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Sample records for chemical shift selective

  1. 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...

  2. 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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2016-02-01

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

  5. Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker

    Energy Technology Data Exchange (ETDEWEB)

    Vernon, Robert [Hospital for Sick Children, Program in Molecular Structure and Function (Canada); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Baker, David [University of Washington, Department of Biochemistry (United States); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Department Chemie, Biomolecular NMR and Munich Center for Integrated Protein Science (Germany)

    2013-10-15

    A new fragment picker has been developed for CS-Rosetta that combines beneficial features of the original fragment picker, MFR, used with CS-Rosetta, and the fragment picker, NNMake, that was used for purely sequence based fragment selection in the context of ROSETTA de-novo structure prediction. Additionally, the new fragment picker has reduced sensitivity to outliers and other difficult to match data points rendering the protocol more robust and less likely to introduce bias towards wrong conformations in cases where data is bad, missing or inconclusive. The fragment picker protocol gives significant improvements on 6 of 23 CS-Rosetta targets. An independent benchmark on 39 protein targets, whose NMR data sets were published only after protocol optimization had been finished, also show significantly improved performance for the new fragment picker (van der Schot et al. in J Biomol NMR, 2013)

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

    International Nuclear Information System (INIS)

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

  7. A Short History of Three Chemical Shifts

    Science.gov (United States)

    Nagaoka, Shin-ichi

    2007-01-01

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

  8. Chemical shift MR imaging of the skin

    International Nuclear Information System (INIS)

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

  9. Geometric effects on carbon-13 chemical shifts

    International Nuclear Information System (INIS)

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

  10. MR chemical shift imaging of human atheroma

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-28

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

  12. Accessible surface area from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

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

  13. Accessible surface area from NMR chemical shifts

    International Nuclear Information System (INIS)

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

  14. 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...

  15. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  18. Probabilistic validation of protein NMR chemical shift assignments

    International Nuclear Information System (INIS)

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

  19. Probabilistic validation of protein NMR chemical shift assignments

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-15

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-10-15

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

  2. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  3. Bayesian inference of protein structure from chemical shift data

    Directory of Open Access Journals (Sweden)

    Lars A. Bratholm

    2015-03-01

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

  4. 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.

  5. Counterion influence on chemical shifts in strychnine salts.

    Science.gov (United States)

    Metaxas, Athena E; Cort, John R

    2013-05-01

    The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here, we characterize the relative influence of different counterions on (1)H and (13)C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD), and chloroform-d (CDCl3) solvents. In organic solvents but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. Slight concentration dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared with the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts. PMID:23495106

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

    Science.gov (United States)

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

    2013-03-01

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

  7. Selected readings in chemical kinetics

    CERN Document Server

    Back, Margaret H

    2013-01-01

    Selected Readings in Chemical Kinetics covers excerpts from 12 papers in the field of general and gas-phase kinetics. The book discusses papers on the laws of connexion between the conditions of a chemical change and its amount; on the reaction velocity of the inversion of the cane sugar by acids; and the calculation in absolute measure of velocity constants and equilibrium constants in gaseous systems. The text then tackles papers on simple gas reactions; on the absolute rate of reactions in condensed phases; on the radiation theory of chemical action; and on the theory of unimolecular reacti

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

    International Nuclear Information System (INIS)

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

  9. SELECTION OF BRILLOUIN SHIFT DISCRIMINATOR FOR BRILLOUIN LIDAR

    Institute of Scientific and Technical Information of China (English)

    吴东; 刘智深

    2002-01-01

    For the measurement of vertical profiles of sound speed in the sea using laser excited Brillouin scattering, a high-resolution measurement of Brillouin frequency shift is required. In this work, a molecular absorption cell was selected as the frequency shift discriminator and several kinds of absorption gases were tried. It was found that the strong line ( # 1095) of 127 I2 at 18783. 3297 cm-1 and two absorption lines of 129 I2 located at the two sides of the # 1095 line of 127 I2 could be used as frequency shift discriminator to detect the changes of the Brillouin frequency shift. This selection is the best one within the range from 532.0131 run to 532.5154 nm. But it is not perfect and there is a lot of work to do before its practical application.

  10. Improving 3D structure prediction from chemical shift data

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Laskowski, Robert; Blaha, Peter

    2012-01-01

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

  12. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-15

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

  13. Anisotropy of the fluorine chemical shift tensor in UF6

    International Nuclear Information System (INIS)

    An 19F magnetic resonance study of polycrystalline UF6 is presented. The low temperature complex line can be analyzed as the superposition of two distinct lines, which is attributed to a distortion of the UF6 octahedron in the solid. The shape of the two components is studied. Their width is much larger than the theoretical dipolar width, and must be explained by large anisotropies of the fluorine chemical shift tensors. The resulting shape functions of the powder spectra are determined. The values of the parameters of the chemical shift tensors yield estimates of the characters of the U-F bonds, and this gives some information on the ground state electronic wave function of the UF6 molecule in the solid. (author)

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

    CERN Document Server

    Fukushima, Kenji

    2016-01-01

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

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

    International Nuclear Information System (INIS)

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

  16. Chemical-shift MRI of exogenous lipoid pneumonia

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-05-01

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

  17. Unnatural selection in chemical systems

    Science.gov (United States)

    Orgel, Leslie E.

    1995-01-01

    The theory of evolution through natural selection was proposed by Darwin and Wallace to explain how the characteristics of populations of animals change with time. An examination of their assumptions shows that the theory has much broader application than they originally envisaged. We now know that in appropriate environments RNA molecules or computer viruses, for example, can evolve. The adventure with which we are concerned is the quest for chemical systems that undergo processes analogous to Darwinian selection in the test tube. The search is not restricted to systems that are closely related to nucleic acids, although most of the available experimental evidence concerns such systems. A population of molecules satisfies all the requirements of the theory is there are different kinds of molecules in the population and if each individual molecule can direct the formation of copies of itself, then a population of molecules will adapt to a varying environment by changing its composition so as to maintain as high as possible a rate of replication. Sol Spiegelman is the inventor of 'unnatural selection'. He showed clearly that populations of RNA molecules evolve when replicated repeatedly by Q beta RNA polymerase under a chosen set of adverse reaction conditions. In the systems that he studied, the initial population was fairly homogeneous and much of the variation was created during the course of the experiment by mutation, that is, error of replication. The term 'unnatural selection' will be used loosely to describe evolution of nucleic acids or other replicatable polymers in vitro. The term 'Natural Selection' will be reserved for the evolution of living organisms and their viruses. Natural Section usually involves the coevolution of nucleic acids and proteins, while 'unnatural selection', as practiced so far, allows replicating nucleic acids to evolve but hold constant the enzymes that catalyze replication. It is widely believed that biology based on DNA, RNA, and

  18. SELECTION OF BRILLOUIN SHIFT DISCRIMINATOR FOR BRILLOUIN LIDAR

    Institute of Scientific and Technical Information of China (English)

    吴东; 刘智深

    2002-01-01

    For the measurement of vertical profiles of sound speed in the sea using laser excited Brillouin scattering, a high-resolution measurement of Brillouin frequency shift is required. In this work, a molecular absorption cell was selec ted as the frequency shift discriminator and several kinds of absorption gases were tri ed. It was found that the strong line (#1095) of 127I2 at 18783.3297 cm-1 and two absorption lines of 129I2 located at the two sides of the #1095 line of 127 I2 could be used as frequency shift discriminator to detect the changes of the Brillouin frequency s hift. This selection is the best one within the range from 532.0131 nm to 532.5154 nm. But it is not perfect and there is a lot of work to do before its practical application.

  19. Substituent effects on 61Ni NMR chemical shifts

    OpenAIRE

    Bühl, Michael; Peters, Dietmund; Herges, Rainer

    2009-01-01

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

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

    International Nuclear Information System (INIS)

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

  1. Computational Assignment of Chemical Shifts for Protein Residues

    CERN Document Server

    Bratholm, Lars A

    2013-01-01

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

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

    Science.gov (United States)

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

    2015-04-14

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

  3. Pitfalls of adrenal imaging with chemical shift MRI

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  5. Applications of Chemical Shift Imaging to Marine Sciences

    Directory of Open Access Journals (Sweden)

    Haakil Lee

    2010-08-01

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

  6. 19-Fluorine nuclear magnetic resonance chemical shift variability in trifluoroacetyl species

    OpenAIRE

    Sloop, Joseph

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

    Lomachuk, Yuriy V.; Titov, Anatoly V.

