambient ionization methods, e.g. paper spray, extraction spray and slug-flow microextraction nanoESI for direct identification of prohibited colorants, carcinogenic primary aromatic amines, allergenic fragrances, preservatives and plasticizers from raw toy samples. The use of paper substrates coated with Co 3 O 4 nanoparticles allowed a great increase in sensitivity for paper spray. Limits of detection as low as 5μgkg -1 were obtained for target analytes. The methods being developed based on the integration of ambient ionization with miniature mass spectrometer represent alternatives to current in-lab MS analysis operation, and would enable fast, outside-the-lab screening of toy products to ensure children's safety and health. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. SiC/Si heterojunction diodes fabricated by self-selective and by blanket rapid thermal chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Yih, P.H.; Li, J.P.; Steckl, A.J. (Univ. of Cincinnati, OH (United States). Dept. of Electrical and Computer Engineering)

    1994-03-01

    SiC/Si heterojunction diodes have been fabricated by two different rapid thermal chemical vapor deposition (RTCVD) processes: a localized self-selective growth and blanket growth. The self-selective growth of crystalline cubic ([beta]) SiC was obtained by propane carbonization of the Si substrate in regions unprotected by an SiO[sub 2] layer, producing planar diodes. Mesa diodes were fabricated using the blanket growth of polycrystalline [beta]-SiC produced by the decomposition of methylsilane (CH[sub 3]SiH[sub 3]). The SiC/Si heterojunction diodes show good rectifying properties for both device structures. Reverse breakdown voltage of 50 V was obtained with the self-selective SiC/Si diode. The mesa diodes exhibited even higher breakdown voltages (V[sub br]) of 150 V and excellent ideality factors of 1.06 at 25 C. The high V[sub br] and good forward rectifying characteristics indicate that the SiC/Si heterojunction diode represents a promising approach for the fabrication of wide-gap emitter SiC/Si heterojunction bipolar transistors.

  13. Towards rapid nanoscale chemical analysis using tip-enhanced Raman spectroscopy with Ag-coated dielectric tips.

    Science.gov (United States)

    Yeo, Boon-Siang; Schmid, Thomas; Zhang, Weihua; Zenobi, Renato

    2007-04-01

    The influence of dielectric substrates on the Raman scattering activities of Ag overlayers has been investigated. Materials with low refractive indices, such as SiO(2), SiO(x) and AlF(3), were found to provide suitable supporting platforms for Ag films to give strong surface-enhanced Raman scattering for dye molecules when illuminated at 488 nm. This finding was then extended to tip-enhanced Raman scattering (TERS). Huge enhancements of 70-80x, corresponding to net enhancements of >10(4), were observed for brilliant cresyl blue test analyte when Ag-coated tips made from or precoated with low refractive index materials were applied. The yield of fabricated tips that significantly enhance the Raman signals was found to be close to 100%. These findings provide crucial steps towards the use of TERS as a robust technique for rapid chemical imaging with nanometer spatial resolution. Figure Silver-coated dielectric tips for tip-enhanced Raman scattering (TERS) are capable of more than 10,000-fold enhancement.

  14. Electronic structure, molecular electrostatic potential, and NMR chemical shifts in cucurbit[n]urils (n = 5-8), ferrocene, and their complexes.

    Science.gov (United States)

    Pinjari, Rahul V; Gejji, Shridhar P

    2008-12-11

    Electronic structure and molecular electrostatic potential (MESP) in ferrocene (FC), cucurbit[n]urils (CB[n]) with n = 5-8, and their host-guest complexes are obtained within the framework of density functional theory. MESP topography that is employed to gauge the dimensions of the CB[n] cavity estimates that the cavity height increases from 7.25 to 7.70 A along CB[n] homologue series, whereas the diameter of the CB[8] (8.57 A) cavity is larger than twice that of CB[5] (3.91 A). MESP investigations reveal deeper minima near ureido oxygens in CB[5] along with large electron-rich regions at its portal. A lateral interaction of the guest FC with hydrophilic exterior of the CB[n] portal and its encapsulation within hydrophobic cavity of the host are analyzed. The present calculations suggest that CB[5] does not yield stable complexes in either case. FC interacts laterally with CB[6], and inclusion of the guest occurs, both parallel as well as perpendicular to the CB[n] axis, in the cavity of higher homologue. Self-consistent reaction field studies indicate that, in the presence of water as a solvent, encapsulation of FC in parallel fashion is favored within CB[7] and CB[8] cavities. NMR chemical shifts (delta(H)) of CB[n] protons remain practically unchanged with an increase in the cavity size; however, they are influenced significantly by water. The spectra thus obtained in aqueous solution agree with those observed experimentally. The delta(H) values in FC-CB[n] complexes indicate deshielding of FC protons directed toward portals, while those pointing toward nitrogens exhibit up-shifts in the spectra.

  15. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts.

    Science.gov (United States)

    Doyle, Colleen M; Rumfeldt, Jessica A; Broom, Helen R; Sekhar, Ashok; Kay, Lewis E; Meiering, Elizabeth M

    2016-03-08

    The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.

  16. Determination of the Tautomeric Equilibria of Pyridoyl Benzoyl -Diketones in the Liquid and Solid State through the use of Deuterium Isotope Effects on 1H and 13C NMR Chemical Shifts and Spin Coupling Constants

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Borisov, Eugeny V.; Lindon, John C.

    2015-01-01

    , in the solution state the 2-bond and 3-bond J(1H–13C) coupling constants have been used to confirm the equilibrium positions. The isotope effects due to deuteriation at the OH position are shown to be superior to chemical shift in determination of equilibrium positions of these almost symmetrical -pyridoyl......-benzoyl methanes. The assignments of the NMR spectra are supported by calculations of the chemical shifts at the DFT level. The equilibrium positions are shown to be different in the liquid and the solid state. In the liquid state the 4-pyridoyl derivative is at the B-form (C-1 is OH), whereas the 2-and 3-pyridoyl...

  17. Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: {sup 1}H and {sup 13}C chemical shift assignments; Constituintes quimicos de Ottonia corcovadensis Miq. da floresta Amazonica - atribuicao dos deslocamentos quimicos dos atomos de hidrogenio e carbono

    Energy Technology Data Exchange (ETDEWEB)

    Facundo, Valdir A. [Rondonia Univ., Porto Velho, RO (Brazil). Dept. de Quimica; Morais, Selene M. [Ceara Univ., Fortaleza, CE (Brazil). Dept. de Quimica e Fisica; Braz Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Setor de Quimica de Produtos Naturais. Lab. de Ciencias Quimicas. Setor de Quimica de Produtos Naturais]. E-mail: braz@uenf.br

    2004-02-01

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

  18. Adherent and Conformal Zn(S,O,OH) Thin Films by Rapid Chemical Bath Deposition with Hexamethylenetetramine Additive.

    Science.gov (United States)

    Opasanont, Borirak; Van, Khoa T; Kuba, Austin G; Choudhury, Kaushik Roy; Baxter, Jason B

    2015-06-03

    ZnS is a wide band gap semiconductor whose many applications, such as photovoltaic buffer layers, require uniform and continuous films down to several nanometers thick. Chemical bath deposition (CBD) is a simple, low-cost, and scalable technique to deposit such inorganic films. However, previous attempts at CBD of ZnS have often resulted in nodular noncontinuous films, slow growth rates at low pH, and high ratio of oxygen impurities at high pH. In this work, ZnS thin films were grown by adding hexamethylenetetramine (HMTA) to a conventional recipe that uses zinc sulfate, nitrilotriacetic acid trisodium salt, and thioacetamide. Dynamic bath characterization showed that HMTA helps the bath to maintain near-neutral pH and also acts as a catalyst, which leads to fast nucleation and deposition rates, continuous films, and less oxygen impurities in the films. Films deposited on glass from HMTA-containing bath were uniform, continuous, and 90 nm thick after 1 h, as opposed to films grown without HMTA that were ∼3 times thinner and more nodular. On Cu2(Zn,Sn)Se4, films grown with HMTA were continuous within 10 min. The films have comparatively few oxygen impurities, with S/(S+O) atomic ratio of 88%, and high optical transmission of 98% at 360 nm. The Zn(S,O,OH) films exhibit excellent adhesion to glass and high resistivity, which make them ideal nucleation layers for other metal sulfides. Their promise as a nucleation layer was demonstrated with the deposition of thin, continuous Sb2S3 overlayers. This novel HMTA chemistry enables rapid deposition of Zn(S,O,OH) thin films to serve as a nucleation layer, a photovoltaic buffer layer, or an extremely thin continuous coating for thin film applications. HMTA may also be applied in a similar manner for solution deposition of other metal chalcogenide and oxide thin films with superior properties.

  19. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection

    Science.gov (United States)

    Sanders-Buell, Eric; Chenine, Agnes-Laurence; Goonetilleke, Nilu; Thomas, Rasmi; Harbolick, Elizabeth A.; Bose, Meera; Pham, Phuc; Oropeza, Celina; Poltavee, Kultida; O’Sullivan, Anne Marie; Costanzo, Margaret C.; Warren, Joanna A.; Slike, Bonnie; Li, Hui; Peachman, Kristina K.; Gao, Feng; Cicala, Claudia; Arthos, James; O’Connell, Robert J.; Sinei, Samuel; Maganga, Lucas; Rao, Mangala; Marovich, Mary A.; Krebs, Shelly J.; Rolland, Morgane; Shaw, George M.

    2017-01-01

    In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL) escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection. PMID:28759651

  20. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection.

    Directory of Open Access Journals (Sweden)

    Gustavo H Kijak

    2017-07-01

    Full Text Available In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI. Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F viruses revealed novel viral profiles that included: a the low-level persistence of minor T/F variants, b the rapid replacement of the major T/F by a minor T/F, and c an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection.

  1. Chemical shift effect predicting lymph node status in rectal cancer using high-resolution MR imaging with node-for-node matched histopathological validation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hongmei; Zhang, Chongda; Ye, Feng; Liu, Yuan; Zhou, Chunwu [Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, ChaoYang District, Beijing (China); Zheng, Zhaoxu [Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Colorectal Oncology, National Cancer Center/Cancer Hospital, ChaoYang District, Beijing (China); Zou, Shuangmei [Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Pathology, National Cancer Center/Cancer Hospital, ChaoYang District, Beijing (China)

    2017-09-15

    To evaluate the value of the chemical shift effect (CSE) as well as other criteria for the prediction of lymph node status. Twenty-nine patients who underwent radical surgery of rectal cancers were studied with pre- and postoperative specimen MRI. Lymph nodes were harvested from transverse whole-mount specimens and compared with in vivo and ex vivo images to obtain a precise slice-for-section match. Preoperative MR characteristics including CSE, as well as other predictors, were evaluated by two readers independently between benign and metastatic nodes. A total of 255 benign and 35 metastatic nodes were obtained; 71.4% and 69.4% of benign nodes were detected with regular CSE for two readers, whereas 80.0% and 74.3% of metastatic nodes with absence of CSE. The CSE rendered areas under the ROC curve (AUC) of 0.879 and 0.845 for predicting nodal status for two readers. The criteria of nodal location, border, signal intensity and minimum distance to the rectal wall were also useful but with AUCs (0.629-0.743) lower than those of CSE. CSE is a reliable predictor for differentiating benign from metastatic nodes. Additional criteria should be taken into account when it is difficult to determine the nodal status by using only a single predictor. (orig.)

  2. Scan time reduction in {sup 23}Na-Magnetic Resonance Imaging using the chemical shift imaging sequence. Evaluation of an iterative reconstruction method

    Energy Technology Data Exchange (ETDEWEB)

    Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology

    2015-07-01

    To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.

  3. {sup 1}H and {sup 13}C NMR Data on Hydroxy/methoxy Flavonoids and the Effects of Substituents on Chemical Shifts

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hyuk; Eom, Sung Lock; Hyun, Ji Ye; Jo, Geun Hyeong; Hwang, Do Seok; Lee, Sun Hee; Yong, Yeon Joong; Lee, Young Han; Lim, Yoong Ho [Konkuk University, Seoul (Korea, Republic of); Park, Jun Cheol [National Institute of Animal Science, Rural Development Administration, Suwon (Korea, Republic of)

    2011-06-15

    Polyphenols have recently been examined for such applications, and they are classified based on their carbon skeletons: phenolic acids with C6-C1 skeleton, hydrocinammates with C6-C{sub 3} skeleton, stilbenes with C6-C2-C6 skeleton, and flavonoids with C6-C{sub 3}-C6 skeleton.2 Of these compounds, flavonoids are ubiquitously found in most plants. Since flavonoids belong to polyphenols, they have many hydroxy groups. From a bioavailability point of view, hydroxy groups prevent cell membrane transport, and hydroxyflavonoids can be metabolized by O-methyltransferases. However, methoxylated flavonoids may not have these problems. Hydroxylated or methoxylated flavonoids are found from natural sources. Nuclear magnetic resonance (NMR) spectroscopy is widely used to identify different compounds including hydroxylated or methoxylated flavonoids. Because the position and the number of substituted hydroxy or/and methoxy groups will change the {sup 1}H and {sup 13}C chemical shifts, it is important to understand these changes so that the structures of newly isolated hydroxy/methoxy-flavonoids can be easily identified.

  4. Flow-suppressed hyperpolarized 13 C chemical shift imaging using velocity-optimized bipolar gradient in mouse liver tumors at 9.4 T.

    Science.gov (United States)

    Lee, Hansol; Lee, Joonsung; Joe, Eunhae; Yang, Seungwook; Song, Jae Eun; Choi, Young-Suk; Wang, Eunkyung; Joo, Chan Gyu; Song, Ho-Taek; Kim, Dong-Hyun

    2017-11-01

    To optimize and investigate the influence of bipolar gradients for flow suppression in metabolic quantification of hyperpolarized 13 C chemical shift imaging (CSI) of mouse liver at 9.4 T. The trade-off between the amount of flow suppression using bipolar gradients and T2* effect from static spins was simulated. A free induction decay CSI sequence with alternations between the flow-suppressed and non-flow-suppressed acquisitions for each repetition time was developed and was applied to liver tumor-bearing mice via injection of hyperpolarized [1-13 C] pyruvate. The in vivo results from flow suppression using the velocity-optimized bipolar gradient were comparable with the simulation results. The vascular signal was adequately suppressed and signal loss in stationary tissue was minimized. Application of the velocity-optimized bipolar gradient to tumor-bearing mice showed reduction in the vessel-derived pyruvate signal contamination, and the average lactate/pyruvate ratio increased by 0.095 (P flow suppression. Optimization of the bipolar gradient is essential because of the short 13 C T2* and high signal in venous flow in the mouse liver. The proposed velocity-optimized bipolar gradient can suppress the vascular signal, minimizing T2*-related signal loss in stationary tissues at 9.4 T. Magn Reson Med 78:1674-1682, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

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

    Science.gov (United States)

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

    2016-04-15

    Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. In vivo application of sub-second spiral chemical shift imaging (CSI) to hyperpolarized 13C metabolic imaging: comparison with phase-encoded CSI.

    Science.gov (United States)

    Mayer, Dirk; Yen, Yi-Fen; Levin, Yakir S; Tropp, James; Pfefferbaum, Adolf; Hurd, Ralph E; Spielman, Daniel M

    2010-06-01

    A fast spiral chemical shift imaging (CSI) has been developed to address the challenge of the limited acquisition window in hyperpolarized (13)C metabolic imaging. The sequence exploits the sparsity of the spectra and prior knowledge of resonance frequencies to reduce the measurement time by undersampling the data in the spectral domain. As a consequence, multiple reconstructions are necessary for any given data set as only frequency components within a selected bandwidth are reconstructed "in-focus" while components outside that band are severely blurred ("spectral tomosynthesis"). A variable-flip-angle scheme was used for optimal use of the longitudinal magnetization. The sequence was applied to sub-second metabolic imaging of the rat in vivo after injection of hyperpolarized [1-(13)C]-pyruvate on a clinical 3T MR scanner. The comparison with conventional CSI based on phase encoding showed similar signal-to-noise ratio (SNR) and spatial resolution in metabolic maps for the substrate and its metabolic products lactate, alanine, and bicarbonate, despite a 50-fold reduction in scan time for the spiral CSI acquisition. The presented results demonstrate that dramatic reductions in scan time are feasible in hyperpolarized (13)C metabolic imaging without a penalty in SNR or spatial resolution. (c) 2010 Elsevier Inc. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    of the exchanging species can be determined independently of the relaxation rates. The applicability of the approach is demonstrated by a detailed analysis of the conformational exchange processes previously observed in the reduced form of the blue copper protein, plastocyanin from the cyanobacteria Anabaena...... shifts were obtained from a series of HSQC spectra recorded in the pH range from 4 to 8. From the R-1 and R-2 relaxation rates, the contribution, R-ex, to the transverse relaxation caused by the exchanges between the different allo-states of the protein were determined. Specifically, it is demonstrated......An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the mus-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift...

  8. Accurate ab initio calculations of O-HO and O-H(-)O proton chemical shifts: towards elucidation of the nature of the hydrogen bond and prediction of hydrogen bond distances.

    Science.gov (United States)

    Siskos, Michael G; Tzakos, Andreas G; Gerothanassis, Ioannis P

    2015-09-07

    The inability to determine precisely the location of labile protons in X-ray molecular structures has been a key barrier to progress in many areas of molecular sciences. We report an approach for predicting hydrogen bond distances beyond the limits of X-ray crystallography based on accurate ab initio calculations of O-HO proton chemical shifts, using a combination of DFT and contactor-like polarizable continuum model (PCM). Very good linear correlation between experimental and computed (at the GIAO/B3LYP/6-311++G(2d,p) level of theory) chemical shifts were obtained with a large set of 43 compounds in CHCl3 exhibiting intramolecular O-HO and intermolecular and intramolecular ionic O-H(-)O hydrogen bonds. The calculated OH chemical shifts exhibit a strong linear dependence on the computed (O)HO hydrogen bond length, in the region of 1.24 to 1.85 Å, of -19.8 ppm Å(-1) and -20.49 ppm Å(-1) with optimization of the structures at the M06-2X/6-31+G(d) and B3LYP/6-31+G(d) level of theory, respectively. A Natural Bond Orbitals (NBO) analysis demonstrates a very good linear correlation between the calculated (1)H chemical shifts and (i) the second-order perturbation stabilization energies, corresponding to charge transfer between the oxygen lone pairs and σ antibonding orbital and (ii) Wiberg bond order of the O-HO and O-H(-)O hydrogen bond. Accurate ab initio calculations of O-HO and O-H(-)O (1)H chemical shifts can provide improved structural and electronic description of hydrogen bonding and a highly accurate measure of distances of short and strong hydrogen bonds.

  9. Toxoplasma gondii infection shifts dendritic cells into an amoeboid rapid migration mode encompassing podosome dissolution, secretion of TIMP-1, and reduced proteolysis of extracellular matrix.

    Science.gov (United States)

    Ólafsson, Einar B; Varas-Godoy, Manuel; Barragan, Antonio

    2018-03-01

    Dendritic cells (DCs) infected by Toxoplasma gondii rapidly acquire a hypermigratory phenotype that promotes systemic parasite dissemination by a "Trojan horse" mechanism in mice. Recent paradigms of leukocyte migration have identified the amoeboid migration mode of DCs as particularly suited for rapid locomotion in extracellular matrix and tissues. Here, we have developed a microscopy-based high-throughput approach to assess motility and matrix degradation by Toxoplasma-challenged murine and human DCs. DCs challenged with T. gondii exhibited dependency on metalloproteinase activity for hypermotility and transmigration but, strikingly, also dramatically reduced pericellular proteolysis. Toxoplasma-challenged DCs up-regulated expression and secretion of tissue inhibitor of metalloproteinases-1 (TIMP-1) and their supernatants impaired matrix degradation by naïve DCs and by-stander DCs dose dependently. Gene silencing of TIMP-1 by short hairpin RNA restored matrix degradation activity in Toxoplasma-infected DCs. Additionally, dissolution of podosome structures in parasitised DCs coincided with abrogated matrix degradation. Toxoplasma lysates inhibited pericellular proteolysis in a MyD88-dependent fashion whereas abrogated proteolysis persevered in Toxoplasma-infected MyD88-deficient DCs. This indicated that both TLR/MyD88-dependent and TLR/MyD88-independent signalling pathways mediated podosome dissolution and the abrogated matrix degradation. We report that increased TIMP-1 secretion and cytoskeletal rearrangements encompassing podosome dissolution are features of Toxoplasma-induced hypermigration of DCs with an impact on matrix degradation. Jointly, the data highlight how an obligate intracellular parasite orchestrates key regulatory cellular processes consistent with non-proteolytic amoeboid migration of the vehicle cells that facilitate its dissemination. © 2017 John Wiley & Sons Ltd.

  10. The use of chemical shift temperature gradients to establish the paramagnetic susceptibility tensor orientation: Implication for structure determination/refinement in paramagnetic metalloproteins

    Energy Technology Data Exchange (ETDEWEB)

    Xia Zhicheng; Nguyen, Bao D.; La Mar, Gerd N. [University of California, Department of Chemistry (United States)

    2000-06-15

    The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation of the anisotropic paramagnetic susceptibility tensor in the molecular frame which is generated interactively with the structure refinement. The use of dipolar shifts as constraints demands knowledge of the diamagnetic shift, which, however, is very often not directly and easily accessible. We demonstrate that temperature gradients of dipolar shifts can serve as alternative constraints for determining the orientation of the magnetic axes, thereby eliminating the need to estimate the diamagnetic shifts. This approach is tested on low-spin, ferric sperm whale cyanometmyoglobin by determining the orientation, anisotropies and anisotropy temperature gradients by the alternate routes of using dipolar shifts and dipolar shift gradients as constraints. The alternate routes ultimately lead to very similar orientation of the magnetic axes, magnetic anisotropies and magnetic anisotropy temperature gradients which, by inference, would lead to an equally valid description of the molecular structure. It is expected that the use of the dipolar shift temperature gradients, rather than the dipolar shifts directly, as constraints will provide an accurate shortcut in a solution structure determination of a paramagnetic metalloprotein.

  11. An optimized method for NMR-based plant seed metabolomic analysis with maximized polar metabolite extraction efficiency, signal-to-noise ratio, and chemical shift consistency.

    Science.gov (United States)

    Wu, Xiangyu; Li, Ning; Li, Hongde; Tang, Huiru

    2014-04-07

    Plant metabolomic analysis has become an essential part of functional genomics and systems biology and requires effective extraction of both primary and secondary metabolites from plant cells. To establish an optimized extraction method for the NMR-based analysis, we used the seeds of mungbean (Vigna radiata cv. Elü no. 1) as a model and systematically investigated the dependence of the metabolite composition in plant extracts on various extraction parameters including cell-breaking methods, extraction solvents, number of extraction repeats, tissue-to-solvent ratio, and extract-to-buffer ratio (for final NMR analysis). We also compared two NMR approaches for quantitative metabolomic analysis from completely relaxed spectra directly and from partially relaxed spectra calculated with T1. By maximizing the extraction efficiency and signal-to-noise ratio but minimizing inter-sample chemical-shift variations and metabolite degradations, we established a parameter-optimized protocol for NMR-based plant seed metabolomic analysis. We concluded that aqueous methanol was the best extraction solvent with an optimal tissue-to-solvent ratio of about 1 : 10-1 : 15 (mg per μL). The combination of tissuelyser homogenization with ultrasonication was the choice of cell-breaking method with three repeated extractions being necessary. For NMR analysis, the optimal extract-to-solvent was around 5-8 mg mL(-1) and completely relaxed spectra were ideal for intrinsically quantitative metabolomic analysis although partially relaxed spectra were employable for comparative metabolomics. This optimized method will offer ensured data quality for high-throughput and reliable plant metabolomics studies.

  12. Rapid analysis of formic acid, acetic acid, and furfural in pretreated wheat straw hydrolysates and ethanol in a bioethanol fermentation using atmospheric pressure chemical ionisation mass spectrometry

    Science.gov (United States)

    2011-01-01

    Atmospheric pressure chemical ionisation mass spectrometry (APCI-MS) offers advantages as a rapid analytical technique for the quantification of three biomass degradation products (acetic acid, formic acid and furfural) within pretreated wheat straw hydrolysates and the analysis of ethanol during fermentation. The data we obtained using APCI-MS correlated significantly with high-performance liquid chromatography analysis whilst offering the analyst minimal sample preparation and faster sample throughput. PMID:21896164

  13. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  14. Tough Shift

    DEFF Research Database (Denmark)

    Brewer, Robert S.; Verdezoto, Nervo; Holst, Thomas

    2015-01-01

    in a student dormitory and found that players did not shift their electricity use, because they were unwilling to change their schedules and found it easier to focus on reducing electricity use. Based on our findings, we discuss the implications for encouraging shifting, and also the challenges of integrating......Modern electrical grids are increasingly reliant on generation from renewable sources that can vary from hour to hour. This variability has led to the desire to shift the times of the day when electricity is consumed to better match generation. One way to achieve these shifts is by encouraging...... people to change their behavior at home. Leveraging prior research on encouraging reductions in residential energy use through game play, we introduce ShareBuddy: a casual mobile game intended to encourage players not only to reduce, but also to shift their electricity use. We conducted two field studies...

  15. Origin of the chemical shift in X-ray absorption near-edge spectroscopy at the Mn K-Edge in manganese oxide compounds

    NARCIS (Netherlands)

    de Vries, AH; Hozoi, L.; Broer, R.

    2003-01-01

    The absorption edge in Mn K-edge X-ray absorption spectra of manganese oxide compounds shows a shift of several electronvolts in going from MnO through LaMnO3 to CaMnO3. On the other hand, in X-ray photoelectron spectra much smaller shifts are observed. To identify the mechanisms that cause the

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-07-01

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

  17. Theoretical investigation of conformational stabilities and 13C NMR chemical shifts of a seven-membered ring thiosugar, (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol

    Science.gov (United States)

    Tai, Chin-Kuen; Yeh, Pao-Ling; Wu, Yun-Sheng; Shih, Tzenge-Lien; Wang, Bo-Cheng

    2014-06-01

    DFT/B3LYP/6-311++G(d,p) calculations have been performed to obtain optimized structures for fourteen conformers of (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol. These conformers are considered as the twist-chair (TC) and twist-boat (TB) conformations. Among all conformers, the TCS5 and TCS6 conformers appear to be the most energetically stable since they contain an intramolecular hydrogen bond between hydroxyl group at C(8) and S atom. Boltzmann weighting factor analysis provides valuable information on the population of the fourteen conformers, including both the TC and TB conformations. The analysis results demonstrate that the TCS2, TCS5, and TCS6 conformers provide a major population contribution with Boltzamann weighting factors larger than 7% as compared to other conformers. For these conformers of (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol, the GIAO/HF, GIAO/DFT/OPBE, GIAO/DFT/B3LYP and GIAO/DFT/mPW1PW91 calculations with the 6-311++G(d,p), 6-311+G(2d,p), cc-pVDZ and cc-pVTZ basis sets were used to obtain their 13C NMR chemical shifts. The calculated 13C NMR chemical shifts of the TCS2, TCS5, and TCS6 conformers show a close correlation with experimental data, within 2.4-3.0 ppm of MAE values. The experimental 13C NMR chemical shifts represent a combination of contributions from all the conformers. In our investigation, the calculated 13C NMR chemical shifts of the mixture of (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol conformers display a remarkable MAE and RMS improvement comparing to those for each individual conformer. The most appropriate calculation method and basis set to evaluate the theoretical 13C NMR chemical shifts for these conformers are OPBE/6-311+G(2d,p). Calculated results represent that the conformation of (3R,4R,5R,7S)-7-(hydroxymethyl)thiepane-3,4,5-triol can be determined by the intramolecular hydrogen bond which could be simulated by the 13C NMR chemical shift calculation.

  18. Comparison of modified two-point dixon and chemical shift encoded MRI water-fat separation methods for fetal fat quantification.

    Science.gov (United States)

    Giza, Stephanie A; Miller, Michael R; Parthasarathy, Prasiddha; de Vrijer, Barbra; McKenzie, Charles A

    2018-01-10

    Fetal fat is indicative of the energy balance within the fetus, which may be disrupted in pregnancy complications such as fetal growth restriction, macrosomia, and gestational diabetes. Water-fat separated MRI is a technique sensitive to tissue lipid content, measured as fat fraction (FF), and can be used to accurately measure fat volumes. Modified two-point Dixon and chemical shift encoded MRI (CSE-MRI) are water-fat separated MRI techniques that could be applied to imaging of fetal fat. Modified two-point Dixon has biases present that are corrected in CSE-MRI which may contribute to differences in the fat measurements. To compare the measurement of fetal fat volume and FF by modified two-point Dixon and CSE-MRI. Cross-sectional study for comparison of two MRI pulse sequences. Twenty-one pregnant women with singleton pregnancies. 1.5T, modified two-point Dixon and CSE-MRI. Manual segmentation of total fetal fat volume and mean FF from modified 2-point Dixon and CSE-MRI FF images. Reliability was assessed by calculating the intraclass correlation coefficient (ICC). Agreement was assessed using a one-sample t-test on the fat measurements difference values (modified two-point Dixon - CSE-MRI). The difference scores were tested against a value of 0, which would indicate that the measurements were identical. The fat volume and FF measured by modified two-point Dixon and CSE-MRI had excellent reliability, demonstrated by ICCs of 0.93 (P < 0.001) and 0.90 (P < 0.001), respectively. They were not in agreement, with CSE-MRI giving mean fat volumes 180 mL greater and mean FF 3.0% smaller than modified two-point Dixon. The reliability between modified two-point Dixon and CSE-MRI indicates that either technique can be used to compare fetal fat measurements in different participants, but they are not in agreement possibly due to uncorrected biases in modified two-point Dixon. 4 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic

  19. Effects of rapid thermal annealing on structural, chemical, and electrical characteristics of atomic-layer deposited lanthanum doped zirconium dioxide thin film on 4H-SiC substrate

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Way Foong, E-mail: wayfoong317@yahoo.com.sg [Institute of Nano Optoelectronics Research and Technology, School of Physics, Universiti Sains Malaysia, 11800 Penang (Malaysia); Centre for Research Initiatives (CRI) Natural Sciences, Universiti Sains Malaysia, 11800 Penang (Malaysia); Quah, Hock Jin, E-mail: jinquah1st@hotmail.com [Institute of Nano Optoelectronics Research and Technology, School of Physics, Universiti Sains Malaysia, 11800 Penang (Malaysia); Centre for Research Initiatives (CRI) Natural Sciences, Universiti Sains Malaysia, 11800 Penang (Malaysia); Lu, Qifeng, E-mail: Qifeng@liverpool.ac.uk [Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3GJ (United Kingdom); Mu, Yifei, E-mail: Y.mu@student.liverpool.ac.uk [Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3GJ (United Kingdom); Ismail, Wan Azli Wan, E-mail: azli.ismail@mimos.my [Advance Analytical Services Lab, MIMOS Wafer Fab, MIMOS Berhad, Technology Park Malaysia, 57000 Kuala Lumpur (Malaysia); Rahim, Bazura Abdul, E-mail: bazura@mimos.my [Advance Analytical Services Lab, MIMOS Wafer Fab, MIMOS Berhad, Technology Park Malaysia, 57000 Kuala Lumpur (Malaysia); Esa, Siti Rahmah, E-mail: rahmah.esa@mimos.my [Advance Analytical Services Lab, MIMOS Wafer Fab, MIMOS Berhad, Technology Park Malaysia, 57000 Kuala Lumpur (Malaysia); Kee, Yeh Yee, E-mail: yy.kee@mimos.my [Advance Analytical Services Lab, MIMOS Wafer Fab, MIMOS Berhad, Technology Park Malaysia, 57000 Kuala Lumpur (Malaysia); Zhao, Ce Zhou, E-mail: cezhou.zhao@xjtlu.edu.cn [Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3GJ (United Kingdom); Department of Electrical and Electronic Engineering, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123 (China); and others

    2016-03-01

    Graphical abstract: - Highlights: • Studies of RTA temperatures on La doped ZrO2 atomic layer deposited on 4HSiC. • Oxygen vacancies improved insulating and catalytic properties of La doped ZrO2. • 700 °C annealed sample showed the highest EB, k value, and sensitivity on O2. • La doped ZrO2 was proposed as a potential metal reactive oxide on 4H-SiC. - Abstract: Effects of rapid thermal annealing at different temperatures (700–900 °C) on structural, chemical, and electrical characteristics of lanthanum (La) doped zirconium oxide (ZrO{sub 2}) atomic layer deposited on 4H-SiC substrates have been investigated. Chemical composition depth profiling analysis using X-ray photoelectron spectroscopy (XPS) and cross-sectional studies using high resolution transmission electron microscopy equipped with energy dispersive X-ray spectroscopy line scan analysis were insufficient to justify the presence of La in the investigated samples. The minute amount of La present in the bulk oxide was confirmed by chemical depth profiles of time-of-flight secondary ion mass spectrometry. The presence of La in the ZrO{sub 2} lattice led to the formation of oxygen vacancies, which was revealed through binding energy shift for XPS O 1s core level spectra of Zr−O. The highest amount of oxygen vacancies in the sample annealed at 700 °C has yielded the acquisition of the highest electric breakdown field (∼ 6.3 MV/cm) and dielectric constant value (k = 23) as well as the highest current–time (I–t) sensor response towards oxygen gas. The attainment of both the insulating and catalytic properties in the La doped ZrO{sub 2} signified the potential of the doped ZrO{sub 2} as a metal reactive oxide on 4H-SiC substrate.

  20. Mining Available Data from the United States Environmental Protection Agency to Support Rapid Life Cycle Inventory Modeling of Chemical Manufacturing

    Science.gov (United States)

    Demands for quick and accurate life cycle assessments create a need for methods to rapidly generate reliable life cycle inventories (LCI). Data mining is a suitable tool for this purpose, especially given the large amount of available governmental data. These data are typically a...

  1. Shape-shifting colloids via stimulated dewetting

    Science.gov (United States)

    Youssef, Mena; Hueckel, Theodore; Yi, Gi-Ra; Sacanna, Stefano

    2016-07-01

    The ability to reconfigure elementary building blocks from one structure to another is key to many biological systems. Bringing the intrinsic adaptability of biological systems to traditional synthetic materials is currently one of the biggest scientific challenges in material engineering. Here we introduce a new design concept for the experimental realization of self-assembling systems with built-in shape-shifting elements. We demonstrate that dewetting forces between an oil phase and solid colloidal substrates can be exploited to engineer shape-shifting particles whose geometry can be changed on demand by a chemical or optical signal. We find this approach to be quite general and applicable to a broad spectrum of materials, including polymers, semiconductors and magnetic materials. This synthetic methodology can be further adopted as a new experimental platform for designing and rapidly prototyping functional colloids, such as reconfigurable micro swimmers, colloidal surfactants and switchable building blocks for self-assembly.

  2. Conformational analysis of a seven-membered ring azasugar, (3R,4R,6S)-trihydroxyazepane: Comparison of GIAO calculation and experimental NMR spectra on 13C chemical shifts

    Science.gov (United States)

    Yeh, Pao-Ling; Tai, Chin-Kuen; Shih, Tzenge-Lien; Hsiao, Hui-Ling; Wang, Bo-Cheng

    2012-06-01

    DFT/B3LYP/6-311++G(d,p) calculation of the relative stable conformations of (3R,4R,6S)-trihydroxyazepane are presented. The GIAO/DFT/OPBE, GIAO/DFT/B3LYP and GIAO/HF single point calculations with 6-311++G(d,p), 6-311+G(2d,p), cc-pVDZ and cc-pVTZ basis sets of (3R,4R,6S)-trihydroxyazepane were conducted to generate their 13C NMR chemical shifts. According to calculation results, 14 (3R,4R,6S)-trihydroxyazepane with optimized structure were generated. There were three conformers which contain the intramolecular hydrogen bonding exhibit a lowest electronic energies and TCN1(eq) was the most stable conformer than others. Boltzmann weighting factor analysis exhibits that TCN1(eq), TCN3(eq) and TCN5(eq) dominate a major contribution among the 14 conformers. The individual calculated NMR results of TCN1(eq), TCN3(eq) and TCN5(eq) represents a quite close correlation with experimental data. Moreover, the experimental 13C NMR chemical shifts gave only the average contribution of all conformers. In our investigation, the calculated 13C NMR chemical shifts of mixture (3R,4R,6S)-trihydroxyazepane exhibit a good agreement with the experimental NMR data. Calculated NMR results of mixture (3R,4R,6S)-trihydroxyazepane conformers display a remarkable MAE and RMS improvement over that of each individual conformer. A good calculation method and basis set choice to evaluate the theoretical chemical shifts for these conformers is HF/cc-pVTZ.

  3. Implementing a Systematic Process for Rapidly Embedding Sustainability within Chemical Engineering Education: A Case Study of James Cook University, Australia

    Science.gov (United States)

    Sheehan, Madoc; Schneider, Phil; Desha, Cheryl

    2012-01-01

    Sustainability has emerged as a primary context for engineering education in the 21st Century, particularly the sub-discipline of chemical engineering. However, there is confusion over how to go about integrating sustainability knowledge and skills systemically within bachelor degrees. This paper addresses this challenge, using a case study of an…

  4. Use of TSHβ:EGFP transgenic zebrafish as a rapid in vivo model for assessing thyroid-disrupting chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Cheng [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei (China); Graduate University of Chinese Academy of Sciences, Beijing (China); Jin, Xia; He, Jiangyan [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei (China); Yin, Zhan, E-mail: zyin@ihb.ac.cn [Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei (China)

    2012-07-15

    Accumulating evidence indicates that a wide range of chemicals have the ability to interfere with the hypothalamic–pituitary–thyroid (HPT) axis. Novel endpoints should be evaluated in addition to existing methods in order to effectively assess the effects of these chemicals on the HPT axis. Thyroid-stimulating hormone subunit β (TSHβ) plays central regulatory roles in the HPT system. We identified the regulatory region that determines the expression level of zebrafish TSHβ in the anterior pituitary. In the transgenic zebrafish with EGFP driven by the TSHβ promoter, the similar responsive patterns between the expression levels of TSHβ:EGFP and endogenous TSHβ mRNA in the pituitary are observed following treatments with goitrogen chemicals and exogenous thyroid hormones (THs). These results suggest that the TSHβ:EGFP transgenic reporter zebrafish may be a useful alternative in vivo model for the assessment of chemicals interfering with the HPT system. Highlights: ► The promoter of zebrafish TSHβ gene has been identified. ► The stable TSHβ:EGFP transgenic zebrafish reporter germline has been generated. ► The EGFP in the transgenic fish recapitulated the pattern of pituitary TSHβ mRNA. ► The transgenic zebrafish may be an in vivo model for EDC assessment.

  5. Rapid prototyping of nano- and micro-patterned substrates for the control of cell neuritogenesis by topographic and chemical cues

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Ajay V.; Gailite, Lasma; Vyas, Varun [European School of Molecular Medicine (SEMM), IFOM-IEO Campus, Via Adamello 16, I-20139 Milano (Italy); CIMAINA and Dipartimento di Fisica, Universita di Milano, via Celoria 16, I-20133 Milano (Italy); Lenardi, Cristina, E-mail: cristina.lenardi@mi.infn.it [CIMAINA and Dipartimento di Scienze Molecolari Applicate ai Biosistemi, Universita di Milano, via Trentacoste 2, I-20134 Milano (Italy); Fondazione Filarete, viale Ortles 22/4, I-20139 Milano (Italy); Forti, Stefania [CIMAINA and Dipartimento di Fisica, Universita di Milano, via Celoria 16, I-20133 Milano (Italy); Matteoli, Michela [Dipartimento di Farmacologia, Chemioterapia e Tossicologia Medica, Universita di Milano, via Vanvitelli 32, I-20139 Milano (Italy); Fondazione Filarete, viale Ortles 22/4, I-20139 Milano (Italy); Milani, Paolo, E-mail: paolo.milani@mi.infn.it [CIMAINA and Dipartimento di Fisica, Universita di Milano, via Celoria 16, I-20133 Milano (Italy); Fondazione Filarete, viale Ortles 22/4, I-20139 Milano (Italy)

    2011-07-20

    Rapid prototyping of titania substrates with micro and nanofeatures is obtained by combining nanosphere lithography with supersonic cluster beam deposition on protein-functionalized glass supports. The proliferation and differentiation of PC12 cells were studied on these substrates. The facile control and modification of the substrate structure at the micro- and nanoscale allowed us to characterize the role of functional and structural features on neuritogenesis and to control this phenomenon by identifying the optimal topography.

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

    Energy Technology Data Exchange (ETDEWEB)

    Sevelsted, Tine F. [Instrument Centre for Solid-State NMR Spectroscopy, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark); Herfort, Duncan [Aalborg Portland A/S,Cementir Holding S.p.A., DK-9100 Aalborg (Denmark); Skibsted, Jørgen, E-mail: jskib@chem.au.dk [Instrument Centre for Solid-State NMR Spectroscopy, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark)

    2013-10-15

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

  7. Solid-phase microextraction low temperature plasma mass spectrometry for the direct and rapid analysis of chemical warfare simulants in complex mixtures.

    Science.gov (United States)

    Dumlao, Morphy C; Jeffress, Laura E; Gooding, J Justin; Donald, William A

    2016-06-21

    Solid-phase microextraction (SPME) is directly integrated with low temperature plasma ionisation mass spectrometry to rapidly detect organophosphate chemical warfare agent simulants and their hydrolysis products in chemical mixtures, including urine. In this sampling and ionization method, the fibre serves: (i) to extract molecules from their native environment, and (ii) as the ionization electrode that is used to desorb and ionize molecules directly from the SPME surface. By use of a custom fabricated SPME fibre consisting of a stainless steel needle coated with a Linde Type A (LTA) zeolitic microporous material and low temperature plasma mass spectrometry, protonated dimethyl methylphosphonate (DMMP), diethyl ethylphosphonate (DEEP) and pinacolyl methylphosphonic acid (PinMPA) can be detected at less than 100 ppb directly in water and urine. Organophosphates were not readily detected by this approach using an uncoated needle in negative control experiments. The use of the LTA coating significantly outperformed the use of a high alumina Zeolite Socony Mobil-5 (ZSM-5) coating of comparable thickness that is significantly less polar than LTA. By conditioning the LTA probe by immersion in an aqueous CuSO4 solution, the ion abundance for protonated DMMP increased by more than 300% compared to that obtained without any conditioning. Sample recovery values were between 96 and 100% for each analyte. The detection of chemical warfare agent analogues and hydrolysis products required less than 2 min per sample. A key advantage of this sampling and ionization method is that analyte ions can be directly and rapidly sampled from chemical mixtures, such as urine and seawater, without sample preparation or chromatography for sensitive detection by mass spectrometry. This ion source should prove beneficial for portable mass spectrometry applications because relatively low detection limits can be obtained without the use of compressed gases, fluid pumps, and lasers. Moreover, the

  8. Microwave assisted rapid growth of Mg(OH){sub 2} nanosheet networks for ethanol chemical sensor application

    Energy Technology Data Exchange (ETDEWEB)

    Al-Hazmi, Faten [Department of Physics, College of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21569 (Saudi Arabia); Umar, Ahmad, E-mail: ahmadumar786@gmail.com [Promising Centre for Sensors and Electronic Devices (PCSED) and Centre for Advanced Materials and Nano-Research (CAMNR), Najran University, P.O. Box 1988, Najran 11001 (Saudi Arabia); Dar, G.N. [Promising Centre for Sensors and Electronic Devices (PCSED) and Centre for Advanced Materials and Nano-Research (CAMNR), Najran University, P.O. Box 1988, Najran 11001 (Saudi Arabia); Al-Ghamdi, A.A.; Al-Sayari, S.A. [Department of Physics, College of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21569 (Saudi Arabia); Al-Hajry, A. [Promising Centre for Sensors and Electronic Devices (PCSED) and Centre for Advanced Materials and Nano-Research (CAMNR), Najran University, P.O. Box 1988, Najran 11001 (Saudi Arabia); Department of Physics, College of Science and Arts, Najran University, P.O. Box 1988, Najran 11001 (Saudi Arabia); Kim, S.H. [Promising Centre for Sensors and Electronic Devices (PCSED) and Centre for Advanced Materials and Nano-Research (CAMNR), Najran University, P.O. Box 1988, Najran 11001 (Saudi Arabia); Al-Tuwirqi, Reem M. [Department of Physics, College of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21569 (Saudi Arabia); Alnowaiserb, Fowzia [Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah (Saudi Arabia); El-Tantawy, Farid [Department of Physics, Faculty of Science, Suez Canal University, Ismailia (Egypt)

    2012-04-05

    Highlights: Black-Right-Pointing-Pointer A facile microwave-assisted synthesis and characterizations of magnesium hydroxide (Mg(OH){sub 2}) nanosheet networks. Black-Right-Pointing-Pointer Fabrication of ethanol sensor based on (Mg(OH){sub 2}) nanosheet networks. Black-Right-Pointing-Pointer Good sensitivity ({approx}3.991 {mu}A cm{sup -2} mM{sup -1}) and lower detection limit (5 {mu}M). Black-Right-Pointing-Pointer This research opens a way to utilize Mg(OH){sub 2} nanostructures for chemical sensors applications. - Abstract: This paper reports a facile microwave-assisted synthesis of magnesium hydroxide (Mg(OH){sub 2}) nanosheet networks and their utilization for the fabrication of efficient ethanol chemical sensor. The synthesized nanosheets networks were characterized in terms of their morphological, structural and optical properties using various analysis techniques such as field emission scanning electron microscopy (FESEM), X-ray diffraction pattern (XRD), Fourier transform infrared (FTIR) and UV-Vis spectroscopy. The detailed morphological and structural investigations reveal that the synthesized (Mg(OH){sub 2}) products are nanosheet networks, grown in high density, and possessing hexagonal crystal structure. The optical band gap of as-synthesized Mg(OH){sub 2} nanosheet networks was examined by UV-Vis absorption spectrum, and found to be 5.76 eV. The synthesized nanosheet networks were used as supporting matrices for the fabrication of I-V technique based efficient ethanol chemical sensor. The fabricated ethanol sensor based on nanosheet networks exhibits good sensitivity ({approx}3.991 {mu}A cm{sup -2} mM{sup -1}) and lower detection limit (5 {mu}M), with linearity (R = 0.9925) in short response time (10.0 s). This work demonstrate that the simply synthesized Mg(OH){sub 2} nanosheet networks can effectively be used for the fabrication of efficient ethanol chemical sensors.

  9. Rapid Monitoring of Mercury in Air from an Organic Chemical Factory in China Using a Portable Mercury Analyzer

    OpenAIRE

    Yasutake, Akira; Cheng, Jin Ping; Kiyono, Masako; Uraguchi, Shimpei; Liu, Xiaojie; Miura, Kyoko; Yasuda, Yoshiaki; Mashyanov, Nikolay

    2011-01-01

    A chemical factory, using a production technology of acetaldehyde with mercury catalysis, was located southeast of Qingzhen City in Guizhou Province, China. Previous research showed heavy mercury pollution through an extensive downstream area. A current investigation of the mercury distribution in ambient air, soils, and plants suggests that mobile mercury species in soils created elevated mercury concentrations in ambient air and vegetation. Mercury concentrations of up to 600 ng/m3 in air o...

  10. Shifting Boundaries

    DEFF Research Database (Denmark)

    Blaagaard, Bolette

    2013-01-01

    within journalistic practice of keeping up the idea as well as the practice of journalistic objectivity. Working on from Schudson (2003), Schudson and Anderson (2009) and Tumber and Prentoulis’ (2003) analyses of journalistic professionalism, the article develops the idea of journalistic objectivity...... further on the question of how the students address and react to this paradigmatic shift....