    2013-01-01

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

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

    CERN Document Server

    Christensen, Anders S

    2015-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-15

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  19. Cardiovascular risk factors and primary selection into shift work

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Kirsten; Garde, Anne Helene; Tüchsen, Finn;

    2008-01-01

    : Altogether 2870 newly educated social and health care workers filled out a questionnaire a few weeks before finishing their formal training and again 1 year after graduation. They answered questions on diabetes, hypertension, lifestyle habits, sociodemographic factors, and general self-efficacy. RESULTS.......04-2.56). Being an ex-smoker was associated with two- or three-shift work including night work (OR 1.85, 95% CI 1.28-2.68). The association between two- and three-shift work and smoking was only of borderline significance (OR 1.37, 95% CI 1.00-1.87). CONCLUSIONS: Compared with future day workers, fixed evening...

  20. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

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

  2. Chemical shifts and coupling constants of C8H10N4O2

    Science.gov (United States)

    Jain, M.

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

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

    Directory of Open Access Journals (Sweden)

    Dalia Z. Zidan

    2014-09-01

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

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

    International Nuclear Information System (INIS)

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

  5. 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...

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2015-09-01

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR and (13)C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and (1)H and (13)C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA (1)H and (13)C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides. PMID:26141454

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-15

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

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

    International Nuclear Information System (INIS)

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

  12. 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.)

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2010-02-01

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

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

    Directory of Open Access Journals (Sweden)

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

    2012-08-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-14

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-07-01

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

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

    International Nuclear Information System (INIS)

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2013-01-01

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

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

    Science.gov (United States)

    Lomachuk, Yuriy V.; Titov, Anatoly V.

    2013-12-01

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

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

    CERN Document Server

    Lomachuk, Yuriy V

    2013-01-01

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

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

    International Nuclear Information System (INIS)

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C', respectively, including outliers

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

    International Nuclear Information System (INIS)

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

  5. Chemical composition of selected Saudi medicinal plants

    Directory of Open Access Journals (Sweden)

    Ihsanullah Daur

    2015-05-01

    Full Text Available Medicinal plants are important in traditional medicine and modern pharmaceutical drugs; therefore, the interest in the analysis of their chemical composition is increasing. In this study, selected medicinal plants including Achillea fragrantissima (Forssk Sch., Amaranthus viridis L., Asteriscus graveolens (Forssk. Less., Chenopodium album L., and Conyza bonariensis (L. Cronquist were collected from the rangeland of western regions (Bahra and Hada areas of Saudi Arabia to study their chemical composition. Eight minerals (Mg, Ca, Cr, Mn, Fe, Co, Cu, and Zn, total phenolic contents, antioxidant activity, and free-radical scavenging ability were examined in order to evaluate the medicinal potential of these plants. All the plants were found to be rich sources of minerals and antioxidants, although there were significant differences (p < 0.05 in their chemical composition, which may provide a rationale for generating custom extracts from specific plants depending on the application. The findings of this study will thus facilitate herbalists in their efforts to incorporate these plants into various formulations based on their chemical composition.

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-01-15

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

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

    Directory of Open Access Journals (Sweden)

    Anders S Christensen

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

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

    CERN Document Server

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

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

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

  13. 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...

  14. 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...

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2016-04-14

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    1996-03-01

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

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

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin

    2011-01-01

    this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that...... changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets......Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues...

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

    DEFF Research Database (Denmark)

    Lægsgaard, Jesper

    2001-01-01

    The chemical shifts of the K alpha radiation line from Al, Si, and Ge ions between their elemental and oxide forms are calculated within the framework of density functional theory using ultrasoft pseudopotentials. It is demonstrated that this theoretical approach yields quantitatively accurate re...... implanted in silica are found to be in excellent agreement with experimental data, providing support for the proposed atomic geometry....

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

    International Nuclear Information System (INIS)

    The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the 1H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson–Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 43 possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA 1H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

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

    Science.gov (United States)

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

    1982-11-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    NARCIS (Netherlands)

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-03-15

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

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

    Science.gov (United States)

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

    2016-02-24

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

  8. Guide to good practices for the selection, training, and qualification of shift technical advisors

    Energy Technology Data Exchange (ETDEWEB)

    1993-02-01

    The DOE Guide to Good Practices For The Selection, Training, and Qualification of Shift Technical Advisors can be used by any DOE nuclear facility that has implemented the shift technical advisor position. DOE Order 5480-20, ``Personnel Selection, Qualification, Training, and Staffing Requirements at DOE Reactor and Non-Reactor Nuclear Facilities,`` states that only Category A reactors must use shift technical advisor position. However, many DOE nuclear facilities have implemented the shift technical advisor position to provide independent on-shift technical advice and counsel to the shift operating personnel to help determine cause and mitigation of facility accidents. Those DOE nuclear facilities that have implemented or are going to implement the shift technical advisor position will find this guide useful. This guide addresses areas that may be covered by other training programs. In these cases, it is unnecessary (and undesirable) to duplicate these areas in the STA training program as long as the specific skills and knowledge essential for STAs are addressed. The guide is presented based on the premise that the trainee has not completed any facility-specific training other than general employee training.

  9. Guide to good practices for the selection, training, and qualification of shift technical advisors

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1993-02-01

    The DOE Guide to Good Practices For the Selection, Training, and Qualification of Shift Technical Advisors can be used by any DOE nuclear facility that has implemented the shift technical advisor (STA) position. DOE Order 5480.20A, Personnel Selection, Qualification and Training Requirements for DOE Nuclear Facilities, states that only Category A reactors must have a shift technical advisor. However, many DOE nuclear facilities have implemented the shift technical advisor position to provide independent on-shift technical advice and counsel to the shift operating personnel to help determine cause and mitigation of facility accidents. Those DOE nuclear facilities that have implemented or are going to implement the shift technical advisor position will find this guide useful. This guide addresses areas that may be covered by other training programs. In these cases, it is unnecessary (and undesirable) to duplicate these areas in the STA training program as long as the specific skills and knowledge essential for STAs are addressed. The guide is based on the premise that the trainee has not completed any facility-specific training other than general employee training.

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

    OpenAIRE

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

    2010-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  13. 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.

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

    International Nuclear Information System (INIS)

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

  15. 1H chemical shift imaging characterization of human brain tumor and edema

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2015-12-14

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

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

    International Nuclear Information System (INIS)

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ1 rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-15

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

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

    Science.gov (United States)

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

    2002-08-01

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

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

    Indian Academy of Sciences (India)

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

    2005-01-01

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

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

    International Nuclear Information System (INIS)

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

  2. DOE handbook: Guide to good practices for the selection, training, and qualification of shift supervisors

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-04-01

    This Department of Energy (DOE) handbook is approved for use by all DOE Components and their contractors. The Handbook incorporates editorial changes to DOE-STD-1061-93, ``Guide to Good Practices for the Selection, Training, and Qualification of shift Supervisors,`` and supersedes DOE-STD-1061-93. Technical content of this Handbook has not changed from the original technical standard. Changes are primarily editorial improvements, redesignation of the standard to a Handbook, and format changes to conform with current Technical Standards Program procedures. This guide, used in conjunction with a facility-specific job analysis, provides a framework for the selection, training, qualification, and professional development of reactor facility and non-reactor nuclear facility shift supervisors. Training and qualification programs based on this guide should provide assurance that shift supervisors perform their jobs safely and competently.

  3. DOE handbook: Guide to good practices for the selection, training, and qualification of shift supervisors

    International Nuclear Information System (INIS)

    This Department of Energy (DOE) handbook is approved for use by all DOE Components and their contractors. The Handbook incorporates editorial changes to DOE-STD-1061-93, ''Guide to Good Practices for the Selection, Training, and Qualification of shift Supervisors,'' and supersedes DOE-STD-1061-93. Technical content of this Handbook has not changed from the original technical standard. Changes are primarily editorial improvements, redesignation of the standard to a Handbook, and format changes to conform with current Technical Standards Program procedures. This guide, used in conjunction with a facility-specific job analysis, provides a framework for the selection, training, qualification, and professional development of reactor facility and non-reactor nuclear facility shift supervisors. Training and qualification programs based on this guide should provide assurance that shift supervisors perform their jobs safely and competently

  4. SiC-BASED HYDROGEN SELECTIVE MEMBRANES FOR WATER-GAS-SHIFT REACTION; F

    International Nuclear Information System (INIS)

    This technical report summarizes our activities conducted in Yr II. In Yr I we successfully demonstrated the feasibility of preparing the hydrogen selective SiC membrane with a chemical vapor deposition (CVD) technique. In addition, a SiC macroporous membrane was fabricated as a substrate candidate for the proposed SiC membrane. In Yr II we have focused on the development of a microporous SiC membrane as an intermediate layer between the substrate and the final membrane layer prepared from CVD. Powders and supported thin silicon carbide films (membranes) were prepared by a sol-gel technique using silica sol precursors as the source of silicon, and phenolic resin as the source of carbon. The powders and films were prepared by the carbothermal reduction reaction between the silica and the carbon source. The XRD analysis indicates that the powders and films consist of SiC, while the surface area measurement indicates that they contain micropores. SEM and AFM studies of the same films also validate this observation. The powders and membranes were also stable under different corrosive and harsh environments. The effects of these different treatments on the internal surface area, pore size distribution, and transport properties, were studied for both the powders and the membranes using the aforementioned techniques and XPS. Finally the SiC membrane materials are shown to have satisfactory hydrothermal stability for the proposed application. In Yr III, we will focus on the demonstration of the potential benefit using the SiC membrane developed from Yr I and II for the water-gas-shift (WGS) reaction

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

    Science.gov (United States)

    Durbeej, Bo; Eriksson, Leif A.