  11. The Chemical Deposition Method for the Decoration of Palladium Particles on Carbon Nanofibers with Rapid Conductivity Changes

    Directory of Open Access Journals (Sweden)

    Hoik Lee

    2016-11-01

    Full Text Available Palladium (Pd metal is well-known for hydrogen sensing material due to its high sensitivity and selectivity toward hydrogen, and is able to detect hydrogen at near room temperature. In this work, palladium-doped carbon nanofibers (Pd/CNFs were successfully produced in a facile manner via electrospinning. Well-organized and uniformly distributed Pd was observed in microscopic images of the resultant nanofibers. Hydrogen causes an increment in the volume of Pd due to the ability of hydrogen atoms to occupy the octahedral interstitial positions within its face centered cubic lattice structure, resulting in the resistance transition of Pd/CNFs. The resistance variation was around 400%, and it responded rapidly within 1 min, even in 5% hydrogen atmosphere conditions at room temperature. This fibrous hybrid material platform will open a new and practical route and stimulate further researches on the development of hydrogen sensing materials with rapid response, even to low concentrations of hydrogen in an atmosphere.

  12. Rapid screening and identification of chemical hazards in surface and drinking water using high resolution mass spectrometry and a case-control filter.

    Science.gov (United States)

    Kaserzon, Sarit L; Heffernan, Amy L; Thompson, Kristie; Mueller, Jochen F; Gomez Ramos, Maria Jose

    2017-09-01

    Access to clean, safe drinking water poses a serious challenge to regulators, and requires analytical strategies capable of rapid screening and identification of potentially hazardous chemicals, specifically in situations when threats to water quality or security require rapid investigations and potential response. This study describes a fast and efficient chemical hazard screening strategy for characterising trace levels of polar organic contaminants in water matrices, based on liquid chromatography high resolution mass spectrometry with post-acquisition 'case-control' data processing. This method allowed for a rapid response time of less than 24 h for the screening of target, suspect and non-target unknown chemicals via direct injection analysis, and a second, more sensitive analysis option requiring sample pre-concentration. The method was validated by fortifying samples with a range of pesticides, pharmaceuticals and personal care products (n = 46); with >90% of target compounds positively screened in samples at 1 ng mL-1, and 46% at 0.1 ng mL-1 when analysed via direct injection. To simulate a contamination event samples were fortified with compounds not present in the commercial library (designated 'non-target compounds'; fipronil and fenitrothion), tentatively identified at 0.2 and 1 ng mL-1, respectively; and a compound not included in any known commercial library or public database (designated 'unknown' compounds; 8Cl- perfluorooctanesulfonic acid), at 0.8 ng mL-1. The method was applied to two 'real-case' scenarios: (1) the assessment of drinking water safety during a high-profile event in Brisbane, Australia; and (2) to screen treated, re-circulated drinking water and pre-treated (raw) water. The validated workflow was effective for rapid prioritisation and screening of suspect and non-target potential hazards at trace levels, and could be applied to a wide range of matrices and investigations where comparison of organic contaminants between

  13. Observing a Chemically and/or Climatically Important Volcano: Facilitating Rapid Response to an Unanticipated yet Inevitable Event

    Science.gov (United States)

    Kaye, J. A.

    2015-12-01

    A large volcanic event has the potential to influence the chemical and/or physical state of the Earth's atmosphere in a significant way. In particular, changes in the trace constituent and/or particulate composition of the stratosphere, as well as the temperature distribution of the troposphere and stratosphere can both take place (and persist over a period of time), as has been observed in several eruptions in recent years (e.g., the Mount Pinatubo eruption in 1991). Characterizing the impacts of these eruptions and predicting their impacts on the evolution of the atmosphere requires observations of gas and particle distributions over time period from as soon after eruption as possible to the longer time period over which the Earth system is affected. This characterization may make use of observation capabilities from ongoing surface-based and existing satellite-based observing systems, and can also benefit significantly from focused airborne campaigns that make use of both in situ and remote sensing instrumentation. This presentation will review the relevant surface- and space-based observing capability operated by NASA in the broader context of the global observing capabilities of the international community, and and will discuss potential approaches to airborne campaigns (platforms, sensors, systems, logistical consideration) that would provide the data most useful for both characterization and forecasting of both the chemical and climatic forcing and impacts associated with the eruption.

  14. An alternative chemical redox method for the production of bispecific antibodies: implication in rapid detection of food borne pathogens.

    Directory of Open Access Journals (Sweden)

    Mohammad Owais

    Full Text Available Bi-functional antibodies with the ability to bind two unrelated epitopes have remarkable potential in diagnostic and bio-sensing applications. In the present study, bispecific antibodies that recognize human red blood cell (RBC and the food borne pathogen Listeria monocytogenes (L. monocytogenes were engineered. The procedure involves initial reduction of a mixture of anti-RBC and anti-Listeria antibodies followed by gradual re-oxidation of the reduced disulphides. This facilitates association of the separated antibody chains and formation of hybrid immunoglobulins with affinity for the L. monocytogenes and human RBC. The bispecific antibodies caused the agglutination of the RBCs only in the presence of L. monocytogenes cells. The agglutination process necessitated the specific presence of L. monocytogenes and the red colored clumps formed were readily visible with naked eyes. The RBC agglutination assay described here provides a remarkably simple approach for the rapid and highly specific screening of various pathogens in their biological niches.

  15. Rapidly induced chemical defenses in maize stems and their effects on short-term growth of Ostrinia nubilalis.

    Science.gov (United States)

    Dafoe, Nicole J; Huffaker, Alisa; Vaughan, Martha M; Duehl, Adrian J; Teal, Peter E; Schmelz, Eric A

    2011-09-01

    Plants damaged by insect herbivory often respond by inducing a suite of defenses that can negatively affect an insect's growth and fecundity. Ostrinia nubilalis (European corn borer, ECB) is one of the most devastating insect pests of maize, and in the current study, we examined the early biochemical changes that occur in maize stems in response to ECB herbivory and how these rapidly induced defenses influence the growth of ECB. We measured the quantities of known maize defense compounds, benzoxazinoids and the kauralexin class of diterpenoid phytoalexins. ECB herbivory resulted in decreased levels of the benzoxazinoid, 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one)-β-D-glucopyranose (DIMBOA-Glc), and a corresponding increase in 2-(2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one)-β-D-glucopyranose (HDMBOA-Glc). Total quantities of benzoxazinoids and kauralexins were increased as early as 24 h after the initiation of ECB feeding. The plant hormones, jasmonic acid (JA) and ethylene (ET), and the transcripts encoding their key biosynthetic enzymes also accumulated in response to ECB herbivory, consistent with a role in defense regulation. The combined pharmacological application of JA and the ET precursor, 1-aminocyclopropane-1-carboxylic acid to stem internode tissue likewise resulted in changes in benzoxazinoids similar to that observed with ECB damage. Despite the fact that maize actively mounts a defense response to ECB stem feeding, no differences in percent weight gain were observed between ECB larvae that fed upon non-wounded control tissues compared to tissues obtained from plants previously subjected to 24 h ECB stem herbivory. These rapid defense responses in maize stems do not appear to negatively impact ECB growth, thus suggesting that ECB have adapted to these induced biochemical changes.

  16. A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space

    Science.gov (United States)

    2012-01-01

    Background The current chemical space of known small molecules is estimated to exceed 1060 structures. Though the largest physical compound repositories contain only a few tens of millions of unique compounds, virtual screening of databases of this size is still difficult. In recent years, the application of physicochemical descriptor-based profiling, such as Lipinski's rule-of-five for drug-likeness and Oprea's criteria of lead-likeness, as early stage filters in drug discovery has gained widespread acceptance. In the current study, we outline a kinase-likeness scoring function based on known kinase inhibitors. Results The method employs a collection of 22,615 known kinase inhibitors from the ChEMBL database. A kinase-likeness score is computed using statistical analysis of nine key physicochemical descriptors for these inhibitors. Based on this score, the kinase-likeness of four publicly and commercially available databases, i.e., National Cancer Institute database (NCI), the Natural Products database (NPD), the National Institute of Health's Molecular Libraries Small Molecule Repository (MLSMR), and the World Drug Index (WDI) database, is analyzed. Three of these databases, i.e., NCI, NPD, and MLSMR are frequently used in the virtual screening of kinase inhibitors, while the fourth WDI database is for comparison since it covers a wide range of known chemical space. Based on the kinase-likeness score, a kinase-focused library is also developed and tested against three different kinase targets selected from three different branches of the human kinome tree. Conclusions Our proposed methodology is one of the first that explores how the narrow chemical space of kinase inhibitors and its relevant physicochemical information can be utilized to build kinase-focused libraries and prioritize pre-existing compound databases for screening. We have shown that focused libraries generated by filtering compounds using the kinase-likeness score have, on average, better docking

  17. In situ DART-MS as a Versatile and Rapid Dereplication Tool in Lichenology: Chemical Fingerprinting of Ophioparma ventosa.

    Science.gov (United States)

    Le Pogam, Pierre; Le Lamer, Anne-Cécile; Legouin, Béatrice; Boustie, Joël; Rondeau, David

    2016-11-01

    Lichens widely occur all over the world and are known to produce unique secondary metabolites with various biological activities. To develop high-throughput screening approaches requiring little to no sample preparation to alleviate the dereplication holdup and accelerate the discovery workflow of new structures from lichens. The extracellular distribution of lichen metabolites is incentive for in situ chemical profiling of lichens using the ambient mass spectrometry DART-MS. For this purpose, the chlorolichen Ophioparma ventosa, producing an array of lichen polyphenolics that encompass the main structural classes associated to lichen chemodiversity, represented a relevant model to assess the versatility of this platform. The feasibility of this approach was first established by analysing the pure compounds known from this species prior to being extended to different solid organs of the lichen. All tested compounds could be detected in positive and negative ion modes, most often with prevalent protonated or deprotonated molecules. Only depsides underwent a significant in-source fragmentation in both ionisation modes, which should be regarded as an added value for their structural elucidation. In situ DART-MS analyses of Ophioparma ventosa provided an extensive chemical profile and noteworthy pinpointed miriquidic acid, an unusual lichen depside so far unknown within this species. At last, in situ DART-MS granted a first insight into the distribution of the metabolites within the lichen. DART-MS represents a versatile tool to the wide field of lichenology, facilitating accelerated and sharp analyses of lichens and bypassing costly and tedious procedures of solvent extraction. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  18. van der Waals Schottky barriers as interface probes of the correlation between chemical potential shifts and charge density wave formation in 1 T -TiSe2 and 2 H -NbSe2

    Science.gov (United States)

    Li, Ang J.; Zhu, Xiaochen; Rhodes, Daniel; Samouce, Christopher C.; Balicas, Luis; Hebard, Arthur F.

    2017-09-01

    Layered transition-metal dichalcogenide (TMD) materials, i.e., 1 T -TiSe2 and 2 H -NbSe2 , harbor a second-order charge density wave (CDW) transition where phonons play a key role for the periodic modulations of conduction electron densities and associated lattice distortions. We systematically study the transport and capacitance characteristics over a wide temperature range of Schottky barriers formed by intimately contacting freshly exfoliated flakes of 1 T -TiSe2 and 2 H -NbSe2 to n -type GaAs semiconductor substrates. The extracted temperature-dependent parameters (zero-bias barrier height, ideality, and built-in potential) reflect changes at the TMD/GaAs interface induced by CDW formation for both TMD materials. The measured built-in potential reveals chemical-potential shifts relating to CDW formation. With decreasing temperature a peak in the chemical-potential shifts during CDW evolution indicates a competition between electron energy redistributions and a combination of lattice strain energies and Coulomb interactions. These modulations of chemical potential in CDW systems, such as 1 T -TiSe2 and 2 H -NbSe2 harboring second-order phase transitions, reflect a corresponding conversion from short-range to long-range order.

  19. Fluid Shifts

    Science.gov (United States)

    Stenger, M. B.; Hargens, A. R.; Dulchavsky, S. A.; Arbeille, P.; Danielson, R. W.; Ebert, D. J.; Garcia, K. M.; Johnston, S. L.; Laurie, S. S.; Lee, S. M. C.; hide

    2017-01-01

    Introduction. NASA's Human Research Program is focused on addressing health risks associated with long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but now more than 50 percent of ISS astronauts have experienced more profound, chronic changes with objective structural findings such as optic disc edema, globe flattening and choroidal folds. These structural and functional changes are referred to as the visual impairment and intracranial pressure (VIIP) syndrome. Development of VIIP symptoms may be related to elevated intracranial pressure (ICP) secondary to spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight and to determine if a relation exists with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as any VIIP-related effects of those shifts, are predicted by the crewmember's pre-flight status and responses to acute hemodynamic manipulations, specifically posture changes and lower body negative pressure. Methods. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, and calcaneus tissue thickness (by ultrasound); (3) vascular dimensions by ultrasound (jugular veins, cerebral and carotid arteries, vertebral arteries and veins, portal vein); (4) vascular dynamics by MRI (head/neck blood flow, cerebrospinal fluid

  20. A rapid chemical-genetic screen utilizing impaired movement phenotypes in C. elegans: Input into genetics of neurodevelopmental disorders.

    Science.gov (United States)

    Schmeisser, Kathrin; Fardghassemi, Yasmin; Parker, J Alex

    2017-07-01

    Autism spectrum disorder (ASD) is the most common neurodevelopmental disorder with a constantly increasing prevalence. Model organisms may be tools to identify underlying cellular and molecular mechanisms, as well as aid the discovery and development of novel therapeutic approaches. A simple animal such as the nematode Caenorhabditis elegans may provide insights into the extreme complexity of ASD genetics. Despite its potential, using C. elegans in ASD research is a controversial approach and has not yet been used extensively in this context. In this study, we present a screening approach of potential C. elegans mutants as potential ASD models. We screened these mutants for motor-deficiency phenotypes, which can be exploited to study underlying mechanisms of the disorder. Selected motor-deficient mutants were then used in a comprehensive drug screen of over 3900 compounds, including many FDA-approved and natural molecules, that were analyzed for their ability to suppress motility defects caused by ASD-associated gene orthologues. This genetic-chemical approach, i.e. establishing C. elegans models for ASD and screening of a well-characterized compound library, might be a promising first step to understand the mechanisms of how gene variations cause neuronal dysfunction, leading to ASD and other neurological disorders. Positively acting compounds could also be promising candidates for preclinical studies. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Rapid assessment of mid-infrared refractive index anisotropy using a prism coupler: chemical vapor deposited ZnS.

    Science.gov (United States)

    Qiao, H A; Lipschultz, Kristen A; Anheier, N C; McCloy, J S

    2012-05-01

    A state-of-the-art mid-infrared prism coupler was used to study suspected anisotropy in the refractive index of forward-looking-infrared grade chemical vapor deposited (CVD) zinc sulfide. Samples were prepared with columnar grain structure in and perpendicular to the sample plane, as well as from different depths in the CVD growth body. This study was motivated by the growing industry concern among optical design engineers, as well as developers of mid-infrared systems, over the reliability of historically accepted index data. Prior photoluminescence and x-ray diffraction measurements have suggested that refractive index may vary according to sample orientation with respect to the grain structure. Measurements were conducted to provide optical dispersion and thermal index (dn/dT) data at discrete laser wavelengths between 0.633 and 10.591 μm at two temperature set points (30 °C and 90 °C). Refractive index measurements between samples exhibited an average standard deviation comparable to the uncertainty of the prism coupler measurement (0.0004 refractive index units), suggesting that the variation in refractive index as a function of sample orientation and CVD deposition time is negligible and should have no impact on subsequent optical designs. Measured dispersion data at mid-infrared wavelengths were also found to agree well with prior published measurements.

  2. Chemical shift assignments for the apo-form of the catalytic domain, the linker region, and the carbohydrate-binding domain of the cellulose-active lytic polysaccharide monooxygenase ScLPMO10C.

    Science.gov (United States)

    Courtade, Gaston; Forsberg, Zarah; Vaaje-Kolstad, Gustav; Eijsink, Vincent G H; Aachmann, Finn L

    2017-10-01

    The apo-form of the 21.4 kDa catalytic domain and the 10.7 kDa carbohydrate binding domain of the AA10 family lytic polysaccharide monooxygenase ScLPMO10C from Streptomyces coelicolor have been isotopically labeled and recombinantly expressed in Escherichia coli. In this paper, we report the 1H, 13C, and 15N chemical shift assignments of each individual domain as well as an ensemble of the assignment for the full-length protein, including its approximately 30-amino acid long linker.

  3. The anisotropic effect of functional groups in 1H NMR spectra is the molecular response property of spatial nucleus independent chemical shifts (NICS)--conformational equilibria of exo/endo tetrahydrodicyclopentadiene derivatives.

    Science.gov (United States)

    Kleinpeter, Erich; Lämmermann, Anica; Kühn, Heiner

    2011-02-21

    The inversion of the flexible five-membered ring in tetrahydrodicyclopentadiene (TH-DCPD) derivatives remains fast on the NMR timescale even at 103 K. Since the intramolecular exchange process could not be sufficiently slowed for spectroscopic evaluation, the conformational equilibrium is thus inaccessible by dynamic NMR. Fortunately, the spatial magnetic properties of the aryl and carbonyl groups attached to the DCPD skeleton can be employed in order to evaluate the conformational state of the system. In this context, the anisotropic effects of the functional groups in the (1)H NMR spectra prove to be the molecular response property of spatial nucleus independent chemical shifts (NICS).

  4. (1)H, (13)C, and (15)N backbone and side-chain chemical shift assignments for the 36 proline-containing, full length 29 kDa human chimera-type galectin-3.

    Science.gov (United States)

    Ippel, Hans; Miller, Michelle C; Berbís, Manuel Alvaro; Suylen, Dennis; André, Sabine; Hackeng, Tilman M; Cañada, F Javier; Weber, Christian; Gabius, Hans-Joachim; Jiménez-Barbero, Jesús; Mayo, Kevin H

    2015-04-01

    Galectin-3, an adhesion/growth regulatory lectin, has a unique trimodular design consisting of the canonical carbohydrate recognition domain, a collagen-like tandem-repeat section, and an N-terminal peptide with two sites for Ser phosphorylation. Structural characterization of the full length protein with its non-lectin part (115 of 250 residues total) will help understand the multi functionality of this potent cellular effector. Here, we report (1)H, (13)C, and (15)N chemical shift assignments as determined by heteronuclear NMR spectroscopy .

  5. Chemical-Induced Read-Through at Premature Termination Codons Determined by a Rapid Dual-Fluorescence System Based on S. cerevisiae.

    Directory of Open Access Journals (Sweden)

    Emiliano Altamura

    Full Text Available Nonsense mutations generate in-frame stop codons in mRNA leading to a premature arrest of translation. Functional consequences of premature termination codons (PTCs include the synthesis of truncated proteins with loss of protein function causing severe inherited or acquired diseases. A therapeutic approach has been recently developed that is based on the use of chemical agents with the ability to suppress PTCs (read-through restoring the synthesis of a functional full-length protein. Research interest for compounds able to induce read-through requires an efficient high throughput large scale screening system. We present a rapid, sensitive and quantitative method based on a dual-fluorescence reporter expressed in the yeast Saccharomyces cerevisiae to monitor and quantitate read-through at PTCs. We have shown that our novel system works equally well in detecting read-through at all three PTCs UGA, UAG and UAA.

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

    Directory of Open Access Journals (Sweden)

    Simone Di Micco

    2013-12-01

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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    The peptide backbones of disordered proteins are routinely characterized by NMR with respect to transient structure and dynamics. Little experimental information is, however, available about the side chain conformations and how structure in the backbone affects the side chains. Methyl chemical sh...

  8. A rapid fabrication of C/C composites by a thermal gradient chemical vapor infiltration method with vaporized kerosene as a precursor

    Energy Technology Data Exchange (ETDEWEB)

    Wang Jiping [State Key Laboratory for Mechanical Behavior of Materials, Xi' an Jiaotong University, Xi' an 710049 (China)]. E-mail: buickwang@hotmail.com; Qian Junmin [State Key Laboratory for Mechanical Behavior of Materials, Xi' an Jiaotong University, Xi' an 710049 (China); Qiao Guanjun [State Key Laboratory for Mechanical Behavior of Materials, Xi' an Jiaotong University, Xi' an 710049 (China); Jin Zhihao [State Key Laboratory for Mechanical Behavior of Materials, Xi' an Jiaotong University, Xi' an 710049 (China)

    2007-01-15

    A thermal gradient, atmospheric pressure chemical vapor infiltration method with simultaneous vaporized kerosene as a precursor for rapid fabrication of C/C composites was studied. By this method, carbon felts (bulk density {approx}0.2 g cm{sup -3}) were densified to C/C composites with density of 1.67 and 1.71 g cm{sup -3} when prepared at 1050 and 1150 deg. C for 6 h, respectively. X-ray diffraction result indicates that the composites have a strong ability to graphitize and the higher deposition temperature leads to the increased graphitization degree. Polarized light microscope and scanning electron microscope images reveal that fibers of the composites prepared for 6 h are surrounded by ring-shaped pyrocarbon matrix with a thickness of {approx}20 {mu}m, and that the matrix is delaminated to 4-6 layer-like regions. The deposition process is analyzed by dividing the reactor into four regions associated with specific functions and the reasons for the rapid fabrication are proposed as the short convection and diffusion path for the precursor and the existing of thermal gradient across the preform.

  9. Shifting Blame?

    DEFF Research Database (Denmark)

    Garofalo, Orsola; Rott, Christina

    2017-01-01

    by the spokesperson if there is room for shifting blame. The increased punishment results from the messenger’s style of delivery: spokespersons are more likely than decision makers to express emotional regret instead of rational need. Receivers seem to punish the former style of communication because they view......Decision makers frequently have a spokesperson communicate their decisions. In this paper, we address two questions. First, does it matter who communicates an unfair decision? Second, does it matter how the unfair decision is communicated? We conduct a modified dictator game experiment in which...... either the decision maker or a spokesperson communicates the decided allocation to recipients, who then determine whether to punish either of them. We find that receivers punish both the decision maker and the spokesperson more often, and more heavily, for unfair allocations communicated...

  10. Rapid and automatic chemical identification of the medicinal flower buds of Lonicera plants by the benchtop and hand-held Fourier transform infrared spectroscopy

    Science.gov (United States)

    Chen, Jianbo; Guo, Baolin; Yan, Rui; Sun, Suqin; Zhou, Qun

    2017-07-01

    With the utilization of the hand-held equipment, Fourier transform infrared (FT-IR) spectroscopy is a promising analytical technique to minimize the time cost for the chemical identification of herbal materials. This research examines the feasibility of the hand-held FT-IR spectrometer for the on-site testing of herbal materials, using Lonicerae Japonicae Flos (LJF) and Lonicerae Flos (LF) as examples. Correlation-based linear discriminant models for LJF and LF are established based on the benchtop and hand-held FT-IR instruments. The benchtop FT-IR models can exactly recognize all articles of LJF and LF. Although a few LF articles are misjudged at the sub-class level, the hand-held FT-IR models are able to exactly discriminate LJF and LF. As a direct and label-free analytical technique, FT-IR spectroscopy has great potential in the rapid and automatic chemical identification of herbal materials either in laboratories or in fields. This is helpful to prevent the spread and use of adulterated herbal materials in time.

  11. 77Se NMR chemical shifts of 9-(arylselanyl)triptycenes: new standard for planar structures of ArSeR and applications to determine the structures in solutions.

    Science.gov (United States)

    Nakamoto, Takashi; Hayashi, Satoko; Nakanishi, Waro

    2008-12-05

    A set of new delta(Se) parameters is proposed as a standard for the planar (pl) orientational effect of p-YC(6)H(4) (Ar) in ArSeR, employing 9-(arylselanyl)triptycenes (1: p-YC(6)H(4)SeTpc). The Se-C(R) bond in ArSeR is placed on the Ar plane in pl and it is perpendicular to the plane in pd. Large upfield shifts are observed for Y = NMe(2), OMe, and Me (-22 to -6 ppm) and large downfield shifts for Y = COOEt, CN, and NO(2) (19-37 ppm), relative to Y = H, with small upfield and moderate downfield shifts by Y of halogens (-1 ppm for Y = F and 4 ppm for Y = Cl and Br). This must be the result of the p(Se)-pi(C(6)H(4))-p(Y) conjugation in 1 (pl). While the character of delta(Se) in 1 (pl) is very similar to that in 9-(arylselanyl)anthracenes (2 (pl)), it is very different from that of 1-(arylselanyl)anthraquinones (3 (pd)). Sets of delta(Se) of 1 and 2 must serve as the standard for pl and that of 3 does for pd in solutions. Structures of various ArSeR in solutions are determined from the viewpoint of the orientational effect based on the standard delta(Se) of 1-3. While the structure of 2-methyl-1-(arylselanyl)naphthalenes is concluded to be all pl in solutions, those of 8-chloro- and 8-bromo-1-(arylselanyl)naphthalenes are all pd, except for Y = COOEt, CN, and NO(2): The equilibrium between pd and pl contributes to those with Y = COOEt, CN, and NO(2). The structure of 1-(arylselanyl)naphthalenes changes depending on Y. The structures of ArSeMe and ArSeCOPh are shown to be pl and pd, respectively, in solutions. Those of ArSePh and ArSeAr seem to change depending on Y. delta(Se) of 1-3 are demonstrated to serve as the standard to determine the structures in solutions. The rules of thumb derived from the characters in delta(Se) for 1-3 are very useful to determine the structures of ArSeR in solutions, in addition to the analysis based on the plots.

  12. Computation provides chemical insight into the diverse hydride NMR chemical shifts of [Ru(NHC)4(L)H]0/+ species (NHC = N-heterocyclic carbene; L = vacant, H2, N2, CO, MeCN, O2, P4, SO2, H-, F- and Cl-) and their [Ru(R2PCH2CH2PR2)2(L)H]+ congeners.

    Science.gov (United States)

    Häller, L Jonas L; Mas-Marzá, Elena; Cybulski, Mateusz K; Sanguramath, Rajashekharayya A; Macgregor, Stuart A; Mahon, Mary F; Raynaud, Christophe; Russell, Christopher A; Whittlesey, Michael K

    2017-02-28

    Relativistic density functional theory calculations, both with and without the effects of spin-orbit coupling, have been employed to model hydride NMR chemical shifts for a series of [Ru(NHC)4(L)H]0/+ species (NHC = N-heterocyclic carbene; L = vacant, H2, N2, CO, MeCN, O2, P4, SO2, H-, F- and Cl-), as well as selected phosphine analogues [Ru(R2PCH2CH2PR2)2(L)H]+ (R = iPr, Cy; L = vacant, O2). Inclusion of spin-orbit coupling provides good agreement with the experimental data. For the NHC systems large variations in hydride chemical shift are shown to arise from the paramagnetic term, with high net shielding (L = vacant, Cl-, F-) being reinforced by the contribution from spin-orbit coupling. Natural chemical shift analysis highlights the major orbital contributions to the paramagnetic term and rationalizes trends via changes in the energies of the occupied Ru dπ orbitals and the unoccupied σ*Ru-H orbital. In [Ru(NHC)4(η2-O2)H]+ a δ-interaction with the O2 ligand results in a low-lying LUMO of dπ character. As a result this orbital can no longer contribute to the paramagnetic shielding, but instead provides additional deshielding via overlap with the remaining (occupied) dπ orbital under the Lz angular momentum operator. These two effects account for the unusual hydride chemical shift of +4.8 ppm observed experimentally for this species. Calculations reproduce hydride chemical shift data observed for [Ru(iPr2PCH2CH2PiPr2)2(η2-O2)H]+ (δ = -6.2 ppm) and [Ru(R2PCH2CH2PR2)2H]+ (ca. -32 ppm, R = iPr, Cy). For the latter, the presence of a weak agostic interaction trans to the hydride ligand is significant, as in its absence (R = Me) calculations predict a chemical shift of -41 ppm, similar to the [Ru(NHC)4H]+ analogues. Depending on the strength of the agostic interaction a variation of up to 18 ppm in hydride chemical shift is possible and this factor (that is not necessarily readily detected experimentally) can aid in the interpretation of hydride chemical shift

  13. The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations.

    Science.gov (United States)

    Vícha, Jan; Babinský, Martin; Demo, Gabriel; Otrusinová, Olga; Jansen, Séverine; Pekárová, Blanka; Žídek, Lukáš; Munzarová, Markéta L

    2016-05-01

    Sequence dependence of (13) C and (15) N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD , and its complexed form, CKI1RD •Mg(2+), was studied by means of MD/DFT calculations. MD simulations of a 20-ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and its sequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/interior position. Using models covering a 10 and a 15 Å environment of Mg(2+), a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg(2+) binding was described better by the 15 Å as compared to the 10 Å model. Thirteen chemical shifts were analyzed in terms of the effect of Mg(2+) insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg(2+) binding. The strongest individual effects were found for (15) N of D70, S74, and V68, where the electrostatics dominated; for (13) Cβ of D69 and (15) N of K76, where the influences were equal, and for (13) Cα of F72 and (13) Cβ of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed. © 2016 Wiley Periodicals, Inc.

  14. Rapid chemical evolution of tropospheric volcanic emissions from Redoubt Volcano, Alaska, based on observations of ozone and halogen-containing gases

    Science.gov (United States)

    Werner, Cynthia A.; Kelly, Peter; Kern, Christoph; Roberts, T.J.; Aluppe, A.

    2013-01-01

    We report results from an observational and modeling study of reactive chemistry in the tropospheric plume emitted by Redoubt Volcano, Alaska. Our measurements include the first observations of Br and I degassing from an Alaskan volcano, the first study of O3 evolution in a volcanic plume, as well as the first detection of BrO in the plume of a passively degassing Alaskan volcano. This study also represents the first detailed spatially-resolved comparison of measured and modeled O3 depletion in a volcanic plume. The composition of the plume was measured on June 20, 2010 using base-treated filter packs (for F, Cl, Br, I, and S) at the crater rim and by an instrumented fixed-wing aircraft on June 21 and August 19, 2010. The aircraft was used to track the chemical evolution of the plume up to ~ 30 km downwind (2 h plume travel time) from the volcano and was equipped to make in situ observations of O3, water vapor, CO2, SO2, and H2S during both flights plus remote spectroscopic observations of SO2 and BrO on the August 19th flight. The airborne data from June 21 reveal rapid chemical O3 destruction in the plume as well as the strong influence chemical heterogeneity in background air had on plume composition. Spectroscopic retrievals from airborne traverses made under the plume on August 19 show that BrO was present ~ 6 km downwind (20 min plume travel time) and in situ measurements revealed several ppbv of O3 loss near the center of the plume at a similar location downwind. Simulations with the PlumeChem model reproduce the timing and magnitude of the observed O3 deficits and suggest that autocatalytic release of reactive bromine and in-plume formation of BrO were primarily responsible for the observed O3 destruction in the plume. The measurements are therefore in general agreement with recent model studies of reactive halogen formation in volcanic plumes, but also show that field studies must pay close attention to variations in the composition of

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

    Science.gov (United States)

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

    2016-03-01

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

  16. Rapid and sensitive serum glucose determination using chemical labeling coupled with black phosphorus-assisted laser desorption/ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    Wang, Qing; Yu, Lei; Qi, Chu-Bo; Ding, Jun; He, Xiao-Mei; Wang, Ren-Qi; Feng, Yu-Qi

    2018-01-01

    Monitoring the concentration of blood glucose in patients is a key component of good medical diagnoses. Therefore, developing an accurate, rapid and sensitive strategy for monitoring blood glucose is of vital importance. We proposed a strategy for serum glucose determination combining 2-(4-boronobenzyl) isoquinolin-2-ium bromide chemical labeling with black phosphorus assisted laser desorption ionization-time of flight mass spectrometry (CL-BP/ALDI-TOF MS). The entire analytical process consisted of 1min of protein precipitation and 3min of chemical labeling in a microwave oven prior to the BP/ALDI-TOF MS analysis. The analysis can be completed in 5min with high throughput and extremely low sample consumption. Good linearity for glucose was obtained with a correlation coefficient (R) of 0.9986. The limit of detection (LOD) and limit of quantification (LOQ) were 11.5 fmol and 37.5 fmol, respectively. Satisfied reproducibility and reliability were gained by evaluation of the intra- and inter-day precisions with relative standard deviations (RSDs) less than 7.2% and relative recoveries ranging from 87.1% to 108.1%, respectively. The proposed strategy was also applied for the analysis of endogenous glucose in various serum samples and the results were consistent with those obtained using the hexokinase method in a clinical laboratory. Considering the results, the proposed CL-BP/ALDI-TOF MS strategy has proven to be reliable, fast, and sensitive for quantitative analysis of serum glucose. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Effects of the gas feeding method on the properties of 3C-SiC/Si(111) grown by rapid thermal chemical vapor deposition

    CERN Document Server

    Shim, H W; Suh, E K

    1998-01-01

    High-quality crystalline 3C-SiC thin films are grown by rapid thermal chemical vapor deposition (RTCVD) on Si(111) by using two different growth processes. The films are grown along the [111] direction at 1200 .deg. C. The quality of the films are investigated by X-ray diffraction, transmission electron microscopy, and transmission electron diffraction. The SiC film grown by flowing the tetramethylsilane (TMS) gas before heating the substrate up to the growth temperature does not contain many voids at the SiC/Si interface, while the SiC grown by heating the substrate before supplying the TMS gas possesses many voids at the interface. The unintentionally doped SiC film grown by gas flow before heating the substrate appears to be n-type with a carrier concentration of 1.48 x 10 sup 1 sup 6 cm sup - sup 3 , a electron mobility of 884 cm sup 2 /V centre dot s, and a resistivity of 0.462 OMEGA centre dot cm. The physical properties, such as the electrical properties, the surface morphology, and the crystallinity, ...

  18. Solid-state (185/187)Re NMR and GIPAW DFT study of perrhenates and Re2(CO)10: chemical shift anisotropy, NMR crystallography, and a metal-metal bond.

    Science.gov (United States)

    Widdifield, Cory M; Perras, Frédéric A; Bryce, David L

    2015-04-21

    Advances in solid-state nuclear magnetic resonance (SSNMR) methods, such as dynamic nuclear polarization (DNP), intricate pulse sequences, and increased applied magnetic fields, allow for the study of systems which even very recently would be impractical. However, SSNMR methods using certain quadrupolar probe nuclei (i.e., I > 1/2), such as (185/187)Re remain far from fully developed due to the exceedingly strong interaction between the quadrupole moment of these nuclei and local electric field gradients (EFGs). We present a detailed high-field (B0 = 21.1 T) experimental SSNMR study on several perrhenates (KReO4, AgReO4, Ca(ReO4)2·2H2O), as well as ReO3 and Re2(CO)10. We propose solid ReO3 as a new rhenium SSNMR chemical shift standard due to its reproducible and sharp (185/187)Re NMR resonances. We show that for KReO4, previously poorly understood high-order quadrupole-induced effects (HOQIE) on the satellite transitions can be used to measure the EFG tensor asymmetry (i.e., ηQ) to nearly an order-of-magnitude greater precision than competing SSNMR and nuclear quadrupole resonance (NQR) approaches. Samples of AgReO4 and Ca(ReO4)2·2H2O enable us to comment on the effects of counter-ions and hydration upon Re(vii) chemical shifts. Calcium-43 and (185/187)Re NMR tensor parameters allow us to conclude that two proposed crystal structures for Ca(ReO4)2·2H2O, which would be considered as distinct, are in fact the same structure. Study of Re2(CO)10 provides insights into the effects of Re-Re bonding on the rhenium NMR tensor parameters and rhenium oxidation state on the Re chemical shift value. As overtone NQR experiments allowed us to precisely measure the (185/187)Re EFG tensor of Re2(CO)10, we were able to measure rhenium chemical shift anisotropy (CSA) for the first time in a powdered sample. Experimental observations are supported by gauge-including projector augmented-wave (GIPAW) density functional theory (DFT) calculations, with NMR tensor calculations also

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-07-01

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

  20. Large species shifts triggered by small forces

    NARCIS (Netherlands)

    Nes, van E.H.; Scheffer, M.

    2004-01-01

    Changes in species composition of communities seem to proceed gradually at first sight, but remarkably rapid shifts are known to occur. Although disrupting disturbances seem an obvious explanation for such shifts, evidence for large disturbances is not always apparent. Here we show that complex

  1. Microfluidic chemical reaction circuits

    Science.gov (United States)

    Lee, Chung-cheng [Irvine, CA; Sui, Guodong [Los Angeles, CA; Elizarov, Arkadij [Valley Village, CA; Kolb, Hartmuth C [Playa del Rey, CA; Huang, Jiang [San Jose, CA; Heath, James R [South Pasadena, CA; Phelps, Michael E [Los Angeles, CA; Quake, Stephen R [Stanford, CA; Tseng, Hsian-rong [Los Angeles, CA; Wyatt, Paul [Tipperary, IE; Daridon, Antoine [Mont-Sur-Rolle, CH

    2012-06-26

    New microfluidic devices, useful for carrying out chemical reactions, are provided. The devices are adapted for on-chip solvent exchange, chemical processes requiring multiple chemical reactions, and rapid concentration of reagents.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-07-15

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

  3. Primary and metastatic intraaxial brain tumors: prospective comparison of multivoxel 2D chemical-shift imaging (CSI) proton MR spectroscopy, perfusion MRI, and histopathological findings in a group of 159 patients.

    Science.gov (United States)

    Bendini, Matteo; Marton, Elisabetta; Feletti, Alberto; Rossi, Sabrina; Curtolo, Stefano; Inches, Ingrid; Ronzon, Monica; Longatti, Pierluigi; Di Paola, Francesco

    2011-02-01

    This study aims to assess the diagnostic value of multivoxel 2D chemical-shift imaging (CSI) proton magnetic resonance (MR) spectroscopy combined with perfusion magnetic resonance imaging (MRI) in the differential diagnosis and grading of brain tumors by comparing neuroimaging data with histopathological findings obtained after resection or biopsy. A total of 159 patients with a previous brain tumor diagnosis underwent multivoxel 2D CSI proton MR spectroscopy and perfusion MRI. MR spectroscopy multivoxel 2D CSI was performed with an echo time of 30, TR 1,500, FOV 160 mm, acquisition time 7 min 34 s. rCBV maps were evaluated during postprocessing. Statistical analysis was performed on the examination of distributive normality, with logarithmic transformations, Fisher's test, and Bonferroni's test. We used the Pearson's test to compare percentages. In the differential diagnosis between GBM and metastases, MR spectroscopy multivoxel 2D CSI, combined with dynamic contrast enhanced MRI (DCE-MRI) perfusion, reached high sensibility and specificity (p CSI spectroscopy and perfusion imaging has shown a high potential in the differential diagnosis and grading of brain tumors. Further exploration into diagnostic procedures that can significantly distinguish between grade III-IV and grade II tumors is needed.

  4. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    1969-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Valdir A. Facundo

    2004-02-01

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

  6. OpenShift Workshop

    CERN Multimedia

    CERN. Geneva; Rodriguez Peon, Alberto

    2017-01-01

    Workshop to introduce developers to the OpenShift platform available at CERN. Several use cases will be shown, including deploying an existing application into OpenShift. We expect attendees to realize about OpenShift features and general architecture of the service.

  7. Rapid screening of chemical warfare nerve agent metabolites in urine by atmospheric solids analysis probe-mass spectroscopy (ASAP-MS).

    Science.gov (United States)

    Zydel, Frank; Smith, J Richard; Pagnotti, Vincent S; Lawrence, Richard J; McEwen, Charles N; Capacio, Benedict R

    2012-01-01

    Exposures to organophosphorus nerve agents (OPNA) remain a threat to both civilian and military populations. Verification of exposures typically involves determinations of urinary metabolites or adducted proteins in blood. Urinary alkyl methylphosphonic acid metabolites resulting from hydrolysis of OPNAs provide a convenient marker for OPNA exposure. In a military setting, urine is a relatively easy sample to obtain, and a rapid turnaround for analyses for the identification of metabolites is critical for field commanders. Timely information on use and identity of OPNAs facilitates decisions regarding employment of personal protective equipment and additional strategies to mitigate additional exposure(s). Herein, we report the development of a rapid mass spectrometric (MS) method to identify OPNA metabolites directly from urine with no sample preparation. Synthetic urine spiked with multiple OPNA metabolites was analyzed using an atmospheric solids analysis probe (ASAP) attached to a high resolution mass spectrometer. The alkyl methylphosphonic acid metabolites resulting from hydrolysis of sarin, cyclosarin, soman, and Russian VX were clearly detectable down to a level of 1.0 ng/ml. The ability to rapidly detect OPNA metabolites in unprepared urine allows for the design of a field-deployable device that could afford field personnel the ability to rapidly screen individuals for specific OPNA exposure. In addition, this provides proof-of-concept evidence that a fieldable ASAP-MS device could afford personnel the ability to rapidly detect OPNAs on skin, equipment, and other porous surfaces. Published 2012. This article is a US Government work and is in the public domain in the USA. Copyright © 2012 John Wiley & Sons, Ltd.

  8. Rapid Induction of Cerebral Organoids From Human Induced Pluripotent Stem Cells Using a Chemically Defined Hydrogel and Defined Cell Culture Medium.

    Science.gov (United States)

    Lindborg, Beth A; Brekke, John H; Vegoe, Amanda L; Ulrich, Connor B; Haider, Kerri T; Subramaniam, Sandhya; Venhuizen, Scott L; Eide, Cindy R; Orchard, Paul J; Chen, Weili; Wang, Qi; Pelaez, Francisco; Scott, Carolyn M; Kokkoli, Efrosini; Keirstead, Susan A; Dutton, James R; Tolar, Jakub; O'Brien, Timothy D

    2016-07-01

    Tissue organoids are a promising technology that may accelerate development of the societal and NIH mandate for precision medicine. Here we describe a robust and simple method for generating cerebral organoids (cOrgs) from human pluripotent stem cells by using a chemically defined hydrogel material and chemically defined culture medium. By using no additional neural induction components, cOrgs appeared on the hydrogel surface within 10-14 days, and under static culture conditions, they attained sizes up to 3 mm in greatest dimension by day 28. Histologically, the organoids showed neural rosette and neural tube-like structures and evidence of early corticogenesis. Immunostaining and quantitative reverse-transcription polymerase chain reaction demonstrated protein and gene expression representative of forebrain, midbrain, and hindbrain development. Physiologic studies showed responses to glutamate and depolarization in many cells, consistent with neural behavior. The method of cerebral organoid generation described here facilitates access to this technology, enables scalable applications, and provides a potential pathway to translational applications where defined components are desirable. Tissue organoids are a promising technology with many potential applications, such as pharmaceutical screens and development of in vitro disease models, particularly for human polygenic conditions where animal models are insufficient. This work describes a robust and simple method for generating cerebral organoids from human induced pluripotent stem cells by using a chemically defined hydrogel material and chemically defined culture medium. This method, by virtue of its simplicity and use of defined materials, greatly facilitates access to cerebral organoid technology, enables scalable applications, and provides a potential pathway to translational applications where defined components are desirable. ©AlphaMed Press.

  9. Rapid determination of chemical composition and classification of bamboo fractions using visible-near infrared spectroscopy coupled with multivariate data analysis.

    Science.gov (United States)

    Yang, Zhong; Li, Kang; Zhang, Maomao; Xin, Donglin; Zhang, Junhua

    2016-01-01

    During conversion of bamboo into biofuels and chemicals, it is necessary to efficiently predict the chemical composition and digestibility of biomass. However, traditional methods for determination of lignocellulosic biomass composition are expensive and time consuming. In this work, a novel and fast method for quantitative and qualitative analysis of chemical composition and enzymatic digestibilities of juvenile bamboo and mature bamboo fractions (bamboo green, bamboo timber, bamboo yellow, bamboo node, and bamboo branch) using visible-near infrared spectra was evaluated. The developed partial least squares models yielded coefficients of determination in calibration of 0.88, 0.94, and 0.96, for cellulose, xylan, and lignin of bamboo fractions in raw spectra, respectively. After visible-near infrared spectra being pretreated, the corresponding coefficients of determination in calibration yielded by the developed partial least squares models are 0.994, 0.990, and 0.996, respectively. The score plots of principal component analysis of mature bamboo, juvenile bamboo, and different fractions of mature bamboo were obviously distinguished in raw spectra. Based on partial least squares discriminant analysis, the classification accuracies of mature bamboo, juvenile bamboo, and different fractions of bamboo (bamboo green, bamboo timber, bamboo yellow, and bamboo branch) all reached 100 %. In addition, high accuracies of evaluation of the enzymatic digestibilities of bamboo fractions after pretreatment with aqueous ammonia were also observed. The results showed the potential of visible-near infrared spectroscopy in combination with multivariate analysis in efficiently analyzing the chemical composition and hydrolysabilities of lignocellulosic biomass, such as bamboo fractions.

  10. Police officers attitude to different shift systems: association with age, present shift schedule, health and sleep/wake complaints.

    Science.gov (United States)

    Kecklund, Göran; Eriksen, Claire Anne; Akerstedt, Torbjörn

    2008-09-01

    It is often claimed that shift workers give priority to long series of days off and therefore prefer compressed work schedules at the expense of what is optimal for long-term health. The aim of the present study was to evaluate the attitude to six new shift systems among a randomly selected sample of police officers. The results showed that the most popular shift system was a rapidly, forward, rotating schedule with at least 16 h of rest between shifts, despite that it had fewer days off compared with some of the compressed shift systems. However, the individual differences were large and many individuals (32%) disliked the rapidly rotating shift system. Young age was associated with a positive attitude to the rapidly rotating shift system. The attitude to the shift system was also influenced by the present schedule, and shift systems that were similar to the present work hours received more positive evaluation. Sleep and health complaints showed no association with the attitude to the shift systems. In conclusion, the shift workers attitude to the new schedules was partly in agreement with the ergonomic recommendations of the design of three-shift systems that will facilitate sufficient sleep and minimize negative health consequences.

  11. Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP8−) for dual biosensing of pH with CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts)

    Science.gov (United States)

    Huang, Yuegao; Coman, Daniel; Ali, Meser M.; Hyder, Fahmeed

    2014-01-01

    Relaxivity based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd3+) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the non-exchangeable or the exchangeable protons on the lanthanide complexes themselves. The non-exchangeable protons (e.g., –CHx, where 3≥x≥1) are detected using a three-dimensional chemical shift imaging method called Biosensor Imaging of Redundant Deviation in Shifts (BIRDS), whereas the exchangeable protons (e.g., –OH or –NHy, where 2≥y≥1) are measured with Chemical Exchange Saturation Transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP8−) chelated with thulium (Tm3+) and ytterbium (Yb3+). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs. using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e., 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP5− than with TmDOTA-4AmP5−. In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging. PMID:24801742

  12. Chemical cardioversion of recent-onset atrial fibrillation in the emergency department using vernakalant hydrochloride achieves safe and rapid restoration of sinus rhythm and facilitates same day discharge.

    Science.gov (United States)

    Stoneman, P; Gilligan, P; Mahon, P; Sheahan, R

    2017-11-01

    Vernakalant hydrochloride is a rapid-acting antiarrhythmic drug licensed in the EU since 2010 for the conversion of recent-onset atrial fibrillation with proven efficacy and safety when compared with placebo and amiodarone in randomized clinical trials. The aim of our study was to determine the feasibility of same day discharge (following 2 h monitoring) from the emergency department after successful cardioversion using vernakalant hydrochloride. Patients with recent-onset atrial fibrillation treated in the emergency department of a large Dublin academic teaching hospital. Patients received a maximum of two weight based 10 min infusions of vernakalant. Hypotensive events (>30% initial blood pressure), arrhythmias, conversion rates, and time to conversion were recorded. Sinus rhythm was restored in 35 out of 42 patients (83%) in an average of 8.8 min (median 8 min), average CHA2DS2-VASc of 0.92, HAS-BLED of 0.21 and average symptoms duration of 12 h. There were no hypotensive or arrhythmogenic events. 41 out of 42 patients were discharged after 2 h of monitoring. Vernakalant hydrochloride has provided a quick, safe, and practical means of achieving rapid restoration of sinus rhythm in our ED population with stable recent-onset AF who would otherwise not have undergone routine electrically cardioversion and same day discharge.