    2003-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-15

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

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

    International Nuclear Information System (INIS)

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13Cβ chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and 13Cβ atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ15N, δ13C', δ13Cα, δ13Cβ, δ1Hα and δ1HN, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

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

    Czech Academy of Sciences Publication Activity Database

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

    2011-01-01

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

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

    Science.gov (United States)

    Grodzka, P.; Facemire, B.

    1977-01-01

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

  10. 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.

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

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

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

    Science.gov (United States)

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

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W. PMID:24496608

  14. 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...

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

    Science.gov (United States)

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

    2009-08-01

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

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

    Science.gov (United States)

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

    2009-09-10

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

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

    DEFF Research Database (Denmark)

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

    2006-01-01

    differences are due to different conformational behavior of the OH and OCH3 groups; while the ortho-disubstituted OH group remains planar in polyphenols due to hydrogen bonding and conjugative stabilization, the steric congestion in ortho-disubstituted anisoles outweighs the conjugative effects and forces the......Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2) to...... Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent...

  18. Chemical modification of nanocrystalline tin dioxide for selective gas sensors

    International Nuclear Information System (INIS)

    Chemical methods for enhancement of the selectivity of semiconductor metal oxide gas sensors are considered taking SnO2 as an example. Theoretical concepts concerning correlations between the metal oxide chemical composition, crystal structure, surface morphology and the oxide surface reactivity are discussed. Application of such concepts to the design of novel, highly selective sensor materials based on nanocrystalline SnO2 is discussed in detail. Experimental data on the determination of the chemical composition, structure, activity in gas–solid chemical interaction and the sensor properties of such materials are analyzed. The applicability of modern concepts of the chemical activity of the surface in gas–solid reactions to the design of novel metal oxide sensor materials with enhanced selectivity is substantiated. The bibliography includes 133 references

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

    Science.gov (United States)

    An, Li

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

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

    Science.gov (United States)

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

    2015-06-01

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-22

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

  3. 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…

  4. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-21

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

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

    International Nuclear Information System (INIS)

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

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

    CERN Document Server

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

    2011-01-01

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

  8. Chemical composition and machinability of selected species from Mozambique

    OpenAIRE

    Lhate, Inacio Arnaldo

    2011-01-01

    The objectives of the current work were to carry out a survey on timber sector in Mozambique and to determine chemical, calorific and machinability features of selected species. Mozambican timber sector was described as dominated by selective harvesting practices on a few hardwood species out of 118 species growing in the forest with potential for industrial timber. Selective logging is believed to be due to the demand in both domestic and international markets of traditionally used, and lack...

  9. Unravelling Selection Shifts Among Foot-and-Mouth Disease Virus (FMDV Serotypes

    Directory of Open Access Journals (Sweden)

    Mario A. Fares

    2006-01-01

    Full Text Available FMDV virus has been increasingly recognised as the most economically severe animal virus with a remarkable degree of antigenic diversity. Using an integrative evolutionary and computational approach we have compelling evidence for heterogeneity in the selection forces shaping the evolution of the seven different FMDV serotypes. Our results show that positive Darwinian selection has governed the evolution of the major antigenic regions of serotypes A, Asia1, O, SAT1 and SAT2, but not C or SAT3. Co-evolution between sites from antigenic regions under positive selection pinpoints their functional communication to generate immune-escape mutants while maintaining their ability to recognise the host-cell receptors. Neural network and functional divergence analyses strongly point to selection shifts between the different serotypes. Our results suggest that, unlike African FMDV serotypes, serotypes with wide geographical distribution have accumulated compensatory mutations as a strategy to ameliorate the effect of slightly deleterious mutations fixed by genetic drift. This strategy may have provided the virus by a flexibility to generate immune-escape mutants and yet recognise host-cell receptors. African serotypes presented no evidence for compensatory mutations. Our results support heterogeneous selective constraints affecting the different serotypes. This points to the possible accelerated rates of evolution diverging serotypes sharing geographical locations as to ameliorate the competition for the host.

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

    Science.gov (United States)

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

    2016-05-30

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

  11. Harnessing the Big Data Paradigm for ICME: Shifting from Materials Selection to Materials Enabled Design

    Science.gov (United States)

    Broderick, Scott R.; Santhanam, Ganesh Ram; Rajan, Krishna

    2016-07-01

    As the size of databases has significantly increased, whether through high throughput computation or through informatics-based modeling, the challenge of selecting the optimal material for specific design requirements has also arisen. Given the multiple, and often conflicting, design requirements, this selection process is not as trivial as sorting the database for a given property value. We suggest that the materials selection process should minimize selector bias, as well as take data uncertainty into account. For this reason, we discuss and apply decision theory for identifying chemical additions to Ni-base alloys. We demonstrate and compare results for both a computational array of chemistries and standard commercial superalloys. We demonstrate how we can use decision theory to select the best chemical additions for enhancing both property and processing, which would not otherwise be easily identifiable. This work is one of the first examples of introducing the mathematical framework of set theory and decision analysis into the domain of the materials selection process.

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

    International Nuclear Information System (INIS)

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

  13. Observation of the Nonlinear Phase Shift Due to Single Post-Selected Photons

    CERN Document Server

    Dmochowski, Amir Feizpour Matin Hallaji Greg

    2015-01-01

    Over the past years, there have been many efforts towards generating interactions between two optical beams so strong that they could be observed at the level of individual photons. Such strong interactions, beyond opening up a new regime in optics, could lead to technologies such as all-optical quantum information processing. However, the extreme weakness of photon-photon scattering has hindered any attempt to observe such interactions at the level of single particles. Here we implement a strong optical nonlinearity using electromagnetically-induced transparency and slow light, and directly measure the resulting nonlinear phase shift for individual photons. This is done by illuminating the sample with a weak classical pulse with as few as 0.5 photons per pulse on average, and using post-selection to determine whether a given pulse contained (approximately) 0 or 1 photons. We present clear data showing the quantized dependence of a probe beam's measured phase shift on the post-selection result, for a range of...

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

    Science.gov (United States)

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

    2015-09-14

    We assess the quality of fragment-based ab initio isotropic (13)C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic (13)C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits. PMID:26374002

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    CERN Document Server

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2008-12-01

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

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

    Science.gov (United States)

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

    2011-07-28

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

  20. SIC-BASED HYDROGEN SELECTIVE MEMBRANES FOR WATER-GAS-SHIFT REACTION

    Energy Technology Data Exchange (ETDEWEB)

    Paul K.T. Liu

    2003-12-01

    A hydrogen selective membrane as a membrane reactor (MR) can significantly improve the power generation efficiency with a reduced capital and operating cost for the waster-gas-shift reaction. Existing hydrogen selective ceramic membranes are not suitable for the proposed MR due to their poor hydrothermal stability. In this project we have focused on the development of innovative silicon carbide (SiC) based hydrogen selective membranes, which can potentially overcome this technical barrier. SiC macro-porous membranes have been successfully fabricated via extrusion of commercially available SiC powder. Also, an SiC hydrogen selective thin film was prepared via our CVD/I technique. This composite membrane demonstrated excellent hydrogen selectivity at high temperature ({approx}600 C). More importantly, this membrane also exhibited a much improved hydrothermal stability at 600 C with 50% steam (atmospheric pressure) for nearly 100 hours. In parallel, we have explored an alternative approach to develop a H{sub 2} selective SiC membrane via pyrolysis of selected pre-ceramic polymers and sol-gel techniques. Building upon the positive progress made in the membrane development study, we conducted an optimization study to develop an H{sub 2} selective SiC membrane with sufficient hydrothermal stability suitable for the WGS environment. In addition, mathematical simulation has been performed to compare the performance of the membrane reactor (MR) vs conventional packed bed reactor for WGS reaction. Our result demonstrates that >99.999% conversion can be accomplished via WGS-MR using the hydrogen selective membrane developed by us. Further, water/CO ratio can be reduced, and >97% hydrogen recovery and <200 ppm CO can be accomplished according to the mathematical simulation. Thus, we believe that the operating economics of WGS can be improved significantly based upon the proposed MR concept. In parallel, gas separations and hydrothermal and long-term-storage stability of the

  1. Chemical rationale for selection of isolates for genome sequencing

    DEFF Research Database (Denmark)

    Rank, Christian; Larsen, Thomas Ostenfeld; Frisvad, Jens Christian

    The advances in gene sequencing will in the near future enable researchers to affordably acquire the full genomes of handpicked isolates. We here present a method to evaluate the chemical potential of an entire species and select representatives for genome sequencing. The selection criteria for new...... strains to be sequenced can be manifold, but for studying the functional phenotype, using a metabolome based approach offers a cheap and rapid assessment of critical strains to cover the chemical diversity. We have applied this methodology on the complex A. flavus/A. oryzae group. Though these two species...

  2. The National Toxicology Program chemical nomination selection and testing process.

    Science.gov (United States)

    Heindel, J J

    1988-01-01

    The NTP is an interagency program of the Federal Government which coordinates toxicological programs at the NIH (NIEHS), FDA (NCTR), and CDC (NIOSH) with input from NCI, NIH, OSHA, CPSC, EPA, and ATSDR. The NTP has the capability to completely characterize the toxicologic profile of a chemical, including studies of chemical disposition, genetic toxicity, immunotoxicity, teratology, reproductive toxicity, carcinogenicity, neurotoxicity, and specific organ toxicity. The NTP encourages nominations of chemicals of human health concern from all sectors of the public, including industry, labor, and the general public. The specific process of nomination, evaluation, and selection of chemicals for testing by the NTP is described. It is a multicomponent system with several evaluations and a public peer review step to assure adequate consideration of all nominated chemicals. The results of NTP studies are all peer reviewed and available to the general public as well as to the scientific community. PMID:2980357

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

    Science.gov (United States)

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-11-15

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  9. Bark chemical analysis explains selective bark damage by rodents

    Czech Academy of Sciences Publication Activity Database

    Heroldová, Marta; Jánová, Eva; Suchomel, J.; Purchart, L.; Homolka, Miloslav

    2009-01-01

    Roč. 2, č. 2 (2009), s. 137-140. ISSN 1803-2451 R&D Projects: GA MZe QH72075 Institutional research plan: CEZ:AV0Z60930519 Keywords : bark damage * bark selection * bark chemical analysis * rowan * beech * spruce * mountain forest regeneration Subject RIV: GK - Forest ry

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

    Institute of Scientific and Technical Information of China (English)

    许波; 李浩然; 王从敏; 许映杰; 韩世钧

    2005-01-01

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

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

    DEFF Research Database (Denmark)

    Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A; Spielman, D.M.

    2000-01-01

    Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations co...... concentration error (<15%). Magn Reson Med 44:10-18, 2000....

  12. 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.

  13. Thermodynamics of natural selection II: Chemical Carnot cycles.

    Science.gov (United States)

    Smith, Eric

    2008-05-21

    This is the second in a series of three papers devoted to energy flow and entropy changes in chemical and biological processes, and to their relations to the thermodynamics of computation. In the first paper of the series, it was shown that a general-form dimensional argument from the second law of thermodynamics captures a number of scaling relations governing growth and development across many domains of life. It was also argued that models of physiology based on reversible transformations provide sensible approximations within which the second-law scaling is realized. This paper provides a formal basis for decomposing general cyclic, fixed-temperature chemical reactions, in terms of the chemical equivalent of Carnot's cycle for heat engines. It is shown that the second law relates the minimal chemical work required to perform a cycle to the Kullback-Leibler divergence produced in its chemical output ensemble from that of a Gibbs equilibrium. Reversible models of physiology are used to create reversible models of natural selection, which relate metabolic energy requirements to information gain under optimal conditions. When dissipation is added to models of selection, the second-law constraint is generalized to a relation between metabolic work and the combined energies of growth and maintenance. PMID:18367209

  14. Monte Carlo optimization for site selection of new chemical plants.

    Science.gov (United States)

    Cai, Tianxing; Wang, Sujing; Xu, Qiang

    2015-11-01

    Geographic distribution of chemical manufacturing sites has significant impact on the business sustainability of industrial development and regional environmental sustainability as well. The common site selection rules have included the evaluation of the air quality impact of a newly constructed chemical manufacturing site to surrounding communities. In order to achieve this target, the simultaneous consideration should cover the regional background air-quality information, the emissions of new manufacturing site, and statistical pattern of local meteorological conditions. According to the above information, the risk assessment can be conducted for the potential air-quality impacts from candidate locations of a new chemical manufacturing site, and thus the optimization of the final site selection can be achieved by minimizing its air-quality impacts. This paper has provided a systematic methodology for the above purpose. There are total two stages of modeling and optimization work: i) Monte Carlo simulation for the purpose to identify background pollutant concentration based on currently existing emission sources and regional statistical meteorological conditions; and ii) multi-objective (simultaneous minimization of both peak pollutant concentration and standard deviation of pollutant concentration spatial distribution at air-quality concern regions) Monte Carlo optimization for optimal location selection of new chemical manufacturing sites according to their design data of potential emission. This study can be helpful to both determination of the potential air-quality impact for geographic distribution of multiple chemical plants with respect to regional statistical meteorological conditions, and the identification of an optimal site for each new chemical manufacturing site with the minimal environment impact to surrounding communities. The efficacy of the developed methodology has been demonstrated through the case studies. PMID:26283263

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-10-01

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

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

    International Nuclear Information System (INIS)

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

  17. 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.

  18. DNA abasic site-selective enhancement of sanguinarine fluorescence with a large emission shift.

    Directory of Open Access Journals (Sweden)

    Fei Wu

    Full Text Available Small molecules that can specifically bind to a DNA abasic site (AP site have received much attention due to their importance in DNA lesion identification, drug discovery, and sensor design. Herein, the AP site binding behavior of sanguinarine (SG, a natural alkaloid, was investigated. In aqueous solution, SG has a short-wavelength alkanolamine emission band and a long-wavelength iminium emission band. At pH 8.3, SG experiences a fluorescence quenching for both bands upon binding to fully matched DNAs without the AP site, while the presence of the AP site induces a strong SG binding and the observed fluorescence enhancement for the iminium band are highly dependent on the nucleobases flanking the AP site, while the alkanolamine band is always quenched. The bases opposite the AP site also exert some modifications on the SG's emission behavior. It was found that the observed quenching for DNAs with Gs and Cs flanking the AP site is most likely caused by electron transfer between the AP site-bound excited-state SG and the nearby Gs. However, the flanking As and Ts that are not easily oxidized favor the enhanced emission. This AP site-selective enhancement of SG fluorescence accompanies a band conversion in the dominate emission from the alkanolamine to iminium band thus with a large emission shift of about 170 nm. Absorption spectra, steady-state and transient-state fluorescence, DNA melting, and electrolyte experiments confirm that the AP site binding of SG occurs and the stacking interaction with the nearby base pairs is likely to prevent the converted SG iminium form from contacting with water that is thus emissive when the AP site neighbors are bases other than guanines. We expect that this fluorophore would be developed as a promising AP site binder having a large emission shift.