  13. Insomnia in shift work.

    Science.gov (United States)

    Vallières, Annie; Azaiez, Aïda; Moreau, Vincent; LeBlanc, Mélanie; Morin, Charles M

    2014-12-01

    Shift work disorder involves insomnia and/or excessive sleepiness associated with the work schedule. The present study examined the impact of insomnia on the perceived physical and psychological health of adults working on night and rotating shift schedules compared to day workers. A total of 418 adults (51% women, mean age 41.4 years), including 51 night workers, 158 rotating shift workers, and 209 day workers were selected from an epidemiological study. An algorithm was used to classify each participant of the two groups (working night or rotating shifts) according to the presence or absence of insomnia symptoms. Each of these individuals was paired with a day worker according to gender, age, and income. Participants completed several questionnaires measuring sleep, health, and psychological variables. Night and rotating shift workers with insomnia presented a sleep profile similar to that of day workers with insomnia. Sleep time was more strongly related to insomnia than to shift work per se. Participants with insomnia in the three groups complained of anxiety, depression, and fatigue, and reported consuming equal amounts of sleep-aid medication. Insomnia also contributed to chronic pain and otorhinolaryngology problems, especially among rotating shift workers. Work productivity and absenteeism were more strongly related to insomnia. The present study highlights insomnia as an important component of the sleep difficulties experienced by shift workers. Insomnia may exacerbate certain physical and mental health problems of shift workers, and impair their quality of life. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Implementing OpenShift

    CERN Document Server

    Miller, Adam

    2013-01-01

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

  15. Rapid Data Assimilation in the Indoor Environment: theory and examples from real-time interpretation of indoor plumes of airborne chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Gadgil, Ashok; Sohn, Michael; Sreedharan, Priya

    2008-09-01

    Releases of acutely toxic airborne contaminants in or near a building can lead to significant human exposures unless prompt response measures are identified and implemented. Commonly, possible responses include conflicting strategies, such as shutting the ventilation system off versus running it in a purge (100percent outside air) mode, or having occupants evacuate versus sheltering in place. The right choice depends in part on quickly identifying the source locations, the amounts released, and the likely future dispersion routes of the pollutants. This paper summarizes recent developments to provide such estimates in real time using an approach called Bayesian Monte Carlo updating. This approach rapidly interprets measurements of airborne pollutant concentrations from multiple sensors placed in the building and computes best estimates and uncertainties of the release conditions. The algorithm is fast, capable of continuously updating the estimates as measurements stream in from sensors. The approach is employed, as illustration, to conduct two specific investigations under different situations.

  16. Rapid Data Assimilation in the Indoor Environment: Theory and Examples from Real-Time Interpretation of Indoor Plumes of Airborne Chemical

    Energy Technology Data Exchange (ETDEWEB)

    Gadgil, Ashok; Gadgil, Ashok; Sohn, Michael; Sreedharan, Priya

    2007-08-01

    Releases of acutely toxic airborne contaminants in or near a building can lead to significant human exposures unless prompt response measures are identified and implemented. Possible responses include conflicting options, such as shutting the ventilation system off versus running it in a purge (100 percent outside air) mode, or having occupants evacuate versus sheltering in place. The right choice depends in part on quickly identifying the source location, the amount released, and the likely future dispersion of the pollutant. This paper summarizes recent developments to provide such estimates in real time using an approach called Bayesian Monte Carlo updating. This approach rapidly interprets measurements of airborne pollutant concentrations from multiple sensors placed in the building, and computes best estimates and uncertainties of the release conditions. The algorithm is fast, and can continuously update the estimates as measurements stream in from sensors. As an illustration, two specific applications of the approach are described.

  17. Regime shifts in the anthropocene: drivers, risks, and resilience.

    Science.gov (United States)

    Rocha, Juan Carlos; Peterson, Garry D; Biggs, Reinette

    2015-01-01

    Many ecosystems can experience regime shifts: surprising, large and persistent changes in the function and structure of ecosystems. Assessing whether continued global change will lead to further regime shifts, or has the potential to trigger cascading regime shifts has been a central question in global change policy. Addressing this issue has, however, been hampered by the focus of regime shift research on specific cases and types of regime shifts. To systematically assess the global risk of regime shifts we conducted a comparative analysis of 25 generic types of regime shifts across marine, terrestrial and polar systems; identifying their drivers, and impacts on ecosystem services. Our results show that the drivers of regime shifts are diverse and co-occur strongly, which suggests that continued global change can be expected to synchronously increase the risk of multiple regime shifts. Furthermore, many regime shift drivers are related to climate change and food production, whose links to the continued expansion of human activities makes them difficult to limit. Because many regime shifts can amplify the drivers of other regime shifts, continued global change can also be expected to increase the risk of cascading regime shifts. Nevertheless, the variety of scales at which regime shift drivers operate provides opportunities for reducing the risk of many types of regime shifts by addressing local or regional drivers, even in the absence of rapid reduction of global drivers.

  18. Shifting employment revisited

    NARCIS (Netherlands)

    Cremers, Jan; Gramuglia, Alessia

    2014-01-01

    The CLR-network examined in 2006 the phenomenon of undeclared labour, with specific regard to the construction sector. The resulting study, Shifting Employment: undeclared labour in construction (Shifting-study hereafter), gave evidence that this is an area particularly affected by undeclared

  19. Shifted Independent Component Analysis

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  20. OpenShift cookbook

    CERN Document Server

    Gulati, Shekhar

    2014-01-01

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

  1. A refined model of the chlorosomal antennae of the green bacterium chlorobium tepidum from proton chemical shift constraints obtained with high-field 2-D and 3-D MAS NMR dipolar correlation spectroscopy

    NARCIS (Netherlands)

    Rossum, van B.E.J.; Steengaard, D.B.; Boender, G.J.; Schaffner, K.; Holzwarth, A.R.; Groot, de H.J.M.

    2001-01-01

    Heteronuclear 2-D and 3-D magic-angle spinning NMR dipolar correlation spectroscopy was applied to determine solid-state 1H shifts for aggregated bacteriochlorophyll c (BChl c) in uniformly 13C-enriched light harvesting chlorosomes of the green photosynthetic bacterium Chlorobium tepidum. A complete

  2. Instantaneous phase shifting deflectometry.

    Science.gov (United States)

    Trumper, Isaac; Choi, Heejoo; Kim, Dae Wook

    2016-11-28

    An instantaneous phase shifting deflectometry measurement method is presented and implemented by measuring a time varying deformable mirror with an iPhone ® 6. The instantaneous method is based on multiplexing phase shifted fringe patterns with color, and decomposing them in x and y using Fourier techniques. Along with experimental data showing the capabilities of the instantaneous deflectometry system, a quantitative comparison with the Fourier transform profilometry method, which is a distinct phase measuring method from the phase shifting approach, is presented. Sources of error, nonlinear color-multiplexing induced error correction, and hardware limitations are discussed.

  3. Shift Performance Test and Analysis of Multipurpose Vehicle

    Directory of Open Access Journals (Sweden)

    Can Yang

    2014-08-01

    Full Text Available This paper presented an analysis of the gear shifting performances of a multipurpose vehicle transmission in driving condition by Ricardo's Gear Shift Quality Assessment (GSQA system. The performances of the transmission included the travel and effort of the gear shift lever and synchronizing time. The mathematic models of the transmission including the gear shift mechanism and synchronizer were developed in MATLAB. The model of the gear shift mechanism was developed to analyze the travel map of the gear shift lever and the model of the synchronizer was developed to obtain the force-time curve of the synchronizer during the slipping time. The model of the synchronizer was used to investigate the relationship between the performances of the transmission and the variation of parameters during gear shifting. The mathematic models of the gear shift mechanism and the synchronizer provided a rapid design and verification method for the transmission with ring spring.

  4. Animal-Free Chemical Safety Assessment

    Directory of Open Access Journals (Sweden)

    George D Loizou

    2016-07-01

    Full Text Available The exponential growth of the Internet of Things and the global popularity and remarkable decline in cost of the mobile phone is driving the digital transformation of medical practice. The rapidly maturing digital, nonmedical world of mobile (wireless devices, cloud computing and social networking is coalescing with the emerging digital medical world of omics data, biosensors and advanced imaging which offers the increasingly realistic prospect of personalized medicine. Described as a potential seismic shift from the current healthcare model to a wellness paradigm that is predictive, preventative, personalized and participatory, this change is based on the development of increasingly sophisticated biosensors which can track and measure key biochemical variables in people. Additional key drivers in this shift are metabolomic and proteomic signatures, which are increasingly being reported as pre-symptomatic, diagnostic and prognostic of toxicity and disease. These advancements also have profound implications for toxicological evaluation and safety assessment of pharmaceuticals and environmental chemicals. An approach based primarily on human in vivo and high-throughput in vitro human cell-line data is a distinct possibility. This would transform current chemical safety assessment practise which operates in a human data poor to a human data rich environment. This could also lead to a seismic shift from the current animal-based to an animal-free chemical safety assessment paradigm.

  5. Rapid screening of anabolic steroids in horse urine with ultra-high-performance liquid chromatography/tandem mass spectrometry after chemical derivatisation.

    Science.gov (United States)

    Wong, Colton H F; Leung, David K K; Tang, Francis P W; Wong, Jenny K Y; Yu, Nola H; Wan, Terence S M

    2012-04-06

    Liquid chromatography/mass spectrometry (LC/MS) has been successfully applied to the detection of anabolic steroids in biological samples. However, the sensitive detection of saturated hydroxysteroids, such as androstanediols, by electrospray ionisation (ESI) is difficult because of their poor ability to ionise. In view of this, chemical derivatisation has been used to enhance the detection sensitivity of hydroxysteroids by LC/MS. This paper describes the development of a sensitive ultra-high-performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS) method for the screening of anabolic steroids in horse urine by incorporating a chemical derivatisation step, using picolinic acid as the derivatisation reagent. The method involved solid-phase extraction (SPE) of both free and conjugated anabolic steroids in horse urine using a polymer-based SPE cartridge (Abs Elut Nexus). The conjugated steroids in the eluate were hydrolysed by methanolysis and the resulting extract was further cleaned up by liquid-liquid extraction. The resulting free steroids in the extract were derivatised with picolinic acid to form the corresponding picolinoyl esters and analysed by UHPLC/MS/MS in the positive ESI mode with selected-reaction-monitoring. Separation of the targeted steroids was performed on a C18 UHPLC column. The instrument turnaround time was 10.5 min inclusive of post-run equilibration. A total of thirty-three anabolic steroids (including 17β-estradiol, 5(10)-estrene-3β,17α-diol, 5α-estrane-3β,17α-diol, 17α-ethyl-5α-estran-3α,17β-diol, 17α-methyl-5α-androstan-3,17β-diols, androstanediols, nandrolone and testosterone) spiked in negative horse urine at the QC levels (ranging from 0.75 to 30 ng/mL) could be consistently detected. The intra-day and inter-day precisions (% RSD) for the peak area ratios were around 7-51% and around 1-72%, respectively. The intra-day and inter-day precisions (% RSD) for the relative retention times were both less than 1% for

  6. Determination of red blood cell fatty acid profiles: Rapid and high-confident analysis by chemical ionization-gas chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Schober, Yvonne; Wahl, Hans Günther; Renz, Harald; Nockher, Wolfgang Andreas

    2017-01-01

    Cellular fatty acid (FA) profiles have been acknowledged as biomarkers in various human diseases. Nevertheless, common FA analysis by gas chromatography mass spectrometry (GC-MS) requires long analysis time. Hence, there is a need for feasible methods for high throughput analysis in clinical studies. FA was extracted from red blood cells (RBC) and derivatized to fatty acid methyl esters (FAME). A method using gas chromatography tandem mass spectrometry (GC-MS/MS) with ammonia-induced chemical ionization (CI) was developed for the analysis of FA profiles in human RBC. We compared this method with classical single GC-MS using electron impact ionization (EI). The FA profiles of 703 RBC samples were determined by GC-MS/MS. In contrast to EI ammonia-induced CI resulted in adequate amounts of molecular ions for further fragmentation of FAME. Specific fragments for confident quantification and fragmentation were determined for 45 FA. The GC-MS/MS method has a total run time of 9min compared to typical analysis times of up to 60min in conventional GC-MS. Intra and inter assay variations were Analysis of RBC FA composition revealed an age-dependent increase of the omega-3 eicosapentaenoic and docosahexaenoic acid, and a decline of the omega-6 linoleic acid with a corresponding rise of the omega-3 index. The combination of ammonia-induced CI and tandem mass spectrometry after GC separation allows for high-throughput, robust and confident analysis of FA profiles in the clinical laboratory. Copyright © 2016. Published by Elsevier B.V.

  7. Combining a Clostridial enzyme exhibiting unusual active site plasticity with a remarkably facile sigmatropic rearrangement: rapid, stereocontrolled entry into densely functionalized fluorinated phosphonates for chemical biology.

    Science.gov (United States)

    Panigrahi, Kaushik; Applegate, Gregory A; Malik, Guillaume; Berkowitz, David B

    2015-03-18

    Described is an efficient stereocontrolled route into valuable, densely functionalized fluorinated phosphonates that takes advantage of (i) a Clostridial enzyme to set the absolute stereochemistry and (ii) a new [3,3]-sigmatropic rearrangement of the thiono-Claisen variety that is among the fastest sigmatropic rearrangements yet reported. Here, a pronounced rate enhancement is achieved by distal fluorination. This rearrangement is completely stereoretentive, parlaying the enzymatically established β-C-O stereochemistry in the substrate into the δ-C-S stereochemistry in the product. The final products are of interest to chemical biology, with a platform for Zn-aminopeptidase A inhibitors being constructed here. The enzyme, Clostridium acetobutylicum (CaADH), recently expressed by our group, reduces a spectrum of γ,δ-unsaturated β-keto-α,α-difluorophosphonate esters (93-99% ee; 10 examples). The resultant β-hydroxy-α,α-difluorophosphonates possess the "L"-stereochemistry, opposite to that previously observed for the CaADH-reduction of ω-keto carboxylate esters ("D"), indicating an unusual active site plasticity. For the thiono-Claisen rearrangement, a notable structure-reactivity relationship is observed. Measured rate constants vary by over 3 orders of magnitude, depending upon thiono-ester structure. Temperature-dependent kinetics reveal an unusually favorable entropy of activation (ΔS(‡) = 14.5 ± 0.6 e.u.). Most notably, a 400-fold rate enhancement is seen upon fluorination of the distal arene ring, arising from favorable enthalpic (ΔΔH(‡) = -2.3 kcal/mol) and entropic (ΔΔS(‡) = 4 e.u., i.e. 1.2 kcal/mol at rt) contributions. The unusual active site plasticity seen here is expected to drive structural biology studies on CaADH, while the exceptionally facile sigmatropic rearrangement is expected to drive computational studies to elucidate its underlying entropic and enthalpic basis.

  8. Rapid adsorption of toxic Pb(II) ions from aqueous solution using multiwall carbon nanotubes synthesized by microwave chemical vapor deposition technique.

    Science.gov (United States)

    Mubarak, Nabisab Mujawar; Sahu, Jaya Narayan; Abdullah, Ezzat Chan; Jayakumar, Natesan Subramanian

    2016-07-01

    Multiwall carbon nanotubes (MWCNTs) were synthesized using a tubular microwave chemical vapor deposition technique, using acetylene and hydrogen as the precursor gases and ferrocene as catalyst. The novel MWCNT samples were tested for their performance in terms of Pb(II) binding. The synthesized MWCNT samples were characterized using Fourier Transform Infrared (FT-IR), Brunauer, Emmett and Teller (BET), Field Emission Scanning Electron Microscopy (FESEM) analysis, and the adsorption of Pb(II) was studied as a function of pH, initial Pb(II) concentration, MWCNT dosage, agitation speed, and adsorption time, and process parameters were optimized. The adsorption data followed both Freundlich and Langmuir isotherms. On the basis of the Langmuir model, Qmax was calculated to be 104.2mg/g for the microwave-synthesized MWCNTs. In order to investigate the dynamic behavior of MWCNTs as an adsorbent, the kinetic data were modeled using pseudo first-order and pseudo second-order equations. Different thermodynamic parameters, viz., ∆H(0), ∆S(0) and ∆G(0) were evaluated and it was found that the adsorption was feasible, spontaneous and endothermic in nature. The statistical analysis revealed that the optimum conditions for the highest removal (99.9%) of Pb(II) are at pH5, MWCNT dosage 0.1g, agitation speed 160r/min and time of 22.5min with the initial concentration of 10mg/L. Our results proved that microwave-synthesized MWCNTs can be used as an effective Pb(II) adsorbent due to their high adsorption capacity as well as the short adsorption time needed to achieve equilibrium. Copyright © 2016. Published by Elsevier B.V.

  9. Shift Verification and Validation

    Energy Technology Data Exchange (ETDEWEB)

    Pandya, Tara M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Evans, Thomas M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Davidson, Gregory G [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Johnson, Seth R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Godfrey, Andrew T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-09-07

    This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over a burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.

  10. The Issue of Calculating the Final Temperature of the Products of Rapid Exothermic Chemical Reactions with Significant Energy Release in a Closed Volume

    Science.gov (United States)

    Lazarev, V.; Geidmanis, D.

    2016-02-01

    The theoretical problem solved in this article is the calculation of thermodynamic parameters such as final temperature, distribution of the liquid and dry saturated vapour phases of the substance that are considered to be in thermodynamic equilibrium, and pressure of the system of several reaction products after adding to the system a certain amount of heat or the thermal effect released during rapid exothermic reaction in a closed volume that occurs so fast that it can be considered to be adiabatic, and when the volume of liquid reagents is several orders of magnitude less than the volume of the reactor. The general multi-substance problem is reduced to a theoretical problem for one substance of calculation thermodynamic parameters of system after adding a certain amount of heat that gives theoretically rigorous isochoric calculation. In this article, we substantiate our view that isochoric pass of calculation is more robust compared to seemingly more natural isobaric pass of calculation, if the later involves quite not trivial calculation of the adiabatic compression of a two-phase system (liquid - dry saturated vapour) that can pass itself into another kind of state (liquid - wet saturated vapour), which requires, apparently, more complex descriptions compared with isochoric calculation because the specific heat capacity of wet saturated vapour can be negative. The solved theoretical problem relates to a practical problem that has been a driver for our research as part of a design of the reactor of the titanium reduction from magnesium and titanium tetrachloride supplied into atmosphere of the reactor at high temperatures when both reagents are in gaseous state. The reaction is known to be exothermic with a high thermal effect, and estimate of the final temperature and pressure of the products of reaction, for instance, designing the reactor allows eliminating the possibility of the reaction products to penetrate backwards into supply tracts of the reagents

  11. Aircraft borne combined measurements of the Fukushima radionuclide Xe-133 and fossil fuel combustion generated pollutants in the TIL - implications for cyclone induced rapid lift and TIL physico-chemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Schlager, Hans; Aufmhoff, Heinfried; Baumann, Robert; Schumann, Ulrich [DLR IPA, Oberpfaffenhofen (Germany); Arnold, Frank [MPI Kernphysik, Heidelberg (Germany); DLR IPA, Oberpfaffenhofen (Germany); Simgen, Hardy; Lindemann, Siegfried; Rauch, Ludwig; Kaether, Frank [MPI Kernphysik, Heidelberg (Germany); Pirjola, Liisa [University of Helsinki, Helsinki (Finland)

    2013-07-01

    The radionuclide Xe-133, released by the March 2011 nuclear disaster at Fukushima/Daiichi (hereafter FD), represents an ideal tracer for atmospheric transport. We report the, to our best knowledge, only aircraft borne measurements of FD Xe-133 in the Tropopause Inversion Layer (TIL), indicating rapid lift of polluted planetary boundary layer air to the TIL. On the same research aircraft (FALCON), we have also conducted on-line measurements of fossil fuel combustion generated pollutant gases (SO{sub 2} and other species), which had increased concentrations in the TIL. In addition, we have conducted supporting model simulations of transport, chemical processes, and aerosol processes. Our investigations reveal a potentially important impact of East-Asian cyclone induced pollutants transport to the TIL. This impact includes particularly aerosol formation.

  12. E-2-Benzylidenebenzocycloalkanones. IV. Studies on transmission of substituent effects on 13C NMR chemical shifts of E-2-(X-benzylidene)-1-tetralones, and -benzosuberones. Comparison with the 13C NMR data of chalcones and E-2-(X-benzylidene)-1-indanones

    Science.gov (United States)

    Perjési, Pál; Linnanto, Juha; Kolehmainen, Erkki; Ősz, Erzsébet; Virtanen, Elina

    2005-04-01

    Single substituent parameter (SSP) and dual substituent parameter (DSP) analyses were applied to study the transmission of substituent effects on selected 13C NMR chemical shifts of the cyclic chalcone analogues, E-2-(4'-X-benzylidene)-1-tetralones ( 2) and E-2-(4'-X-benzylidene)-1-benzosuberones ( 3). In order to study how the geometry of the cyclic chalcone analogues affects the transmission of substituent effects similar investigations with the respective chalcones ( 4) were also performed. The results obtained earlier with the five-membered analogue E-2-(4'-X-benzylidene)-1-indanones ( 1) were also involved in the comparisons. Geometry optimization of the unsubstituted 1a, 2a, 3a and 4a as well as the substituted 2 and 3 was performed by ab initio quantum chemical calculations. Both SSP and DSP analyses reflected that resonance effects contribute more to the chemical shift of C-α (C2), while inductive effects primarily affect that of C-β (C10) of the enone moiety of all the four series. This latter effect, however, is far not as pronounced as that of the former one. It was found that DSP analysis data ( ρF and ρR values) of transmission of substituent effects on the δC2 data can serve as a measure of choice to study the conformation (planarity) of the investigated enones in the four series.

  13. Pheromones-based sexual selection in a rapidly changing world.

    Science.gov (United States)

    Henneken, Jessica; Jones, Therésa M

    2017-12-01

    Insects utilise chemical cues for a range of different purposes and the complexity and degree of specificity of these signals is arguably unparalleled in the animal kingdom. Chemical signals are particularly important for insect reproduction and the selective pressures driving their evolution and maintenance have been the subject of previous reviews. However, the world in which chemical cues evolved and are maintained is changing at an unprecedented rate. How (or indeed whether) chemical signals used in sexual selection will respond is largely unknown. Here, we explore how recent increases in urbanisation and associated anthropogenic impacts may affect how chemical signals are produced and perceived. We focus on four anthropomorphic influences which have the potential to interact with pheromone-mediated sexual selection processes; climatic temperature shifts, exposure to chemical pollutants, the presence of artificial light at night and nutrient availability. Our aim is to provide a broad overview of key areas where the rapidly changing environment of the future might specifically affect pheromones utilised in sexual selection. Copyright © 2017. Published by Elsevier Inc.

  14. A New Paradigm for Chemical Engineering?

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    businesses has been observed. There is an increasing trend within the chemical industry to focus on products and the sustainable processes that can make them. Do these changes point to a paradigm shift in chemical engineering as a discipline? Historically, two previous paradigm shifts in chemical engineering...... corresponded to major shifts in chemical engineering as a discipline, which affected not only the education of chemical engineers, but also the development of chemical engineering as a discipline. Has the time come for a new paradigm shift that will prepare the current and future chemical engineering graduates...... to tackle the complex problems facing the chemicals based industries and serve the modern society more efficiently? The lecture will review the current status of chemical engineering as a discipline, the proposals for the third paradigm, the need for such a paradigm shift and related educational issues....