  19. Motivational Shifts in Aging Monkeys and the Origins of Social Selectivity.

    Science.gov (United States)

    Almeling, Laura; Hammerschmidt, Kurt; Sennhenn-Reulen, Holger; Freund, Alexandra M; Fischer, Julia

    2016-07-11

    As humans age, they become more selective regarding their personal goals [1] and social partners [2]. Whereas the selectivity in goals has been attributed to losses in resources (e.g., physical strength) [3], the increasing focus on emotionally meaningful partners is, according to socioemotional selectivity theory, driven by the awareness of one's decreasing future lifetime [2]. Similar to humans, aging monkeys show physical losses [4] and reductions in social activity [2, 5-7]. To disentangle a general resource loss and the awareness of decreasing time, we combined field experiments with behavioral observations in a large age-heterogeneous population of Barbary macaques (Macaca sylvanus) at La Forêt des Singes. Novel object tests revealed a loss of interest in the nonsocial environment in early adulthood, which was modulated by the availability of a food reward. Experiments using vocal and visual representations of social partners indicated that monkeys maintained an interest in social stimuli and a preferential interest in friends and socially important individuals into old age. Old females engaged in fewer social interactions, although other group members continued to invest in relationships with them. Consequently, reductions in sociality were not due to a decrease in social interest. In conclusion, some of the motivational shifts observed in aging humans, particularly the increasing focus on social over nonsocial stimuli, may occur in the absence of a limited time perspective and are most likely deeply rooted in primate evolution. Our findings highlight the value of nonhuman primates as valuable models for understanding human aging [8, 9]. PMID:27345168

  20. Novel selection methods for DNA-encoded chemical libraries

    Science.gov (United States)

    Chan, Alix I.; McGregor, Lynn M.; Liu, David R.

    2015-01-01

    Driven by the need for new compounds to serve as biological probes and leads for therapeutic development and the growing accessibility of DNA technologies including high-throughput sequencing, many academic and industrial groups have begun to use DNA-encoded chemical libraries as a source of bioactive small molecules. In this review, we describe the technologies that have enabled the selection of compounds with desired activities from these libraries. These methods exploit the sensitivity of in vitro selection coupled with DNA amplification to overcome some of the limitations and costs associated with conventional screening methods. In addition, we highlight newer techniques with the potential to be applied to the high-throughput evaluation of DNA-encoded chemical libraries. PMID:25723146

  1. Nanoporous membranes with electrochemically switchable, chemically stabilized ionic selectivity

    Science.gov (United States)

    Small, Leo J.; Wheeler, David R.; Spoerke, Erik D.

    2015-10-01

    Nanopore size, shape, and surface charge all play important roles in regulating ionic transport through nanoporous membranes. The ability to control these parameters in situ provides a means to create ion transport systems tunable in real time. Here, we present a new strategy to address this challenge, utilizing three unique electrochemically switchable chemistries to manipulate the terminal functional group and control the resulting surface charge throughout ensembles of gold plated nanopores in ion-tracked polycarbonate membranes 3 cm2 in area. We demonstrate the diazonium mediated surface functionalization with (1) nitrophenyl chemistry, (2) quinone chemistry, and (3) previously unreported trimethyl lock chemistry. Unlike other works, these chemistries are chemically stabilized, eliminating the need for a continuously applied gate voltage to maintain a given state and retain ionic selectivity. The effect of surface functionalization and nanopore geometry on selective ion transport through these functionalized membranes is characterized in aqueous solutions of sodium chloride at pH = 5.7. The nitrophenyl surface allows for ionic selectivity to be irreversibly switched in situ from cation-selective to anion-selective upon reduction to an aminophenyl surface. The quinone-terminated surface enables reversible changes between no ionic selectivity and a slight cationic selectivity. Alternatively, the trimethyl lock allows ionic selectivity to be reversibly switched by up to a factor of 8, approaching ideal selectivity, as a carboxylic acid group is electrochemically revealed or hidden. By varying the pore shape from cylindrical to conical, it is demonstrated that a controllable directionality can be imparted to the ionic selectivity. Combining control of nanopore geometry with stable, switchable chemistries facilitates superior control of molecular transport across the membrane, enabling tunable ion transport systems.Nanopore size, shape, and surface charge all play

  2. Chemical recycling of mixed waste plastics by selective pyrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Tatsumoto, K.; Meglen, R.; Evans, R. [National Renewable Energy Laboratory, Golden, CO (United States)

    1995-05-01

    The goal of this work is to use selective pyrolysis to produce high-value chemicals from waste plastics mixtures. Selectivity is achieved by exploiting differences in reaction rates, catalysis, and coreactants. Target wastes are molecular mixtures such as; blends or composites, or mixtures from manufactured products such as; carpets and post-consumer mixed-plastic wastes. The experimental approach has been to use small-scale experiments using molecular beam mass spectrometry (MBMS), which provides rapid analysis of reaction products and permits rapid screening of process parameters. Rapid screening experiments permit exploration of many potential waste stream applications for the selective pyrolysis process. After initial screening, small-scale, fixed-bed and fluidized-bed reactors are used to provide products for conventional chemical analysis, to determine material balances, and to test the concept under conditions that will be used at a larger scale. Computer assisted data interpretation and intelligent chemical processing are used to extract process-relevant information from these experiments. An important element of this project employs technoeconomic assessments and market analyses of durables, the availability of other wastes, and end-product uses to identify target applications that have the potential for economic success.

  3. Shift endpoint trace selection algorithm and wavelet analysis to detect the endpoint using optical emission spectroscopy

    Science.gov (United States)

    Ben Zakour, Sihem; Taleb, Hassen

    2016-06-01

    Endpoint detection (EPD) is very important undertaking on the side of getting a good understanding and figuring out if a plasma etching process is done on the right way. It is truly a crucial part of supplying repeatable effects in every single wafer. When the film to be etched has been completely erased, the endpoint is reached. In order to ensure the desired device performance on the produced integrated circuit, many sensors are used to detect the endpoint, such as the optical, electrical, acoustical/vibrational, thermal, and frictional. But, except the optical sensor, the other ones show their weaknesses due to the environmental conditions which affect the exactness of reaching endpoint. Unfortunately, some exposed area to the film to be etched is very low (method to determine the wind-up of the etch process. This work has provided a means to improve the endpoint detection sensitivity by collecting a huge numbers of full spectral data containing 1201 spectra for each run, then a new unsophisticated algorithm is proposed to select the important endpoint traces named shift endpoint trace selection (SETS). Then, a sensitivity analysis of linear methods named principal component analysis (PCA) and factor analysis (FA), and the nonlinear method called wavelet analysis (WA) for both approximation and details will be studied to compare performances of the methods mentioned above. The signal to noise ratio (SNR) is not only computed based on the main etch (ME) period but also the over etch (OE) period. Moreover, a new unused statistic for EPD, coefficient of variation (CV), is proposed to reach the endpoint in plasma etches process.

  4. Chemically selective soft x-ray patterning of polymers

    Energy Technology Data Exchange (ETDEWEB)

    Wang, J.; Stover, H.D.; Hitchcock, A.P.; Tyliszczak, T.

    2007-06-19

    The chemically selective modification of polymer mixtures by monochromated soft X-rays has been explored using the high-brightness fine-focused 50 nm beam of a scanning transmission X-ray microscope. Four different polymer systems were examined: a polymethylmethacrylate (PMMA) polyacrylonitrile (PAN) bilayer film; a PMMA-blend-PAN microphase-separated film; a poly(MMA-co-AN) copolymer film; and a poly(ethyl cyanoacrylate) homopolymer film. A high level of chemically selective modification was achieved for the PMMA/PAN bilayer; in particular, irradiation at 288.45 eV selectively removed the carbonyl group from PMMA while irradiation at 286.80 eV selectively reduced the nitrile group of PAN, even when these irradiations were carried out at the same (x,y) position of the sample. In the last two homogeneous polymer systems, similar amounts of damage to the nitrile and carbonyl groups occurred during irradiation at either 286.80 or 288.45 eV. This is attributed to damage transfer between the C=N and C=O groups mediated by primary electrons, secondary electrons or radical/ionic processes, aided by their close spatial proximity. Although the overall thickness of the bilayer sample at 70 nm is smaller than the lateral line spreading of 100 nm, the interface between the layers appears to effectively block the transport of energy, and hence damage, between the two layers. The origins of the line spreading in homogeneous phases and possible origins of the damage blocking effect of the interface are discussed. To demonstrate chemically selective patterning, high-resolution multi-wavelength patterns were created in the PMMA/PAN bilayer system.

  5. Effect of night-shift work on selected physiological indicators in power plant workers

    Energy Technology Data Exchange (ETDEWEB)

    Chizynski, K.

    1983-01-01

    Ninety-two workers of Thermal-electric Power Station have been examined. The subjects have been classified into three age-dependent groups: 21-30, 31-40 and over 40 years. Each of the subjects has undergone tests of selected physiological indices before and after the night shift. The examinations included: body temperature measurement, pulse rate, respiration rate, arterial blood pressure. The measurements promoted calculation of: Kerdoe's index pulse respiration rate, mean arterial pressure, stroke and minute volumes. Changes in physiological indices due to night work have been compared in particular age groups by the ''t'' Student test for two mean values of small samples. The night work results in hypertonia of the vegetative parasympathetic system which is consistent with the circadiem rhythmicity of human physiological functions. The 21-30 years age group exhibits strong excitation of the vegetative sympathetic system due to great nervous and emotional tension accompanying operators' work.

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

    International Nuclear Information System (INIS)

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

  7. The direct peptide reactivity assay: selectivity of chemical respiratory allergens.

    Science.gov (United States)

    Lalko, Jon F; Kimber, Ian; Gerberick, G Frank; Foertsch, Leslie M; Api, Anne Marie; Dearman, Rebecca J

    2012-10-01

    It is well known that some chemicals are capable of causing allergic diseases of the skin and respiratory tract. Commonly, though not exclusively, chemical allergens are associated with the selective development of skin or respiratory sensitization. The reason for this divergence is unclear, although it is hypothesized that the nature of interactions between the chemical hapten and proteins is influential. The direct peptide reactivity assay (DPRA) has been developed as a screen for the identification of skin-sensitizing chemicals, and here we describe the use of this method to explore whether differences exist between skin and respiratory allergens with respect to their peptide-binding properties. Known skin and respiratory sensitizers were reacted with synthetic peptides containing either lysine (Lys) or cysteine (Cys) for 24 h. The samples were analyzed by HPLC/UV, and the loss of peptide from the reaction mixture was expressed as the percent depletion compared with the control. The potential for preferential reactivity was evaluated by comparing the ratio of Lys to Cys depletion (Lys:Cys ratio). The results demonstrate that the majority of respiratory allergens are reactive in the DPRA, and that in contrast to most skin-sensitizing chemicals, preferentially react with the Lys peptide. These data suggest that skin and respiratory chemical allergens can result in different protein conjugates, which may in turn influence the quality of induced immune responses. Overall, these investigations reveal that the DPRA has considerable potential to be incorporated into tiered testing approaches for the identification and characterization of chemical respiratory allergens. PMID:22713598

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

    OpenAIRE

    Wassenhove, Luk; Lebreton, Baptiste; Letizia, Paolo

    2007-01-01

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

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

    Science.gov (United States)

    Fenzke, Dieter; Hunger, Michael; Pfeifer, Harry

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

  10. Reactive chromophores for sensitive and selective detection of chemical warfare agents and toxic industrial chemicals

    Science.gov (United States)

    Frye-Mason, Greg; Leuschen, Martin; Wald, Lara; Paul, Kateri; Hancock, Lawrence F.

    2005-05-01

    A reactive chromophore developed at MIT exhibits sensitive and selective detection of surrogates for G-class nerve agents. This reporter acts by reacting with the agent to form an intermediate that goes through an internal cyclization reaction. The reaction locks the molecule into a form that provides a strong fluorescent signal. Using a fluorescent sensor platform, Nomadics has demonstrated rapid and sensitive detection of reactive simulants such as diethyl chloro-phosphate (simulant for sarin, soman, and related agents) and diethyl cyanophosphate (simulant for tabun). Since the unreacted chromophore does not fluoresce at the excitation wavelength used for the cyclized reporter, the onset of fluo-rescence can be easily detected. This fluorescence-based detection method provides very high sensitivity and could enable rapid detection at permissible exposure levels. Tests with potential interferents show that the reporter is very selective, with responses from only a few highly toxic, electrophilic chemicals such as phosgene, thionyl chloride, and strong acids such as HF, HCl, and nitric acid. Dimethyl methyl phosphonate (DMMP), a common and inactive simu-lant for other CW detectors, is not reactive enough to generate a signal. The unique selectivity to chemical reactivity means that a highly toxic and hazardous chemical is present when the reporter responds and illustrates that this sensor can provide very low false alarm rates. Current efforts focus on demonstrating the sensitivity and range of agents and toxic industrial chemicals detected with this reporter as well as developing additional fluorescent reporters for a range of chemical reactivity classes. The goal is to produce a hand-held sensor that can sensitively detect a broad range of chemical warfare agent and toxic industrial chemical threats.

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  13. The evolution of the placenta drives a shift in sexual selection in livebearing fish

    NARCIS (Netherlands)

    Pollux, B.J.A.; Meredith, R.W.; Springer, M.S.; Garland, T.; Reznick, D.N.

    2014-01-01

    The evolution of the placenta from a non-placental ancestor causes a shift of maternal investment from pre- to post-fertilization, creating a venue for parent–offspring conflicts during pregnancy1, 2, 3, 4. Theory predicts that the rise of these conflicts should drive a shift from a reliance on pre-

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

    Science.gov (United States)

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

    2015-10-01

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

  15. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-02-01

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

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

    Indian Academy of Sciences (India)

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

    2013-11-01

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

  18. Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals.

    Science.gov (United States)

    Chikina, Maria; Robinson, Joseph D; Clark, Nathan L

    2016-09-01

    Mammal species have made the transition to the marine environment several times, and their lineages represent one of the classical examples of convergent evolution in morphological and physiological traits. Nevertheless, the genetic mechanisms of their phenotypic transition are poorly understood, and investigations into convergence at the molecular level have been inconclusive. While past studies have searched for convergent changes at specific amino acid sites, we propose an alternative strategy to identify those genes that experienced convergent changes in their selective pressures, visible as changes in evolutionary rate specifically in the marine lineages. We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment. Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. These marine-accelerated genes are highly enriched for pathways that control recognized functional adaptations in marine mammals, including muscle physiology, lipid-metabolism, sensory systems, and skin and connective tissue. The accelerations resulted from both adaptive evolution as seen in skin and lung genes, and loss of function as in gustatory and olfactory genes. In regard to sensory systems, this finding provides further evidence that reduced senses of taste and smell are ubiquitous in marine mammals. Our analysis demonstrates the feasibility of identifying genes underlying convergent organism-level characteristics on a genome-wide scale and without prior knowledge of adaptations, and provides a powerful approach for investigating the physiological functions of mammalian genes. PMID:27329977

  19. Control of optical spin Hall shift in phase-discontinuity metasurface by weak value measurement post-selection.

    Science.gov (United States)

    Lee, Y U; Wu, J W

    2015-01-01

    Spin Hall effect of light is a spin-dependent transverse shift of optical beam propagating along a curved trajectory, where the refractive index gradient plays a role of the electric field in spin Hall effect of solid-state systems. In order to observe optical spin Hall shift in a refraction taking place at air-glass interface, an amplification technique was necessary such as quantum weak measurement. In phase-discontinuity metasurface (PMS) a rapid phase-change along metasurface takes place over subwavelength distance, which leads to a large refractive index gradient for refraction beam enabling a direct detection of optical spin Hall shift without amplification. Here, we identify that the relative optical spin Hall shift depends on incidence angle at PMS, and demonstrate a control of optical spin Hall shift by constructing weak value measurement with a variable phase retardance in the post-selection. Capability of optical spin Hall shift control permits a tunable precision metrology applicable to nanoscale photonics such as angular momentum transfer and sensing. PMID:26354387

  20. Maltodextrins from chemically modified starches. Selected physicochemical properties.

    Science.gov (United States)

    Pycia, Karolina; Juszczak, Lesław; Gałkowska, Dorota; Witczak, Mariusz; Jaworska, Grażyna

    2016-08-01

    The aim of this work was to evaluate the effect of chemical modification of starch (cross-linking and/or stabilisation) on selected rheological and functional properties of maltodextrins of dextrose equivalent of 6, 11 and 16. It was found that values of glass transition temperatures were decreasing with dextrose equivalent of maltodextrin. The highest values of glass transition temperature (TG) were determined for maltodextrin of DE 6-obtained from distarch phosphate and acetylated distarch phosphate. Increase in DE value of maltodextrin was also accompanied by decrease and increase in values of intrinsic viscosity and the critical concentration, respectively; however, there was no significant effect of kind of chemical modification of starch on the values of these parameters. Maltodextrin solutions at concentrations of from 10 to 70 % exhibited Newtonian flow behaviour. In the case of 50% solutions of maltodextrins of DE 6 the highest viscosity was produced by maltodextrin from native potato starch, while the lowest one by maltodextrin from acetylated starch. On the other hand, among the maltodextrin of DE 11 this one produced from acetylated starch showed the highest viscosity. All the maltodextrins exhibited surfactant properties in a water-air system, with the strongest effect observed for maltodextrins produced from double chemically modified starches and from acetylated starch. The surface activity was increasing with increasing of the DE value of maltodextrin. Moreover, values of surface tension were decreasing with increasing in maltodextrin concentration in the system. PMID:27112878

  1. Reactive chemically modified piezoelectric crystal detectors: A new class of high-selectivity sensors

    International Nuclear Information System (INIS)