  15. Contributors to shift work tolerance in South Korean nurses working rotating shift.

    Science.gov (United States)

    Jung, Hye-Sun; Lee, Bokim

    2015-05-01

    Shift workers have rapidly increased in South Korea; however, there is no published research exploring shift work tolerance among South Korean workers. This study aimed to investigate factors related to shift work tolerance in South Korean nurses. The sample comprised of 660 nurses who worked shifts in a large hospital in South Korea. A structured questionnaire included following comprehensive variables: demographic (age and number of children), individual (morningness and self-esteem), psychosocial (social support and job stress), lifestyle (alcohol consumption, physical activity, and BMI), and working condition factors (number of night shifts and working hours). Shift work tolerance was measured in terms of insomnia, fatigue, and depression. The results of hierarchical regressions indicate that all variables, except for three, number of children, BMI, and working hours, were related to at least one of the symptoms associated with shift work tolerance. Based on these results, we offer some practical implications to help improve shift work tolerance of workers. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Nurses' shift reports

    DEFF Research Database (Denmark)

    Buus, Niels; Hoeck, Bente; Hamilton, Bridget Elizabeth

    2017-01-01

    practices were described as highly conventionalised and locally situated, but with occasional opportunities for improvisation and negotiation between nurses. Finally, shift reports were described as multifunctional meetings, with individual and social effects for nurses and teams. CONCLUSION: Innovations...... in between-shift communications can benefit from this analysis, by providing for the many functions of handovers that are revealed in field studies. RELEVANCE TO CLINICAL PRACTICE: Leaders and practising nurses may consider what are the best opportunities for nurses to work up clinical knowledge......AIMS AND OBJECTIVES: To identify reporting practices that feature in studies of nurses' shift reports across diverse nursing specialities. The objectives were to perform an exhaustive systematic literature search and to critically review the quality and findings of qualitative field studies...

  17. Dealing with a Paradigm Shift

    Science.gov (United States)

    Pack, Allan I.

    2015-01-01

    Recent changes in policies by insurance companies with respect to mandating home sleep apnea testing rather than in-laboratory studies have a large impact on the financial viability of clinical sleep centers. Coping with this disruptive change requires forward planning. First, it is important to be well positioned with respect to facilities so that these can be quickly downsized to control costs. There is also a need to develop, in advance, an accredited home sleep study program so that centers can respond to the rapidly changing environment. Following the change there is a need to control costs by rapidly downsizing the technology workforce. Technologists can be retrained for other essential roles. Centralizing the precertification process with knowledgeable, well-trained staff and a robust auditing process is an essential component. The approach taken at the University of Pennsylvania to this change is described as is how one can ensure continued financial viability of a comprehensive sleep center program in a major academic medical center. Citation: Pack AI. Dealing with a paradigm shift. J Clin Sleep Med 2015;11(8):925–929. PMID:26094918

  18. A rapid and high-precision method for sulfur isotope δ(34)S determination with a multiple-collector inductively coupled plasma mass spectrometer: matrix effect correction and applications for water samples without chemical purification.

    Science.gov (United States)

    Lin, An-Jun; Yang, Tao; Jiang, Shao-Yong

    2014-04-15

    Previous studies have indicated that prior chemical purification of samples, although complex and time-consuming, is essential in obtaining precise and accurate results for sulfur isotope ratios using multiple-collector inductively coupled plasma mass spectrometry (MC-ICP-MS). In this study, we introduce a new, rapid and precise MC-ICP-MS method for sulfur isotope determination from water samples without chemical purification. The analytical work was performed on an MC-ICP-MS instrument with medium mass resolution (m/Δm ~ 3000). Standard-sample bracketing (SSB) was used to correct samples throughout the analytical sessions. Reference materials included an Alfa-S (ammonium sulfate) standard solution, ammonium sulfate provided by the lab of the authors and fresh seawater from the South China Sea. A range of matrix-matched Alfa-S standard solutions and ammonium sulfate solutions was used to investigate the matrix (salinity) effect (matrix was added in the form of NaCl). A seawater sample was used to confirm the reliability of the method. Using matrix-matched (salinity-matched) Alfa-S as the working standard, the measured δ(34)S value of AS (-6.73 ± 0.09‰) was consistent with the reference value (-6.78 ± 0.07‰) within the uncertainty, suggesting that this method could be recommended for the measurement of water samples without prior chemical purification. The δ(34)S value determination for the unpurified seawater also yielded excellent results (21.03 ± 0.18‰) that are consistent with the reference value (20.99‰), thus confirming the feasibility of the technique. The data and the results indicate that it is feasible to use MC-ICP-MS and matrix-matched working standards to measure the sulfur isotopic compositions of water samples directly without chemical purification. In comparison with the existing MC-ICP-MS techniques, the new method is better for directly measuring δ(34)S values in water samples with complex matrices; therefore, it can

  19. Illuminating geographical patterns in species' range shifts.

    Science.gov (United States)

    Grenouillet, Gaël; Comte, Lise

    2014-10-01

    Species' range shifts in response to ongoing climate change have been widely documented, but although complex spatial patterns in species' responses are expected to be common, comprehensive comparisons of species' ranges over time have undergone little investigation. Here, we outline a modeling framework based on historical and current species distribution records for disentangling different drivers (i.e. climatic vs. nonclimatic) and assessing distinct facets (i.e. colonization, extirpation, persistence, and lags) of species' range shifts. We used extensive monitoring data for stream fish assemblages throughout France to assess range shifts for 32 fish species between an initial period (1980-1992) and a contemporary one (2003-2009). Our results provide strong evidence that the responses of individual species varied considerably and exhibited complex mosaics of spatial rearrangements. By dissociating range shifts in climatically suitable and unsuitable habitats, we demonstrated that patterns in climate-driven colonization and extirpation were less marked than those attributed to nonclimatic drivers, although this situation could rapidly shift in the near future. We also found evidence that range shifts could be related to some species' traits and that the traits involved varied depending on the facet of range shift considered. The persistence of populations in climatically unsuitable areas was greater for short-lived species, whereas the extent of the lag behind climate change was greater for long-lived, restricted-range, and low-elevation species. We further demonstrated that nonclimatic extirpations were primarily related to the size of the species' range, whereas climate-driven extirpations were better explained by thermal tolerance. Thus, the proposed framework demonstrated its potential for markedly improving our understanding of the key processes involved in range shifting and also offers a template for informing management decisions. Conservation strategies

  20. Label-free surface-enhanced infrared spectro-electro-chemical analysis of the Redox potential shift of cytochrome c complexed with a cardiolipin-containing lipid membrane of varied composition

    Science.gov (United States)

    Liu, Li; Wu, Lie; Zeng, Li; Jiang, Xiu-E.

    2015-12-01

    In this study, a lipid membrane was fabricated by fusing cardiolipin-phosphatidylcholine (CL_PC, 1:4) vesicles onto a hydrophobic surface of 1-dodecanethiol (DT) preadsorbed on a nanostructured gold film. By changing the concentration of the DT adsorption solution, we constructed a series of CL_PC-DT bilayers with different hydrophobicity to study the effects of lipid membrane characteristics on the adsorption conformation of cytochrome c (Cyt c). Electrochemical analysis showed that the formal potential is 0.24 V for Cyt c-CL_PC-DT(10), 0.2 V for Cyt c-CL_PC-DT(20), and 0.16 V for Cyt c-CL_PC-DT(40) — a gradual positive shift with the decreasing DT concentration — relative to the potential of native cyt c (0.02 V). Potential-induced surface-enhanced infrared adsorption difference spectroscopy revealed that the gradual positive shift of the formal potential of CL-bound cyt c is determined by the environment with the gradually lowered dielectric constant for the heme cofactor in CL-bound cyt c (Fe3+). Project supported by the National Natural Science Foundation of China (Grant Nos. 91227114, 21322510, and 21105097), the China Postdoctoral Science Foundation (Grant No. 2013M530998), the Natural Science Foundation of Jilin Province, China (Grant No. 201215092), and the President Funds of the Chinese Academy of Sciences.

  1. A high performance liquid chromatography fingerprinting and ultra high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry chemical profiling approach to rapidly find characteristic chemical markers for quality evaluation of dispensing granules, a case study on Chuanxiong Rhizoma.

    Science.gov (United States)

    Zhang, Xiao-Lin; Liu, Li-Fang; Zhu, Ling-Ying; Bai, Ying-Jia; Mao, Qian; Li, Song-Lin; Chen, Shi-Lin; Xu, Hong-Xi

    2014-01-01

    A high performance liquid chromatography-photodiode array detector (HPLC-PDA) fingerprinting and ultra high performance liquid chromatography-photodiode array detector coupled with quadrupole time-of-flight mass spectrometry (UHPLC-PDA-QTOF-MS/MS) based chemical profiling approach was developed to rapidly find characteristic chemical markers for quality control of dispensing granules, taking Chuanxiong Rhizoma (CR) as a model herb. Firstly, CR crude drugs, their traditional decoctions and CR dispensing granules were analyzed by HPLC-PDA to rapidly establish the fingerprints and thereby generate the simulative median chromatograms of CR crude drugs, decoctions and dispensing granules, and by comparing the simulative median chromatograms, major characteristic peaks of CR decoctions and dispensing granules could be determined. Secondary, UHPLC-PDA-QTOF-MS/MS was used to identify the major characteristic peaks of CR decoctions and dispensing granules. The identities of three major peaks were elucidated and confirmed to be ferulic acid (1), senkyunolide I (2) and senkyunolide H (3) by comparing the mass/UV spectra and retention times with that of the reference compounds. Thirdly, an HPLC-PDA method was validated to quantify the three characteristic components in commercial CR dispensing granules. The average contents of ferulic acid and senkyunolide H were found to be less than 1.0mg/g, whereas that of senkyunolide I was 4.40mg/g in CR dispensing granules, which indicated that senkyunolide I might be chosen as a suitable quantitative marker, while ferulic acid and senkyunolide H as qualitative markers for the quality evaluation of CR dispensing granules. It is suggested that this newly established approach could be used to practically and rapidly find suitable marker compounds for quality control of dispensing granules derived from other medicinal herbs. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Shifting employment revisited

    NARCIS (Netherlands)

    Cremers, J.; Gramuglia, A.

    2014-01-01

    The CLR-network examined in 2006 the phenomenon of undeclared labour, with specific regard to the construction sector. The resulting study, Shifting Employment: undeclared labour in construction, gave evidence that this is an area particularly affected by undeclared activities with one of the

  3. Shifting tasks in telecare

    DEFF Research Database (Denmark)

    Nickelsen, Niels Christian Mossfeldt

    2017-01-01

    with focus on shifting tasks was undertaken. Furthermore, the method of ‘Interview to double’ was used the analytical ambition being to explore the becoming of tasks and relations. Analytically the study draws predominantly on Stars notion of ‘infrastructure’. Infrastructure is seen as human and non...

  4. Capacitive chemical sensor

    Science.gov (United States)

    Manginell, Ronald P; Moorman, Matthew W; Wheeler, David R

    2014-05-27

    A microfabricated capacitive chemical sensor can be used as an autonomous chemical sensor or as an analyte-sensitive chemical preconcentrator in a larger microanalytical system. The capacitive chemical sensor detects changes in sensing film dielectric properties, such as the dielectric constant, conductivity, or dimensionality. These changes result from the interaction of a target analyte with the sensing film. This capability provides a low-power, self-heating chemical sensor suitable for remote and unattended sensing applications. The capacitive chemical sensor also enables a smart, analyte-sensitive chemical preconcentrator. After sorption of the sample by the sensing film, the film can be rapidly heated to release the sample for further analysis. Therefore, the capacitive chemical sensor can optimize the sample collection time prior to release to enable the rapid and accurate analysis of analytes by a microanalytical system.

  5. Understanding and controlling chromaticity shift in LED devices

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Lynn; Mills, Karmann; Lamvik, Michael; Perkins, Curtis; Bobashev, Georgiy; Young, Joseph; Yaga, Robert; Johnson, Cortina

    2017-05-30

    Chromaticity shift in light-emitting diode (LED) devices arises from multiple mechanisms, and at least five different chromaticity shift modes (CSMs) have been identified to date. This paper focuses on the impacts of irreversible phosphor degradation as a cause of chromaticity shifts in LED devices. The nitride phosphors used to produce warm white LEDs are especially vulnerable to degradation due to thermal and chemical effects such as reactions with oxygen and water. As a result, LED devices utilizing these phosphors were found to undergo either a green shift or, less commonly, a red shift depending on the phosphor mix in the LED devices. These types of chromaticity shifts are classified as CSM-2 (green shift) and CSM-5 (red shift). This paper provides an overview of the kinetic processes responsible for green and red chromaticity shifts along with examples from accelerated stress testing of 6” downlights. Both CSMs appear to proceed through analogous mechanisms that are initiated at the surface of the phosphor. A green shift is produced by the surface oxidation of the nitride phosphor that changes the emission profile to lower wavelengths. As the surface oxidation reaction proceeds, reactant limitations slow the rate and bulk oxidation processes become more prevalent. We found that a red chromaticity shift arises from quenching of the green phosphor, also possibly due to surface reactions of oxygen, which shift the emission chromaticity in the red direction. In conclusion, we discuss the implications of these findings on projecting chromaticity.

  6. Rapid Prototyping

    Science.gov (United States)

    1999-01-01

    Javelin, a Lone Peak Engineering Inc. Company has introduced the SteamRoller(TM) System as a commercial product. The system was designed by Javelin during a Phase II NASA funded small commercial product. The purpose of the invention was to allow automated-feed of flexible ceramic tapes to the Laminated Object Manufacturing rapid prototyping equipment. The ceramic material that Javelin was working with during the Phase II project is silicon nitride. This engineered ceramic material is of interest for space-based component.

  7. Effects of shift rotation and the flexibility of a shift system on daytime alertness and cardiovascular risk factors.

    Science.gov (United States)

    Viitasalo, Katriina; Kuosma, Eeva; Laitinen, Jaana; Härmä, Mikko

    2008-06-01

    A controlled intervention study was conducted to evaluate the effects of two changes in shift characteristics on alertness and cardiovascular risk factors: a change in shift rotation (direction and speed) and a change in the flexibility of the shift system. Altogether 84 male workers currently working in a backward-rotating shift system volunteered for the study. A total of 40 men changed to a rapidly forward-rotating shift system, 22 changed to a more flexible shift system, and 22 remained with the old shift system. Health effects were studied with the use of clinical measurements, blood tests, and questionnaires before and after the shift changes. Analyses of variance were used with repeated measures to study associations of cardiovascular risk factors and daytime sleepiness according to the change in shift systems. The mean number of days on which the workers reported sleepiness decreased in the group with the forward-rotating shift system when compared with that of the group on the old shift system (from 2.9 to 2.1 days/week, P=0.02). Systolic blood pressure decreased (from 142 to 136 mm Hg, P=0.049), and heart rate showed a declining trend (from 66 to 60 beats/minute, P=0.06) in the flexible shift system when the three groups were compared. The study indicates that a faster speed, together with a change to the forward direction, in shift rotation alleviates daytime sleepiness. Combining individual flexibility with company-based flexibility in a shift system may have favorable effects on shift workers' blood pressure.

  8. The shifting beverage landscape.

    Science.gov (United States)

    Storey, Maureen

    2010-04-26

    STOREY, M.L. The shifting beverage landscape. PHYSIOL BEHAV, 2010. - Simultaneous lifestyle changes have occurred in the last few decades, creating an imbalance in energy intake and energy expenditure that has led to overweight and obesity. Trends in the food supply show that total daily calories available per capita increased 28% since 1970. Total energy intake among men and women has also increased dramatically since that time. Some have suggested that intake of beverages has had a disproportional impact on obesity. Data collected by the Beverage Marketing Corporation between 1988-2008 demonstrate that, in reality, fewer calories per ounce are being produced by the beverage industry. Moreover, data from the National Cancer Institute show that soft drink intake represents 5.5% of daily calories. Data from NHANES 1999-2003 vs. 2003-06 may demonstrate a shift in beverage consumption for age/gender groups, ages 6 to>60years. The beverages provided in schools have significantly changed since 2006 when the beverage industry implemented School Beverage Guidelines. This voluntary action has removed full-calorie soft drinks from participating schools across the country. This shift to lower-calorie and smaller-portion beverages in school has led to a significant decrease in total beverage calories in schools. These data support the concept that to prevent and treat obesity, public health efforts should focus on energy balance and that a narrow focus on sweetened beverages is unlikely to have any meaningful impact on this complex problem. Copyright 2010 Elsevier Inc. All rights reserved.

  9. Upward ant distribution shift corresponds with minimum, not maximum, temperature tolerance

    Science.gov (United States)

    Robert J. Warren; Lacy. Chick

    2013-01-01

    Rapid climate change may prompt species distribution shifts upward and poleward, but species movement in itself is not sufficient to establish climate causation. Other dynamics, such as disturbance history, may prompt species distribution shifts resembling those expected from rapid climate change. Links between species distributions, regional climate trends and...

  10. Catastrophic shifts in ecosystems

    Science.gov (United States)

    Scheffer, Marten; Carpenter, Steve; Foley, Jonathan A.; Folke, Carl; Walker, Brian

    2001-10-01

    All ecosystems are exposed to gradual changes in climate, nutrient loading, habitat fragmentation or biotic exploitation. Nature is usually assumed to respond to gradual change in a smooth way. However, studies on lakes, coral reefs, oceans, forests and arid lands have shown that smooth change can be interrupted by sudden drastic switches to a contrasting state. Although diverse events can trigger such shifts, recent studies show that a loss of resilience usually paves the way for a switch to an alternative state. This suggests that strategies for sustainable management of such ecosystems should focus on maintaining resilience.

  11. Computational study of hydrogen shifts and ring-opening mechanisms in α-pinene ozonolysis products

    DEFF Research Database (Denmark)

    Kurtén, Theo; Rissanen, Matti P.; Mackeprang, Kasper

    2015-01-01

    Autoxidation by sequential peroxy radical hydrogen shifts (H-shifts) and O2 additions has recently emerged as a promising mechanism for the rapid formation of highly oxidized, low-volatility organic compounds in the atmosphere. A key prerequisite for autoxidation is that the H-shifts of the initial...

  12. Shifted excitation Raman difference spectroscopy for authentication of cheese and cheese analogues

    Science.gov (United States)

    Sowoidnich, Kay; Kronfeldt, Heinz-Detlef

    2016-04-01

    Food authentication and the detection of adulterated products are recent major issues in the food industry as these topics are of global importance for quality control and food safety. To effectively address this challenge requires fast, reliable and non-destructive analytical techniques. Shifted Excitation Raman Difference Spectroscopy (SERDS) is well suited for identification purposes as it combines the chemically specific information obtained by Raman spectroscopy with the ability for efficient fluorescence rejection. The two slightly shifted excitation wavelengths necessary for SERDS are realized by specially designed microsystem diode lasers. At 671 nm the laser (optical power: 50 mW, spectral shift: 0.7 nm) is based on an external cavity configuration whereas an emission at 783 nm (optical power: 110 mW, spectral shift: 0.5 nm) is achieved by a distributed feedback laser. To investigate the feasibility of SERDS for rapid and nondestructive authentication purposes four types of cheese and three different cheese analogues were selected. Each sample was probed at 8 different positions using integration times of 3-10 seconds and 10 spectra were recorded at each spot. Principal components analysis was applied to the SERDS spectra revealing variations in fat and protein signals as primary distinction criterion between cheese and cheese analogues for both excitation wavelengths. Furthermore, to some extent, minor compositional differences could be identified to discriminate between individual species of cheese and cheese analogues. These findings highlight the potential of SERDS for rapid food authentication potentially paving the way for future applications of portable SERDS systems for non-invasive in situ analysis.

  13. Repetition and Translation Shifts

    Directory of Open Access Journals (Sweden)

    Simon Zupan

    2006-06-01

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

  14. Alcaloides iboga de Peschiera affinis (Apocynaceae - Atribuição inequívoca dos deslocamentos químicos dos átomos de hidrogênio e carbono: atividade antioxidante Iboga alkaloids from Peschiera affinis (Apocynaceae - unequivocal 1H and 13C chemical shift assignments: antioxidant activity

    Directory of Open Access Journals (Sweden)

    Allana Kellen L. Santos

    2009-01-01

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

  15. Accurate phase-shift velocimetry in rock.

    Science.gov (United States)

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models. Copyright © 2016. Published by Elsevier Inc.

  16. ADAPTIVE NOISE CANCELLATION OF DOPPLER SHIFTED SIGNALS: A LINEAR FRAMEWORK

    OpenAIRE

    Stewart, R. W.; Weiss, S.

    1996-01-01

    In this paper we investigate the performance of single channel adaptive noise cancellation techniques for situations where the noise signal received by the two microphones cannot be related by a fixed weight canceller's (linear) digital filter due to Doppler shift on the two signals. A mathematical signal model is produced, which shows that the adaptive filter is in fact required to identify a time-varying system which incorporates Doppler shift, and potential rapid variations in signal power...

  17. Trends in shifting cultivation and the REDD mechanism

    DEFF Research Database (Denmark)

    Mertz, Ole

    2009-01-01

    In many parts of the forest-agriculture frontiers of the tropics, particularly in Southeast Asia, shifting cultivation is rapidly being transformed to other land uses. Yet, there is rather limited knowledge on the spatial and demographic extent of shifting cultivation and the consequences...... of the transitions taking place. The proposed mechanism for reduced greenhouse gas emissions from deforestation and degradation (REDD) can be both a challenge and opportunity for shifting cultivators. Very limited literature is available on this dilemma, but a few sources point to benefits from ‘compensated...

  18. Energy phase shift as mechanism for catalysis

    KAUST Repository

    Beke-Somfai, Tamás

    2012-05-01

    Catalysts are agents that by binding reactant molecules lower the energy barriers to chemical reaction. After reaction the catalyst is regenerated, its unbinding energy recruited from the environment, which is associated with an inevitable loss of energy. We show that combining several catalytic sites to become energetically and temporally phase-shifted relative to each other provides a possibility to sustain the overall reaction by internal \\'energy recycling\\', bypassing the need for thermal activation, and in principle allowing the system to work adiabatically. Using an analytical model for superimposed, phase-shifted potentials of F 1-ATP synthase provides a description integrating main characteristics of this rotary enzyme complex. © 2012 Elsevier B.V. All rights reserved.

  19. Measurements of isotope shifts and hyperfine structure in Ti II

    Energy Technology Data Exchange (ETDEWEB)

    Nouri, Z; Rosner, S D; Holt, R A [Department of Physics and Astronomy, University of Western Ontario, London, ON N6A 3K7 (Canada); Li, R [TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6 T 2A3 (Canada); Scholl, T J, E-mail: rholt@uwo.c [Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1 (Canada)

    2010-06-01

    We have applied fast-ion-beam laser-fluorescence spectroscopy to measure the isotope shifts of 38 transitions in the wavelength range 429-457 nm and the hyperfine structures (hfs) of 22 levels in Ti II. The isotope shift and hfs measurements are the first for these transitions and levels. These atomic data are essential for astrophysical studies of chemical abundances, allowing correction for saturation and the effects of blended lines.

  20. Quantized beam shifts in graphene

    Energy Technology Data Exchange (ETDEWEB)

    de Melo Kort-Kamp, Wilton Junior [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sinitsyn, Nikolai [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dalvit, Diego Alejandro Roberto [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-08

    We predict the existence of quantized Imbert-Fedorov, Goos-Hanchen, and photonic spin Hall shifts for light beams impinging on a graphene-on-substrate system in an external magnetic field. In the quantum Hall regime the Imbert-Fedorov and photonic spin Hall shifts are quantized in integer multiples of the fine structure constant α, while the Goos-Hanchen ones in multiples of α2. We investigate the influence on these shifts of magnetic field, temperature, and material dispersion and dissipation. An experimental demonstration of quantized beam shifts could be achieved at terahertz frequencies for moderate values of the magnetic field.

  1. Work shifts in Emergency Medicine

    Directory of Open Access Journals (Sweden)

    Roberto Recupero

    2007-06-01

    Full Text Available Emergency Medicine is known as a high stress specialty. The adverse effect of constantly rotating shifts is the single most important reason given for premature attrition from the field. In this work problems tied with night shift work will be taken into account and some solutions to reduce the impact of night work on the emergency physicians will be proposed.