    A great number of works have focused on the study of properties of modified piezoelectric quartz crystal detectors (PQCDs) coated with sorbing substrates and on applying sensors based on them for the analysis of diluted gas mixtures and solutions. This work offers a new class of gravemetric sensors characterized by a reversible chemical reaction that occurs on their surface. Silica films are proposed as a sorbing coating of quartz detectors, and a chemical modification of a surface is suggested for covalent fixation of the necessary compounds. PQCDs were chemically modified with reactive diene derivatives that can also act as dienophiles. Hexachlorocyclopentadiene (HCCPD, resonater I) and cyclopentadiene (CPD, resonator II) were fixed on a PQCD surface in several stages. After treatment with the resonaters, the PQCD in a CPD gas phase exhibited time dependent frequency shifts from 20-100 Hz. The results suggest that there is a reversible chemical reaction on the electrode surface of resonators I and II when they interact with CPD vapors. Therefore, PQCDs modified with reactive dienes were prepared for the first time and may be employed as selective sensors for CPD

  2. Fractional enrichment of proteins using [2-{sup 13}C]-glycerol as the carbon source facilitates measurement of excited state {sup 13}Cα chemical shifts with improved sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Ahlner, Alexandra; Andresen, Cecilia; Khan, Shahid N. [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden); Kay, Lewis E. [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry, One King’s College Circle (Canada); Lundström, Patrik, E-mail: patlu@ifm.liu.se [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden)

    2015-07-15

    A selective isotope labeling scheme based on the utilization of [2-{sup 13}C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state {sup 13}Cα chemical shifts using Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-{sup 13}C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state {sup 13}Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s{sup −1}, despite the small fraction of {sup 13}Cα–{sup 13}Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using {sup 13}Cα spin probes.

  3. Acoustic bubble: Controlled and selective micropropulsion and chemical waveform generator

    Science.gov (United States)

    Ahmed, Daniel

    The physics governing swimming at the microscale---where viscous forces dominate over inertial---is distinctly different than that at the macroscale. Devices capable of finely controlled swimming at the microscale could enable bold ideas such as targeted drug delivery, non-invasive microsurgery, and precise materials assembly. Progress has already been made towards such artificial microswimmers using several means of actuation: chemical reactions and applied magnetic, electric or acoustic fields. However, the prevailing goal of selective actuation of a single microswimmer from within a group, the first step towards collaborative, guided action by a group of swimmers, has so far not been achieved. Here I present a new class of microswimmer that accomplishes for the first time selective actuation (Chapter 1). The swimmer design eschews the commonly-held design paradigm that microswimmers must use non-reciprocal motion to achieve propulsion; instead, the swimmer is propelled by oscillatory motion of an air bubble trapped within the swimmer's polymer body. This oscillatory motion is driven by a low-power biocompatible acoustic field to the ambient liquid, with meaningful swimmer propulsion occurring only at resonance frequencies of the bubble. This acoustically-powered microswimmer performs controllable rapid translational and rotational motion even in highly viscous liquid. By using a group of swimmers each with a different bubble size (and thus different resonance frequencies) selective actuation of a single swimmer from among the group can be readily achieved. Cellular response to chemical microenvironments depends on the spatiotemporal characteristics of the stimulus, which is central to many biological processes including gene expression, cell migration, differentiation, apoptosis, and intercellular signaling. To date, studies have been limited to digital (or step) chemical stimulation with little control over the temporal counterparts. Microfluidic approaches

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

    Science.gov (United States)

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

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated. PMID:27335085

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  7. Improved procedures for the selective chemical fragmentation of rhamnogalacturonans.

    Science.gov (United States)

    Deng, Chenghua; O'Neill, Malcolm A; Hahn, Michael G; York, William S

    2009-09-28

    The structural characterization of branched rhamnogalacturonans (RGs) requires the availability of methods that selectively cleave the Rhap-(1-->4)-alpha-GalAp linkage and thereby generate oligosaccharide fragments that are suitable for mass spectrometric and NMR spectroscopic analyses. Enzymic cleavage of this linkage is often ineffective, especially in highly branched RGs. Therefore, we have developed an improved chemical fragmentation method based on beta-elimination of esterified 4-linked GalpA residues. At least 85% of the carboxyl groups of the GalA residues in Arabidopsis thaliana seed mucilage RG is esterified using methyl iodide or 3-iodopropanol in Me(2)SO containing 8% water and 1% tetrabutylammonium fluoride. However, beta-elimination fragmentation at pH 7.3 and 120 degrees C is far more extensive with hydroxypropyl-esterified RG than with methyl-esterified RG. The non-reducing 4-deoxy-beta-l-threo-hex-4-enepyranosyluronic acid residue formed by the beta-elimination reaction is completely removed by treatment with aqueous N-bromosuccinimide, thereby simplifying the structural characterization of the chemically generated oligoglycosyl fragments. This newly developed procedure was used to selectively fragment the branched RG from peppergrass seed mucilage. The products were characterized using MALDI-TOF mass spectrometry, glycosyl residue composition analysis, and 1 and 2D NMR spectroscopy. Our data show that the most abundant low-molecular weight fragments contained a backbone rhamnose residue substituted at O-4 with a single sidechain, and suggest that peppergrass seed mucilage RG is composed mainly of the repeating unit 4-O-methyl-alpha-d-GlcpA-(1-->4)-beta-d-Galp-(1-->4)-[-->4)-alpha-d-GalpA-(1-->2)-]-alpha-l-Rhap-(1-->. PMID:19162261

  8. Behavior of Selected Endocrine Disrupting Chemicals in Sewage Treatment Plant

    Science.gov (United States)

    Wang, Xinze; Lu, Jiaming; Ollivier, Natacha; Saturnino, Anais; Gomez, Elena; Casellas, Claude; Picot, Bernadette

    2010-11-01

    The behavior of endocrine disrupting chemicals in sewage treatment plant affects their final fate in water environment. We selected six endocrine disrupting chemicals: 4 alkylphenols (4-tert-octylphenol, octylphenol, 4-nonylphenol, bisphenol A) and 2 steroids (17α-ethinylestradiol and estriol) as targets, their removal and transformation in wastewater treatment plant were studied. Five mixed liquors were sampled respectively from different stages of Minhang wastewater treatment plant in Shanghai. EDCs concentration were analyzed with GC-MS. The main removal pathways of EDCs include initial adsorption by suspended solids and following biodegradation in biological sludge. The removal efficiency of six targets was more than 86%. The concentration of OP and 4-n-NP in water significantly increased in anoxic stage, the reason may be the releases of EDCs from sludge to water on the condition of low DO. And it was also found that the EDCs could be released to water phase in the secondary clarifier, which may cause potential risk of EDCs entering the environment with discharge.

  9. Development of microforming process combined with selective chemical vapor deposition

    Directory of Open Access Journals (Sweden)

    Koshimizu Kazushi

    2015-01-01

    Full Text Available Microforming has been received much attention in the recent decades due to the wide use of microparts in electronics and medical purpose. For the further functionalization of these micro devices, high functional surface with noble metals and nanomaterials are strongly required in bio- and medical fields, such as bio-sensors. To realize the efficient manufacturing process, which can deform the submillimeter scale bulk structure and can construct the micro to nanometer scale structures in one process, the present study proposes a combined process of microforming for metal foils with a selective chemical vapor deposition (SCVD on the active surface of work materials. To clarify the availability of this proposed process, the feasibility of SCVD of functional materials to active surface of titanium (Ti was investigated. CVD of iron (Fe and carbon nanotubes (CNTs which construct CNTs on the patterned surface of active Ti and non-active oxidation layer were conducted. Ti thin films on silicon substrate and Fe were used as work materials and functional materials, respectively. CNTs were grown on only Ti surface. Consequently, the selectivity of the active surface of Ti to the synthesis of Fe particles in CVD process was confirmed.

  10. Parallel shifts in ecology and natural selection in an island lizard

    OpenAIRE

    Smith Thomas B; Buermann Wolfgang; Calsbeek Ryan

    2009-01-01

    Abstract Background Natural selection is a potent evolutionary force that shapes phenotypic variation to match ecological conditions. However, we know little about the year-to-year consistency of selection, or how inter-annual variation in ecology shapes adaptive landscapes and ultimately adaptive radiations. Here we combine remote sensing data, field experiments, and a four-year study of natural selection to show that changes in vegetation structure associated with a severe drought altered b...