  2. 15N NMR chemical shifts in papaverine decomposition products

    Science.gov (United States)

    Czyrski, Andrzej; Girreser, Ulrich; Hermann, Tadeusz

    2013-03-01

    Papaverine can be easily oxidized to papaverinol, papaveraldine and 2,3,9,10-tetramethoxy-12-oxo-12H-indolo[2,1-a]isoquinolinium chloride. On addition of alkali solution the latter compound forms 2-(2-carboxy-4,5-dimethoxyphenyl)-6,7-dimethoxyisoquinolinium inner salt. Together with these structures the interesting 13-(3,4-dimethoxyphenyl)-2,3,8,9-tetramethoxy-6a-12a-diazadibenzo[a,g]fluorenylium chloride is discussed, which is formed in the Gadamer-Schulemann reaction of papaverine as a side product. This letter reports the 15N NMR spectra of the above mentioned compounds.

  3. Chemical shift assignments of calmodulin constructs with EF hand mutations.

    Science.gov (United States)

    Piazza, Michael; Guillemette, J Guy; Dieckmann, Thorsten

    2016-04-01

    Calmodulin (CaM) is a ubiquitous cytosolic Ca(2+)-binding protein able to bind and regulate hundreds of different proteins. It consists of two globular domains joined by a flexible central linker region. Each one of these domains contains two EF hand pairs capable of binding to Ca(2+). Upon Ca(2+) binding CaM undergoes a conformational change exposing hydrophobic patches that interact with its intracellular target proteins. CaM is able to bind to target proteins in the Ca(2+)-replete and Ca(2+)-deplete forms. To study the Ca(2+)-dependent/independent properties of binding and activation of target proteins by CaM, CaM constructs with Ca(2+) binding disrupting mutations of Asp to Ala at position one of each EF hand have been used. One target protein of CaM is nitric oxide synthase, which catalyzes the production of nitric oxide. At elevated Ca(2+) concentrations, CaM binds to neuronal NOS and endothelial NOS, making them the Ca(2+)-dependent NOS enzymes. In contrast, inducible NOS is transcriptionally regulated in vivo and binds to CaM at basal levels of Ca(2+). Here we report the NMR backbone and sidechain resonance assignments of C-lobe Ca(2+)-replete and deplete CaM12, N-lobe Ca(2+)-replete and deplete CaM34, CaM1234 in the absence of Ca(2+) and N-lobe Ca(2+)-replete CaM34 with the iNOS CaM-binding domain peptide.

  4. Is there a shift to "active nanostructures"?

    Science.gov (United States)

    Subramanian, Vrishali; Youtie, Jan; Porter, Alan L.; Shapira, Philip

    2010-01-01

    It has been suggested that an important transition in the long-run trajectory of nanotechnology development is a shift from passive to active nanostructures. Such a shift could present different or increased societal impacts and require new approaches for risk assessment. An active nanostructure "changes or evolves its state during its operation," according to the National Science Foundation's (2006) Active Nanostructures and Nanosystems grant solicitation. Active nanostructure examples include nanoelectromechanical systems (NEMS), nanomachines, self-healing materials, targeted drugs and chemicals, energy storage devices, and sensors. This article considers two questions: (a) Is there a "shift" to active nanostructures? (b) How can we characterize the prototypical areas into which active nanostructures may emerge? We build upon the NSF definition of active nanostructures to develop a research publication search strategy, with a particular intent to distinguish between passive and active nanotechnologies. We perform bibliometric analyses and describe the main publication trends from 1995 to 2008. We then describe the prototypes of research that emerge based on reading the abstracts and review papers encountered in our search. Preliminary results suggest that there is a sharp rise in active nanostructures publications in 2006, and this rise is maintained in 2007 and through to early 2008. We present a typology that can be used to describe the kind of active nanostructures that may be commercialized and regulated in the future.

  5. Changes in forest productivity across Alaska consistent with biome shift.

    Science.gov (United States)

    Beck, Pieter S A; Juday, Glenn P; Alix, Claire; Barber, Valerie A; Winslow, Stephen E; Sousa, Emily E; Heiser, Patricia; Herriges, James D; Goetz, Scott J

    2011-04-01

    Global vegetation models predict that boreal forests are particularly sensitive to a biome shift during the 21st century. This shift would manifest itself first at the biome's margins, with evergreen forest expanding into current tundra while being replaced by grasslands or temperate forest at the biome's southern edge. We evaluated changes in forest productivity since 1982 across boreal Alaska by linking satellite estimates of primary productivity and a large tree-ring data set. Trends in both records show consistent growth increases at the boreal-tundra ecotones that contrast with drought-induced productivity declines throughout interior Alaska. These patterns support the hypothesized effects of an initiating biome shift. Ultimately, tree dispersal rates, habitat availability and the rate of future climate change, and how it changes disturbance regimes, are expected to determine where the boreal biome will undergo a gradual geographic range shift, and where a more rapid decline. © 2011 Blackwell Publishing Ltd/CNRS.

  6. Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

    Science.gov (United States)

    Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

    2016-05-05

    Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes.

  7. Chemical Emergencies

    Science.gov (United States)

    When a hazardous chemical has been released, it may harm people's health. Chemical releases can be unintentional, as in the case of an ... the case of a terrorist attack with a chemical weapon. Some hazardous chemicals have been developed by ...

  8. Stress shift in rhythmical speech

    Science.gov (United States)

    Quené, Hugo; Port, Robert

    2002-05-01

    In phrases like thirteen men, stress in thirteen is often shifted forward from its canonical final position. Presumably, the occurrence of this optional stress shift may be partly controlled by the rhythm of speech. Work on rhythmic speech production has demonstrated that given a repetition cycle, T, its harmonic fractions like T/2 attract stressed vowel onsets. Comparing phrases like ceMENT thirTEEN and GALaxy thirTEEN, differing in the number of weak syllables between strong ones, it was predicted that, during rhythmic production, the harmonic locations would attract shifted stress. Since shifting stress results in more even distribution of syllables through the cycle, we expected that faster repetition rates would also result in more stress shift. Dependent variables were the relative stress in the second word of each pair, and the location of onset of the nuclear vowel of the stressed syllable. Results confirmed the predictions, first, that with more intermediate unstressed syllables, stress was shifted forward more often (thereby locating the stressed vowel onset closer to T/2) and, second, that stress shifted forward more often at faster speaking rates. [Work supported by Fulbright Visiting Scholar program and by Utrecht University, The Netherlands.

  9. Piezoelectric Ceramics of the (1 − x)Bi0.50Na0.50TiO3–xBa0.90Ca0.10TiO3 Lead-Free Solid Solution: Chemical Shift of the Morphotropic Phase Boundary, a Case Study for x = 0.06

    Science.gov (United States)

    Vivar-Ocampo, Rodrigo; Pardo, Lorena; Ávila, David; Morán, Emilio; González, Amador M.; Bucio, Lauro; Villafuerte-Castrejón, María-Elena

    2017-01-01

    Research and development of lead-free piezoelectric materials are still the hottest topics in the field of piezoelectricity. One of the most promising lead-free family of compounds to replace lead zirconate–titanate for actuators is that of Bi0.50Na0.50TiO3 (BNT) based solid solutions. The pseudo-binary (1 − x)Bi0.50Na0.50TiO3–xBa1 − yCayTiO3 system has been proposed for high temperature capacitors and not yet fully explored as piezoelectric material. In this work, the solid solution with x = 0.06 and y = 0.10 was obtained by two different synthesis routes: solid state and Pechini, aiming at using reduced temperatures, both in synthesis (<800 °C) and sintering (<1150 °C), while maintaining appropriated piezoelectric performance. Crystal structure, ceramic grain size, and morphology depend on the synthesis route and were analyzed by X-ray diffraction, together with scanning and transmission electron microscopy. The effects of processing and ceramic microstructure on the structural, dielectric, ferroelectric, and piezoelectric properties were discussed in terms of a shift of the Morphotropic Phase Boundary, chemically induced by the synthesis route. PMID:28773096

  10. Explaining (Missing) Regulator Paradigm Shifts

    DEFF Research Database (Denmark)

    Wigger, Angela; Buch-Hansen, Hubert

    2014-01-01

    of competition regulation is heaving into sight. It sets out to explain this from the vantage point of a critical political economy perspective, which identifies the circumstances under which a crisis can result in a regulatory paradigm shift. Contrasting the current situation with the shift in EC/EU competition...... capitalism; the social power configuration underpinning the neoliberal order remains unaltered; no clear counter-project has surfaced; the European Commission has been (and remains) in a position to oppose radical changes; and finally, there are no signs of a wider paradigm shift in the EU's regulatory...

  11. Controllable optical phase shift over one radian from a single isolated atom.

    Science.gov (United States)

    Jechow, A; Norton, B G; Händel, S; Blūms, V; Streed, E W; Kielpinski, D

    2013-03-15

    Fundamental optics such as lenses and prisms work by applying phase shifts of several radians to incoming light, and rapid control of such phase shifts is crucial to telecommunications. However, large, controllable optical phase shifts have remained elusive for isolated quantum systems. We have used a single trapped atomic ion to induce and measure a large optical phase shift of 1.3±0.1 radians in light scattered by the atom. Spatial interferometry between the scattered light and unscattered illumination light enables us to isolate the phase shift in the scattered component. The phase shift achieves the maximum value allowed by atomic theory over the accessible range of laser frequencies, pointing out new opportunities in microscopy and nanophotonics. Single-atom phase shifts of this magnitude open up new quantum information protocols, in particular long-range quantum phase-shift-keying cryptography.

  12. Developmental evolution facilitates rapid adaptation.

    Science.gov (United States)

    Lin, Hui; Kazlauskas, Romas J; Travisano, Michael

    2017-11-21

    Developmental evolution has frequently been identified as a mode for rapid adaptation, but direct observations of the selective benefits and associated mechanisms of developmental evolution are necessarily challenging to obtain. Here we show rapid evolution of greatly increased rates of dispersal by developmental changes when populations experience stringent selection. Replicate populations of the filamentous fungus Trichoderma citrinoviride underwent 85 serial transfers, under conditions initially favoring growth but not dispersal. T. citrinoviride populations shifted away from multicellular growth toward increased dispersal by producing one thousand times more single-celled asexual conidial spores, three times sooner than the ancestral genotype. Conidia of selected lines also germinated fifty percent faster. Gene expression changed substantially between the ancestral and selected fungi, especially for spore production and growth, demonstrating rapid evolution of tight regulatory control for down-regulation of growth and up-regulation of conidia production between 18 and 24 hours of growth. These changes involved both developmentally fixed and plastic changes in gene expression, showing that complex developmental changes can serve as a mechanism for rapid adaptation.

  13. Structural and geographic shifts in the Washington warehousing industry : transportation impacts for the Green River Valley.

    Science.gov (United States)

    2009-07-01

    Establishment level employment data indicate that the warehousing industry has experienced rapid growth and : restructuring since 1998. This restructuring has resulted in geographic shifts at the national, regional, and local scales. : Uneven growth ...

  14. A Rapid Analysis of Variations in Conformational Behavior during Dihydrofolate Reductase Catalysis.

    Science.gov (United States)

    Hughes, Robert L; Johnson, Luke A; Behiry, Enas M; Loveridge, E Joel; Allemann, Rudolf K

    2017-04-18

    Protein flexibility is central to enzyme catalysis, yet it remains challenging both to predict conformational behavior on the basis of analysis of amino acid sequence and protein structure and to provide the necessary breadth of experimental support to any such predictions. Here a generic and rapid procedure for identifying conformational changes during dihydrofolate reductase (DHFR) catalysis is described. Using DHFR from Escherichia coli (EcDHFR), selective side-chain 13 C labeling of methionine and tryptophan residues is shown to be sufficient to detect the closed-to-occluded conformational transition that follows the chemical step in the catalytic cycle, with clear chemical shift perturbations found for both methionine methyl and tryptophan indole groups. In contrast, no such perturbations are seen for the DHFR from the psychrophile Moritella profunda, where the equivalent conformational change is absent. Like EcDHFR, Salmonella enterica DHFR shows experimental evidence of a large-scale conformational change following hydride transfer that relies on conservation of a key hydrogen bonding interaction between the M20 and GH loops, directly comparable to the closed-to-occluded conformational change observed in EcDHFR. For the hyperthermophile Thermotoga maritima, no chemical shift perturbations were observed, suggesting that no major conformational change occurs during the catalytic cycle. In spite of their conserved tertiary structures, DHFRs display variations in conformational sampling that occurs concurrently with catalysis.

  15. Tree-species range shifts in a changing climate: detecting, modeling, assisting

    Science.gov (United States)

    Louis R. Iverson; Donald. McKenzie

    2013-01-01

    In these times of rapidly changing climate, the science of detecting and modeling shifts in the ranges of tree species is advancing of necessity. We briefly review the current state of the science on several fronts. First, we review current and historical evidence for shifting ranges and migration. Next, we review two broad categories of methods, focused on the spatial...

  16. Socio-economic perspectives on shifting cultivation landscapes in Northern Laos

    DEFF Research Database (Denmark)

    Heinimann, Andreas; Hett, Cornelia; Hurni, Kaspar

    2013-01-01

    Despite the rapid agricultural transition that has occurred in the past decade, shifting cultivation remains a widespread agricultural practice in the northern uplands of Lao PDR. Little information is available on the basic socio-economic situation and respective possible patterns in shifting...

  17. Chemical bond fundamental aspects of chemical bonding

    CERN Document Server

    Frenking, Gernot

    2014-01-01

    This is the perfect complement to ""Chemical Bonding - Across the Periodic Table"" by the same editors, who are two of the top scientists working on this topic, each with extensive experience and important connections within the community. The resulting book is a unique overview of the different approaches used for describing a chemical bond, including molecular-orbital based, valence-bond based, ELF, AIM and density-functional based methods. It takes into account the many developments that have taken place in the field over the past few decades due to the rapid advances in quantum chemica

  18. A new digestion and chemical separation technique for rapid and highly reproducible determination of Lu/Hf and Hf isotope ratios in geological materials by mc-ICP-MS

    DEFF Research Database (Denmark)

    Bizzarro, Martin; Baker, J.A.; Ulfbeck, D.

    2003-01-01

    A new digestion procedure and chemical separation technique has been developed for measurement of Lu/Hf and Hf isotope ratios that does not require high-pressure bombs or use of HF or HClO acids. Samples are digested in dilute HCl or HNO after flux-fusion at 1100 °C in the presence of lithium...

  19. Doppler Shift Oscillations from a Hot Line Observed by IRIS

    Science.gov (United States)

    Li, D.; Ning, Z. J.; Huang, Y.; Chen, N.-H.; Zhang, Q. M.; Su, Y. N.; Su, W.

    2017-11-01

    We present a detailed investigation of the Doppler shift oscillations in a hot loop during an M7.1 flare on 2014 October 27 observed by the Interface Region Imaging Spectrograph. The periodic oscillations are observed in the Doppler shift of Fe xxi 1354.09 Å (log T˜ 7.05), and the dominant period is about 3.1 minutes. However, such 3.1 minute oscillations are not found in the line-integrated intensity of Fe xxi 1354.09 Å, AIA EUV fluxes, or microwave emissions. Solar Dynamics Observatory/AIA and Hinode/XRT imaging observations indicate that the Doppler shift oscillations locate at the hot loop-top region (≥11 MK). Moreover, the differential emission measure results show that the temperature is increasing rapidly when the Doppler shift oscillates, but the number density does not exhibit the corresponding increases nor oscillations, implying that the flare loop is likely to oscillate in an incompressible mode. All of these facts suggest that the Doppler shift oscillations at the shorter period are most likely the standing kink oscillations in a flare loop. Meanwhile, a longer period of about 10 minutes is identified in the time series of Doppler shift and line-integrated intensity, GOES SXR fluxes, and AIA EUV light curves, indicating the periodic energy release in this flare, which may be caused by a slow mode wave.

  20. shift

    African Journals Online (AJOL)

    during the course of an academic year at the University of Witwatersrand following recent reforms in training and assessment methods Method: All fifth ... Assessment of Psychiatry in medical education at the. University of Witwatersrand ... or two examiners, to assess mainly clinical competence; multiple-choice questions ...

  1. Paradigm Shifts in Ophthalmic Diagnostics.

    Science.gov (United States)

    Sebag, J; Sadun, Alfredo A; Pierce, Eric A

    2016-08-01

    Future advances in ophthalmology will see a paradigm shift in diagnostics from a focus on dysfunction and disease to better measures of psychophysical function and health. Practical methods to define genotypes will be increasingly important and non-invasive nanotechnologies are needed to detect molecular changes that predate histopathology. This is not a review nor meant to be comprehensive. Specific topics have been selected to illustrate the principles of important paradigm shifts that will influence the future of ophthalmic diagnostics. It is our impression that future evaluation of vision will go beyond visual acuity to assess ocular health in terms of psychophysical function. The definition of disease will incorporate genotype into what has historically been a phenotype-centric discipline. Non-invasive nanotechnologies will enable a paradigm shift from disease detection on a cellular level to a sub-cellular molecular level. Vision can be evaluated beyond visual acuity by measuring contrast sensitivity, color vision, and macular function, as these provide better insights into the impact of aging and disease. Distortions can be quantified and the psychophysical basis of vision can be better evaluated than in the past by designing tests that assess particular macular cell function(s). Advances in our understanding of the genetic basis of eye diseases will enable better characterization of ocular health and disease. Non-invasive nanotechnologies can assess molecular changes in the lens, vitreous, and macula that predate visible pathology. Oxygen metabolism and circulatory physiology are measurable indices of ocular health that can detect variations of physiology and early disease. This overview of paradigm shifts in ophthalmology suggests that the future will see significant improvements in ophthalmic diagnostics. The selected topics illustrate the principles of these paradigm shifts and should serve as a guide to further research and development. Indeed

  2. The shifting foundations of nursing.

    Science.gov (United States)

    Law, Kate; Aranda, Kay

    2010-08-01

    In this paper we argue that the concerns generated by the development of Foundation Degrees and the Assistant and Associate Practitioner roles have rekindled some of the unresolved debates regarding the status and identity of nursing and nurses. Through the application of the sociological theories of professionalisation and nostalgia we have identified the shifting and unresolved nature of nursing. We argue that these theories continue to have resonance in the current climate of change and 'upskilling' of the health care workforce and argue, that the shifts illuminated are perhaps so significant as to demonstrate that we have entered a post-nursing era. Copyright 2009 Elsevier Ltd. All rights reserved.

  3. Repeated climate-linked host shifts have promoted diversification in a temperate clade of leaf-mining flies.

    Science.gov (United States)

    Winkler, Isaac S; Mitter, Charles; Scheffer, Sonja J

    2009-10-27

    A central but little-tested prediction of "escape and radiation" coevolution is that colonization of novel, chemically defended host plant clades accelerates insect herbivore diversification. That theory, in turn, exemplifies one side of a broader debate about the relative influence on clade dynamics of intrinsic (biotic) vs. extrinsic (physical-environmental) forces. Here, we use a fossil-calibrated molecular chronogram to compare the effects of a major biotic factor (repeated shift to a chemically divergent host plant clade) and a major abiotic factor (global climate change) on the macroevolutionary dynamics of a large Cenozoic radiation of phytophagous insects, the leaf-mining fly genus Phytomyza (Diptera: Agromyzidae). We find one of the first statistically supported examples of consistently elevated net diversification accompanying shift to new plant clades. In contrast, we detect no significant direct effect on diversification of major global climate events in the early and late Oligocene. The broader paleoclimatic context strongly suggests, however, that climate change has at times had a strong indirect influence through its effect on the biotic environment. Repeated rapid Miocene radiation of these flies on temperate herbaceous asterids closely corresponds to the dramatic, climate-driven expansion of seasonal, open habitats.

  4. Predator-induced phenotypic plasticity in Daphnia pulex: Uncoupling morphological defenses and life history shifts

    NARCIS (Netherlands)

    Repka, S.; Pihlajamaa, K.

    1996-01-01

    Chemical cues from a predator Chaoborus sp. induce morphological defense (neck spine) and life history shifts (later reproduction, decreased fecundity but larger juvenile size) in the waterflea Daphnia pulex. These shifts have been interpreted either as costs of defense or as separate adaptation. In

  5. Metabolical shifts towards alternative BTEX biodegradation intermediates induced by perfluorinated compounds in firefighting foams.

    Science.gov (United States)

    Montagnolli, Renato Nallin; Lopes, Paulo Renato Matos; Cruz, Jaqueline Matos; Claro, Marina Turini; Quiterio, Gabriela Mercuri; Bidoia, Ederio Dino

    2017-04-01

    The type and concentration of perfluorinated compounds (PFCs) can induce different types of enzymes and promote alternate patterns of BTEX transformation. However, it is not known how the presence of active fluorocarbon-degrading microbial populations affects the transformation of BTEX. In addition to chemical analysis at the molecular level, our research approached the aqueous film forming fire-fighting foams (AFFF) and BTEX co-contamination at a large-scale with respirometers to quantify the total microbial metabolism of soil via CO2 output levels. The intended outcome of this research was to obtain and characterize shifts in BTEX degradation at a set realistic environmental condition while measuring byproducts and CO2 production. Both methodologies complimentarily provided an in-depth knowledge of the environmental behavior of fire-fighting foams. The biodegradation was monitored using headspace sampling and two types of gas chromatography: thermal conductivity detector and flame ionization detector. Headspace samples were periodically withdrawn for BTEX biodegradation and CO2 production analysis. Our research suggests the discovery of an altered metabolic pathway in aromatic hydrocarbons biodegradation that is directly affected by fluorinated substances. The fluorinated compounds affected the BTEX biodegradation kinetics, as PFCs may contribute to a shift in styrene and catechol concentrations in co-contamination scenarios. A faster production of styrene and catechol was detected. Catechol is also rapidly consumed, thus undergoing further metabolic stages earlier under the presence of PFCs. The release of AFFF compounds not only changes byproducts output but also drastically disturbs the soil microbiota according to the highly variable CO2 yields. Therefore, we observed a high sensitivity of microbial consortia due to PFCs in the AFFF formulation, therefore shifting their BTEX degradation routes in terms of intermediate products concentration. Copyright © 2016

  6. Crichton's phase-shift ambiguity

    NARCIS (Netherlands)

    Atkinson, D.; Johnson, P.W.; Mehta, N.; Roo, M. de

    1973-01-01

    A re-examination of the SPD phase-shift ambiguity is made with a view to understanding certain singular features of the elastic unitarity constraint. An explicit solution of Crichton's equations is presented, and certain features of this solution are displayed graphically. In particular, it is shown

  7. Environmental Protection: a shifting focus

    NARCIS (Netherlands)

    Dr. ir. Jan Venselaar

    2004-01-01

    The last two decades have seen a fundamental change in the way chemistry handles environmental issues. A shift in focus has occurred from 'end-of-pipe' to prevention and process integration. Presently an even more fundamental change is brought about by the need for sustainable development. It is

  8. Anthropometric changes and fluid shifts

    Science.gov (United States)

    Thornton, W. E.; Hoffler, G. W.; Rummel, J. A.

    1974-01-01

    Several observations of body size, shape, posture, and configuration were made to document changes resulting from direct effects of weightlessness during the Skylab 4 mission. After the crewmen were placed in orbit, a number of anatomical and anthropometric changes occurred including a straightening of the thoracolumbar spine, a general decrease in truncal girth, and an increase in height. By the time of the earliest in-flight measurement on mission day 3, all crewmen had lost more than two liters of extravascular fluid from the calf and thigh. The puffy facies, the bird legs effect, the engorgement of upper body veins, and the reduced volume of lower body veins were all documented with photographs. Center-of-mass measurements confirmed a fluid shift cephalad. This shift remained throughout the mission until recovery, when a sharp reversal occurred; a major portion of the reversal was completed in a few hours. The anatomical changes are of considerable scientific interest and of import to the human factors design engineer, but the shifts of blood and extravascular fluid are of more consequence. It is hypothesized that the driving force for the fluid shift is the intrinsic and unopposed lower limb elasticity that forces venous blood and then other fluid cephalad.

  9. Does the ARFIMA really shift?

    DEFF Research Database (Denmark)

    Monache, Davide Delle; Grassi, Stefano; Santucci de Magistris, Paolo

    Short memory models contaminated by level shifts have long-memory features similar to those associated to processes generated under fractional integration. In this paper, we propose a robust testing procedure, based on an encompassing parametric specification, that allows to disentangle the level...

  10. The Shift Needed for Sustainability

    Science.gov (United States)

    Smith, Peter A. C.; Sharicz, Carol

    2011-01-01

    Purpose: The purpose of this action research is to begin to assess to what extent organizations have in practice begun to make the shift towards triple bottom line (TBL) sustainability. Design/methodology/approach: A definition of TBL sustainability is provided, and key elements of TBL sustainability considered necessary to success are identified…

  11. Shift Work: Improving Daytime Sleep

    Science.gov (United States)

    ... Good daytime sleep is possible, though, if shift work is a necessary part of your work life. To promote better sleep during the day: ... Take naps. Napping late in the day before work might help you make up your sleep debt. ...

  12. Shifts in historical streamflow extremes in the Colorado River Basin

    OpenAIRE

    Kurt C. Solander; Katrina E. Bennett; Richard S. Middleton

    2017-01-01

    The global phenomenon of climate change-induced shifts in precipitation leading to “wet regions getting wetter” and “dry regions getting drier” has been widely studied. However, the propagation of these changes in atmospheric moisture within stream channels is not a direct relationship due to differences in the timing of how changing precipitation patterns interact with various land surfaces. Streamflow is of particular interest in the Colorado River Basin (CRB) due to the region’s rapidly gr...

  13. Protein structure refinement using a quantum mechanics-based chemical shielding predictor

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Jensen, Jan Halborg

    2017-01-01

    chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field...... the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1–0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted...

  14. Measurement of hyperfine structure and isotope shifts in Gd II

    Science.gov (United States)

    Del Papa, Dylan F.; Rose, Christopher D. M.; Rosner, S. David; Holt, Richard A.

    2017-07-01

    We have applied fast-ion-beam laser-fluorescence spectroscopy to measure the isotope shifts of 73 optical transitions in the wavelength range 421.5-455.8 nm and the hyperfine structures of 35 even parity and 33 odd parity levels in Gd II. Many of the isotope shifts and hyperfine structure measurements are the first for these transitions and levels. These atomic data can be used to correct for saturation and blending in the analysis of stellar spectra to determine chemical abundances. As a result, they have an important impact on studies of the history of nucleosynthesis in the Universe and on the use of photospheric abundance anomalies in Chemically Peculiar stars to infer indirect information about stellar interiors.

  15. VP Anaphors and Object Shift

    DEFF Research Database (Denmark)

    Ørsnes, Bjarne

    2013-01-01

    The article discusses the placement of the VP anaphor det ‘it’ as a complement of verbs selecting VP complements in Danish. With verbs that only allow a VP complement, the VP anaphor must be in SpecCP regardless of its information structure properties. If SpecCP is occupied by an operator......, the anaphor can be in situ, but it cannot shift. With verbs that allow its VP complement to alternate with an NP complement, the VP anaphor can be in SpecCP, shifted or in situ according to the information structural properties of the anaphor. Only if SpecCP is occupied by an operator, must a topical anaphor...

  16. Hadronic shift in pionic hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Hennebach, M.; Gotta, D. [Forschungszentrum Juelich, Institut fuer Kernphysik, Juelich (Germany); Anagnostopoulos, D.F. [University of Ioannina, Department of Materials Science and Engineering, Ioannina (Greece); Dax, A.; Liu, Y.W.; Markushin, V.E.; Simons, L.M. [Paul Scherrer Institut, Laboratory for Particle Physics, Villigen (Switzerland); Fuhrmann, H.; Gruber, A.; Hirtl, A.; Zmeskal, J. [Austrian Academy of Sciences, Stefan Meyer Institute for Subatomic Physics, Vienna (Austria); Indelicato, P. [UPMC Univ. Paris 06, Laboratoire Kastler Brossel, Sorbonne Universites, Paris (France); CNRS, Laboratoire Kastler Brossel, Paris (France); Departement de Physique de l' Ecole Normale Superieure, Laboratoire Kastler Brossel, Paris (France); Manil, B. [UPMC Univ. Paris 06, Laboratoire Kastler Brossel, Sorbonne Universites, Paris (France); Rusi el Hassani, A.J. [Universite Abdelmalek Essaadi, Faculte des Sciences et Techniques, Tanger (Morocco); Trassinelli, M. [Sorbonne Universites, Institut des NanoSciences de Paris, Paris (France); CNRS, Institut des NanoSciences de Paris, Paris (France)

    2014-12-01

    The hadronic shift in pionic hydrogen has been redetermined to be ε {sub 1s} = 7.086 ± 0.007(stat) ± 0.006(sys) eV by X-ray spectroscopy of ground-state transitions applying various energy calibration schemes. The experiment was performed at the high-intensity low-energy pion beam of the Paul Scherrer Institut by using the cyclotron trap and an ultimate-resolution Bragg spectrometer with bent crystals. (orig.)

  17. Into the Era of shifts

    DEFF Research Database (Denmark)

    Dencik, Lars

    2005-01-01

    Globalization and new communication technologies shape new increasingly unpredictable living conditions. Societies as individuals face a world og growing predictive impotence. Traditions loose their power as guides for maneuvering - where traditions was reflection will be. At the same time peoples......, life styles, experiences and sexuality. Even thougts and feelings.In the era of shifts we shall be living with ever more design in an ever less designed world....

  18. Rapid mixing kinetic techniques.

    Science.gov (United States)

    Martin, Stephen R; Schilstra, Maria J

    2013-01-01

    Almost all of the elementary steps in a biochemical reaction scheme are either unimolecular or bimolecular processes that frequently occur on sub-second, often sub-millisecond, time scales. The traditional approach in kinetic studies is to mix two or more reagents and monitor the changes in concentrations with time. Conventional spectrophotometers cannot generally be used to study reactions that are complete within less than about 20 s, as it takes that amount of time to manually mix the reagents and activate the instrument. Rapid mixing techniques, which generally achieve mixing in less than 2 ms, overcome this limitation. This chapter is concerned with the use of these techniques in the study of reactions which reach equilibrium; the application of these methods to the study of enzyme kinetics is described in several excellent texts (Cornish-Bowden, Fundamentals of enzyme kinetics. Portland Press, 1995; Gutfreund, Kinetics for the life sciences. Receptors, transmitters and catalysis. Cambridge University Press, 1995).There are various ways to monitor changes in concentration of reactants, intermediates and products after mixing, but the most common way is to use changes in optical signals (absorbance or fluorescence) which often accompany reactions. Although absorbance can sometimes be used, fluorescence is often preferred because of its greater sensitivity, particularly in monitoring conformational changes. Such methods are continuous with good time resolution but they seldom permit the direct determination of the concentrations of individual species. Alternatively, samples may be taken from the reaction volume, mixed with a chemical quenching agent to stop the reaction, and their contents assessed by techniques such as HPLC. These methods can directly determine the concentrations of different species, but are discontinuous and have a limited time resolution.

  19. Shift Work and Endocrine Disorders

    Directory of Open Access Journals (Sweden)

    M. A. Ulhôa

    2015-01-01

    Full Text Available The objective of this review was to investigate the impact of shift and night work on metabolic processes and the role of alterations in the sleep-wake cycle and feeding times and environmental changes in the occurrence of metabolic disorders. The literature review was performed by searching three electronic databases for relevant studies published in the last 10 years. The methodological quality of each study was assessed, and best-evidence synthesis was applied to draw conclusions. The literature has shown changes in concentrations of melatonin, cortisol, ghrelin, and leptin among shift workers. Melatonin has been implicated for its role in the synthesis and action of insulin. The action of this hormone also regulates the expression of transporter glucose type 4 or triggers phosphorylation of the insulin receptor. Therefore, a reduction in melatonin can be associated with an increase in insulin resistance and a propensity for the development of diabetes. Moreover, shift work can negatively affect sleep and contribute to sedentarism, unhealthy eating habits, and stress. Recent studies on metabolic processes have increasingly revealed their complexity. Physiological changes induced in workers who invert their activity-rest cycle to fulfill work hours include disruptions in metabolic processes.

  20. Prevalence of myopic shifts among patients seeking cataract surgery

    Directory of Open Access Journals (Sweden)

    Rafael Iribarren

    2013-06-01

    Full Text Available Modern cataract surgery by phacoemulsification is a widely accepted procedure with a rapid recovery time. The prescription of specific intraocular lens, implanted during surgery, makes it possible to anticipate whether the patient will need reading glasses after the procedure. The present study analyses a sample of cataract surgery patients to show the frequency of myopic shifts related to nuclear opacity, which can result in clear near vision before surgery. A non-selected sample of consecutive patients who underwent elective cataract surgery in a private clinic was studied retrospectively. The myopic shift in refraction was assessed by comparing the old prescription with the spectacle correction at the time of interviewing.The mean age of the 229 subjects studied was 71.5 ± 10.4 years (109, 47.6%, males. A myopic shift in refraction, defined as at least - 0.5 diopters, was present in 37.1% of subjects (95% CI: 30.8%-43.4%. The mean change in refraction in these subjects was -2.52 ± 1.52 diopters. The percentage of subjects who had developed a myopic shift was significantly greater in those who presented greater nuclear opalescence. There were also differences in the mean myopic shift by refractive group, with the emmetropes having the greatest myopic shift. In this study of patients seeking cataract surgery in a clinical setting, more than one third had myopic shifts in refraction. This must be taken into account in order that patients maintain the benefit of clear near vision after surgery.

  1. The Cryo-Thermochromatographic Separator (CTS) A new rapid separation and alpha-detection system for on-line chemical studies of highly volatile osmium and hassium (Z=108) tetroxides

    CERN Document Server

    Kirbach, U W; Gregorich, K E; Lee, D M; Ninov, V; Omtvedt, J P; Patin, J B; Seward, N K; Strellis, D A; Sudowe, R; Türler, A; Wilk, P A; Zielinski, P M; Hoffman, D C; Nitsche, H

    2002-01-01

    The Cryo-Thermochromatographic Separator (CTS) was designed and constructed for rapid, continuous on-line separation and simultaneous detection of highly volatile compounds of short-lived alpha-decaying isotopes of osmium and hassium (Hs, Z=108). A flowing carrier gas containing the volatile species is passed through a channel formed by two facing rows of 32 alpha-particle detectors, cooled to form a temperature gradient extending from 247 K at the channel entrance down to 176 K at the exit. The volatile species adsorb onto the SiO sub 2 -coated detector surfaces at a characteristic deposition temperature and are identified by their observed alpha-decay energies. The CTS was tested on-line with OsO sub 4 prepared from sup 1 sup 6 sup 9 sup - sup 1 sup 7 sup 3 Os isotopes produced in sup 1 sup 1 sup 8 sup , sup 1 sup 2 sup 0 Sn( sup 5 sup 6 Fe, 3,4,5n) reactions. An adsorption enthalpy for OsO sub 4 of -40.2+-1.5 kJ/mol on SiO sub 2 was deduced by comparing the measured deposition distribution with Monte Carlo...

  2. Elevated salivary cortisol levels as a result of sleep deprivation in a shift worker.

    Science.gov (United States)

    Lac, G; Chamoux, A

    2003-03-01

    This paper reports a case from a group of 63 shift-workers for whom adaptation to shift-work was evaluated through measurement of salivary cortisol levels. Workers' saliva was sampled and cortisol levels measured at intervals of 2 h during morning, evening and night shifts. For one subject among the 63, very high values of cortisol (an approximately 6-fold increase) were observed for the morning (M) shift, but with normal values found for evening (E) and night (N) shifts. Individual mean and peak cortisol values were 48.4 and 67.8 nmol/l against group mean and peak cortisol values of 8.9 and 11.0 nmol/l. Retrospective questioning showed that this subject was healthy and there were no indicators of long-term stress. This cortisol rise was deduced to be caused by sleep deprivation as a result of rapidly rotating shift patterns.

  3. Principles of chemical kinetics

    CERN Document Server

    House, James E

    2007-01-01

    James House's revised Principles of Chemical Kinetics provides a clear and logical description of chemical kinetics in a manner unlike any other book of its kind. Clearly written with detailed derivations, the text allows students to move rapidly from theoretical concepts of rates of reaction to concrete applications. Unlike other texts, House presents a balanced treatment of kinetic reactions in gas, solution, and solid states. The entire text has been revised and includes many new sections and an additional chapter on applications of kinetics. The topics covered include quantitative rela

  4. Redox regime shifts in microbially mediated biogeochemical cycles

    Directory of Open Access Journals (Sweden)

    T. Bush

    2015-06-01

    Full Text Available Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet they are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point". These redox regime shifts occur in parameter ranges that are relevant to the present-day sulfur cycle in the natural environment and the present-day nitrogen cycle in eutrophic terrestrial environments. These shifts may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

  5. Chemical use

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a summary of research and activities related to chemical use on Neal Smith National Wildlife Refuge between 1992 and 2009. The chemicals used on the Refuge...

  6. Feasibility of Rapid-Sequence {sup 31}P Magnetic Resonance Spectroscopy in Cardiac Patients

    Energy Technology Data Exchange (ETDEWEB)

    Chida, K.; Otani, H.; Saito, H.; Nagasaka, T.; Kagaya, Y.; Kohzuki, M.; Zuguchi, M.; Shirato, K. [Tohoku Univ., School of Health Sciences, Sendai (Japan). Dept. of Radiological Technology

    2005-07-01

    Purpose: To determine the clinical feasibility of rapid-sequence phosphorus-31 magnetic resonance spectroscopy ({sup 31}P -MRS) of the heart with cardiac patients using a 5T clinical MR system. Material and Methods: Twenty cardiac patients, i.e. dilated cardiomyopathy (DCM)3 cases, hypertrophic cardiomyopathy (HCM) 3 cases, hypertensive heart diseases (HHD) 3 cases, and aortic regurgitation (AR) case were examined using rapid cardiac {sup 31}P-MRS. Complete three-dimensional localization was performed using a two-dimensional phosphorus chemical-shift imaging sequence in combination with 30-mm axial slice-selective excitation. The rapid-sequence {sup 31}P-MRS procedure was phase encoded in arrays of 8x8 steps with an average of 4 acquisitions. The total examination time, including proton imaging and shimming, for the rapid cardiac {sup 31}P-MRS procedure, ranged from 0 to 5 min, depending on the heart rate. Student's t test was used to compare creatine phosphate (PCr)/adenosine triphosphate (ATP) ratios from the cardiac patients with those of the control subjects (n{approx_equal}13). Results: The myocardial PCr/ATP ratio obtained by rapid {sup 31}P-MRS was significantly lower (P <0.001) in DCM patients (1.82{+-}0.33, mean{+-}SD), and in patients with global myocardial dysfunction (combined data for 20 patients:.89{+-}0.32) than in normal volunteers (2.96{+-}0.59). These results are similar to previous studies. Conclusion: Rapid-sequence {sup 31}P-MRS may be a valid diagnostic tool for patients with cardiac disease.

  7. Geometric phase shifting digital holography.

    Science.gov (United States)

    Jackin, Boaz Jessie; Narayanamurthy, C S; Yatagai, Toyohiko

    2016-06-01

    A new phase shifting digital holographic technique using a purely geometric phase in Michelson interferometric geometry is proposed. The geometric phase in the system does not depend upon either optical path length or wavelength, unlike dynamic phase. The amount of geometric phase generated is controllable through a rotating wave plate. The new approach has unique features and major advantages in holographic measurement of transparent and reflecting three-dimensional (3D) objects. Experimental results on surface shape measurement and imaging of 3D objects are presented using the proposed method.

  8. Chemical genomics in plant biology.

    Science.gov (United States)

    Sadhukhan, Ayan; Sahoo, Lingaraj; Panda, Sanjib Kumar

    2012-06-01

    Chemical genomics is a newly emerged and rapidly progressing field in biology, where small chemical molecules bind specifically and reversibly to protein(s) to modulate their function(s), leading to the delineation and subsequent unravelling of biological processes. This approach overcomes problems like lethality and redundancy of classical genetics. Armed with the powerful techniques of combinatorial synthesis, high-throughput screening and target discovery chemical genomics expands its scope to diverse areas in biology. The well-established genetic system of Arabidopsis model allows chemical genomics to enter into the realm of plant biology exploring signaling pathways of growth regulators, endomembrane signaling cascades, plant defense mechanisms and many more events.

  9. Enhancing Thai Students' Learning of Chemical Kinetics

    Science.gov (United States)

    Chairam, Sanoe; Somsook, Ekasith; Coll, Richard K.

    2009-01-01

    Chemical kinetics is an extremely important concept for introductory chemistry courses. The literature suggests that instruction in chemical kinetics is often teacher-dominated at both the secondary school and tertiary levels, and this is the case in Thailand--the educational context for this inquiry. The work reported here seeks to shift students…

  10. Rapid Prototyping Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The ARDEC Rapid Prototyping (RP) Laboratory was established in December 1992 to provide low cost RP capabilities to the ARDEC engineering community. The Stratasys,...

  11. [Investigation of the actual conditions of hospital nurses working on three rotating shifts: questionnaire results of shift work schedules, feelings of sleep and fatigue, and depression].

    Science.gov (United States)

    Matsumoto, M; Kamata, S; Naoe, H; Mutoh, F; Chiba, S

    1996-01-01

    These studies were performed to clarify (1) the actual conditions concerning rotating shift schedules of nurses in Japanese university and college hospitals and to evaluate (2) some aspects of the physical and mental health, and (3) sleep profile of hospital nurses working on counter-clockwise shift rotation. Two questionnaire surveys and the OSA sleep inventory (OSA) were carried out. The subjects in the study (1) were a total of 80 nursing directors in university and college hospitals. The questionnaire covered 4 categories, such as the schedule most frequently adopted and reasons for using the schedule. The questionnaires were returned by 67 directors (83.8%). The subjects in the study (2) were 189 nurses working on three-shift work schedules at Asahikawa Medical College Hospital. The items in the questionnaire covered 7 categories, as follows: 1) feeling of sleep after each shift (8 items); 2) feeling of fatigue after each shift (30 items); 3) physical symptoms; 4) inter-personal problems; 5) all the items on Zung's self-rating depression scale (SDS); 6) all the items on the Horne and Ostberg morningness-eveningness questionnaire; and 7) 24 items on the Maudsley personality inventory. The questionnaires were returned by 156 nurses (82.5%), whose mean age and duration of shift-work employment were 27.2 +/- 5.1 and 5.0 +/- 4.3 years (mean +/- SD), respectively. For 152 nurses (97.4%) of those returning the questionnaire, the working schedule consisted of 2 consecutive night shifts and 2 consecutive evening shifts, following a variable number of day shifts (rapid and counterclockwise shift rotation). The subjects in the study (3) were 8 healthy nurses working on above-mentioned three rotating shifts at the psychiatric ward of Asahikawa Medical College Hospital, whose mean age was 29.4 +/- 5.8 years (mean +/- SD). All the subjects recorded their sleep-logs and underwent OSA everyday for 30 consecutive days. Of the 240 OSA data, 95 data (16 after day shift, 17 after

  12. Influence of Rapid Thermal Annealing on the Characteristics of InGaN/GaN MQWs

    Directory of Open Access Journals (Sweden)

    Tian Yuan

    2016-01-01

    Full Text Available N-type InGaN/GaN multiple-quantum-wells (MQWs were grown on sapphire substrates by metal organic chemical vapor deposition (MOCVD. The crystal quality and optical properties of samples after rapid thermal annealing (RTA at different temperatures in a range from 400 to 800°C are investigated by X-ray diffraction (XRD and photoluminescence (PL spectrum. The experimental results show that the peaks of InGaN, InN and In can be observed in all samples. And the results are induced by the phase separation and In-clusters. The luminescence peak of the samples annealed showed a red shift. It is caused by strain stress relaxation during the RTA process. Furthermore, some defects can be eliminated and the best annealing temperature is from 500°C to 700°C.

  13. Paradigm shifts in corneal transplantation.

    Science.gov (United States)

    Tan, Donald T H; Anshu, Arundhati; Mehta, Jodhbir S

    2009-04-01

    Conventional corneal transplantation, in the form of penetrating keratoplasty (PK), involves full-thickness replacement of the cornea, and is a highly successful procedure. However, the cornea is anatomically a multi-layered structure. Pathology may only affect individual layers of the cornea, hence selective lamellar surgical replacement of only the diseased corneal layers whilst retaining unaffected layers represents a new paradigm shift in the field. Recent advancements in surgical techniques and instrumentation have resulted in several forms of manual, microkeratome and femto-second laser-assisted lamellar transplantation procedures. Anterior lamellar keratoplasty (ALK) aims at replacing only diseased or scarred corneal stroma, whilst retaining the unaffected corneal endothelial layer, thus obviating the risk of endothelial allograft rejection. Posterior lamellar keratoplasty/endothelial keratoplasty (PLK/EK) involves the replacement of the dysfunctional endothelial cell layer only. Whilst significant technical and surgical challenges are involved in performing lamellar micro-dissection of a tissue which is only 0.5 mm thick, the benefits of a more controlled surgical procedure and improved graft survival rates have resulted in a shift away from conventional PK. This review details the current advances in emerging lamellar corneal surgical procedures and highlights the main advantages and disadvantages of these new lamellar corneal procedures.

  14. Cortisol shifts financial risk preferences

    Science.gov (United States)

    Kandasamy, Narayanan; Hardy, Ben; Page, Lionel; Schaffner, Markus; Graggaber, Johann; Powlson, Andrew S.; Fletcher, Paul C.; Gurnell, Mark; Coates, John

    2014-01-01

    Risk taking is central to human activity. Consequently, it lies at the focal point of behavioral sciences such as neuroscience, economics, and finance. Many influential models from these sciences assume that financial risk preferences form a stable trait. Is this assumption justified and, if not, what causes the appetite for risk to fluctuate? We have previously found that traders experience a sustained increase in the stress hormone cortisol when the amount of uncertainty, in the form of market volatility, increases. Here we ask whether these elevated cortisol levels shift risk preferences. Using a double-blind, placebo-controlled, cross-over protocol we raised cortisol levels in volunteers over 8 d to the same extent previously observed in traders. We then tested for the utility and probability weighting functions underlying their risk taking and found that participants became more risk-averse. We also observed that the weighting of probabilities became more distorted among men relative to women. These results suggest that risk preferences are highly dynamic. Specifically, the stress response calibrates risk taking to our circumstances, reducing it in times of prolonged uncertainty, such as a financial crisis. Physiology-induced shifts in risk preferences may thus be an underappreciated cause of market instability. PMID:24550472

  15. Cortisol shifts financial risk preferences.

    Science.gov (United States)

    Kandasamy, Narayanan; Hardy, Ben; Page, Lionel; Schaffner, Markus; Graggaber, Johann; Powlson, Andrew S; Fletcher, Paul C; Gurnell, Mark; Coates, John

    2014-03-04

    Risk taking is central to human activity. Consequently, it lies at the focal point of behavioral sciences such as neuroscience, economics, and finance. Many influential models from these sciences assume that financial risk preferences form a stable trait. Is this assumption justified and, if not, what causes the appetite for risk to fluctuate? We have previously found that traders experience a sustained increase in the stress hormone cortisol when the amount of uncertainty, in the form of market volatility, increases. Here we ask whether these elevated cortisol levels shift risk preferences. Using a double-blind, placebo-controlled, cross-over protocol we raised cortisol levels in volunteers over 8 d to the same extent previously observed in traders. We then tested for the utility and probability weighting functions underlying their risk taking and found that participants became more risk-averse. We also observed that the weighting of probabilities became more distorted among men relative to women. These results suggest that risk preferences are highly dynamic. Specifically, the stress response calibrates risk taking to our circumstances, reducing it in times of prolonged uncertainty, such as a financial crisis. Physiology-induced shifts in risk preferences may thus be an underappreciated cause of market instability.