  11. Is it time for a paradigm shift in understanding embryo selection?

    OpenAIRE

    Gleicher, Norbert; Kushnir, Vitaly A.; Barad, David H

    2015-01-01

    Background Embryo selection has been an integral feature of in vitro fertilization (IVF) almost since its inception. Since the advent of extended blastocyst stage embryo culture, and especially with increasing popularity of elective single embryo transfer (eSET), the concept of embryo selection has increasingly become a mainstay of routine IVF. Discussion We here, however, argue that embryo selection via blastocyst stage embryo transfer (BSET), as currently practiced, at best improves IVF out...

  12. The Role of Sexual Selection in the Evolution of Chemical Signals in Insects

    OpenAIRE

    Sandra Steiger; Johannes Stökl

    2014-01-01

    Chemical communication is the most ancient and widespread form of communication. Yet we are only beginning to grasp the complexity of chemical signals and the role they play in sexual selection. Focusing on insects, we review here the recent progress in the field of olfactory-based sexual selection. We will show that there is mounting empirical evidence that sexual selection affects the evolution of chemical traits, but form and strength of selection differ between species. Studies indicate t...

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

    International Nuclear Information System (INIS)

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

  14. Covariance of phenotypically plastic traits induces an adaptive shift in host selection behaviour

    OpenAIRE

    Henry, Lee M; Roitberg, Bernard D.; Gillespie, David R

    2006-01-01

    Flexibility in adult body size allows generalist parasitoids to use many host species at a cost of producing a range of adult sizes. Consequently, host selection behaviour must also maintain a level of flexibility as adult size is related to capture efficiency. In the present study, we investigated covariance of two plastic traits—size at pupation and host size selection behaviour—using Aphidius ervi reared on either Acyrthosiphon pisum or Aulacorthum solani, generating females of disparate s...

  15. Recent host-shifts in ranaviruses: signatures of positive selection in the viral genome

    OpenAIRE

    Abrams, A. Jeanine; Cannatella, David C; Hillis, David M.; Sawyer, Sara L

    2013-01-01

    Ranaviruses have been implicated in recent declines in global amphibian populations. Compared with the family Iridoviridae, to which the genus Ranavirus belongs, ranaviruses have a wide host range in that species/strains are known to infect fish, amphibians and reptiles, presumably due to recent host-switching events. We used eight sequenced ranavirus genomes and two selection-detection methods (site based and branch based) to identify genes that exhibited signatures of positive selection, po...

  16. 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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-01-01

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

  2. Selected area chemical vapor deposition of thin films for conductometric microelectronic chemical sensors

    Science.gov (United States)

    Majoo, Sanjeev

    Recent advances in microelectronics and silicon processing have been exploited to fabricate miniaturized chemical sensors. Although the capability of chemical sensing technology has grown steadily, it has been outpaced by the increasing demands for more reliable, inexpensive, and selective sensors. The diversity of applications requires the deployment of different sensing materials that have rich interfacial chemistry. However, several promising sensor materials are often incompatible with silicon micromachining and their deposition requires complicated masking steps. The new approach described here is to first micromachine a generic, instrumented, conductometric, microelectronic sensor platform that is fully functional except for the front-end sensing element. This generic platform contains a thin dielectric membrane, an integrated boron-doped silicon heater, and conductance electrodes. The membrane has low thermal mass and excellent thermal isolation. A proprietary selected-area chemical vapor deposition (SACVD) process in a cold-wall reactor at low pressures was then used to achieve maskless, self-lithographic deposition of thin films. The temperature-programmable integrated microheater initiates localized thermal decomposition/reaction of suitable CVD precursors confined to a small heated area (500 mum in diameter), and this creates the active sensing element. Platinum and titania (TiOsb2) films were deposited from pyrolysis of organometallic precursors, tetrakistrifluorophosphine platinum Pt(PFsb3)sb4 and titanium tetraisopropoxide Ti(OCH(CHsb3)sb2rbrack sb4, respectively. Deposition of gold metal films from chlorotriethylphosphine gold (Csb2Hsb5)sb3PAuCl precursor was also attempted but without success. The conductance electrodes permit in situ monitoring of film growth. The as-deposited films were characterized in situ by conductance measurements and optical microscopy and ex situ by electron microscopy and spectroscopy methods. Devices equipped with

  3. Analysis of the Preference Shift of Customer Brand Selection and Its Matrix Structure

    OpenAIRE

    竹安, 数博; 樋口, 友紀; Takeyasu, Kazuhiro; HIGUCHI, Yuki

    2008-01-01

    It is often observed that consumers select the upper class brand when they buy the next time. Suppose that the former buying data and the current buying data are gathered. Also suppose that the upper brand is located upper in the variable array. Then the transition matrix becomes an upper triangle matrix under the supposition that the former buying variables are set input and the current buying variables are set output. If the top brand were selected from the lower brand in jumping way, corre...

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

    Science.gov (United States)

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

    2014-04-28

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

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

    Science.gov (United States)

    Miura, Yoshinori

    2016-05-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2016-08-31

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

  9. Chemical composition of buckwheat plant parts and selected buckwheat products

    Directory of Open Access Journals (Sweden)

    Petra Vojtíšková

    2014-11-01

    Full Text Available Chemical composition plant parts (roots, stalks, leaves, blossoms of common buckwheat (Fagopyrum esculentum Moench and selected products made from its seeds (peels, whole seed, wholemeal flour, broken seeds, crunchy products Natural and Cocoa, flour, and pasta was determined. Samples were dried and ground to a fine powder. All analyses were performed according to the Commission Regulation no. 152/2009, while rutin concentration was determined by the modified HPLC method. The lowest content of moisture was found in roots (4.3% and in peels (almost 8% and the highest moisture (nearly 11% was discovered in seeds. The lowest amount of crude protein (3.5% was found in peels, the highest crude protein amount (>13% in both flours and leaves (23%. The starch content (>50% in dry matter differs from one sample to another. Only in peels the content of starch was about 3.5%. From all examined samples, the lowest content of fat was found in crunchy products Cocoa, 1.7%. The lowest amount of histidine was determined in all studied samples, except peels, the highest content of glutamic acid was determined in almost all samples, except peels. Whole-meal flour is very rich source of Ca and Fe. The content of these elements was 1172 mg.kg-1 and 45.9 mg.kg-1, respectively. On the other hand, the highest content of Pb (>1 mg.kg-1 was found in broken seeds. The greatest concentration of rutin was determined in blossoms and leaves (83.6 and 69.9 mg.g-1, respectively. On the other hand, the lowest concentrations of rutin were found in buckwheat products (generally less then 1 mg.g-1, i.e. in wholemeal flour, 702 μg.kg-1, the lowest almost 10 μg.kg-1 in pasta.

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  13. Subtype-selective nicotinic acetylcholine receptor agonists can improve cognitive flexibility in an attentional set shifting task.

    Science.gov (United States)

    Wood, Christopher; Kohli, Shivali; Malcolm, Emma; Allison, Claire; Shoaib, Mohammed

    2016-06-01

    Nicotinic acetylcholine receptors (nAChRs) are considered to be viable targets to enhance cognition in patients diagnosed with schizophrenia. Activation of nAChRs with selective nicotinic receptor agonists may provide effective means to pharmacologically treat cognitive deficits observed in schizophrenia. Cognitive flexibility is one aspect of cognition, which can be assessed in a rodent model of the attentional set-shifting task (ASST). The aim of the present study was two-fold, firstly, to evaluate the efficacy of a series of subtype selective nAChR agonists, such as those that target α7 and α4β2 nAChR subtypes in non-compromised rodents. Secondly, nicotine as a prototypic agonist was evaluated for its effects to restore attentional deficits produced by sub-chronic ketamine exposure in the ASST. Male hooded Lister rats underwent habituation, consisting of a simple odour and medium discrimination with subsequent assessment 24 h later. In experimentally naïve rats, α7 subtype selective agonists, compound-A and SSR180711 along with PNU-120596, an α7 positive allosteric modulator (PAM), were compared against the β2* selective agonist, 5IA-85380. All compounds except for PNU-120596 were observed to significantly improve extra-dimensional (ED) shift performance, nicotine, 5IA-85380 and SSR180711 further enhanced the final reversal (REV3) stage of the task. In another experiment, sub-chronic ketamine treatment produced robust deficits during the ED and the REV3 stages of the discriminations; rodents required significantly more trials to reach criterion during these discriminations. These deficits were attenuated in rodents treated acutely with nicotine (0.1 mg/kg SC) 10 min prior to the ED shift. These results highlight the potential utility of targeting nAChRs to enhance cognitive flexibility, particularly the α7 and β2* receptor subtypes. The improvement with nicotine was much greater in rodents that were impaired following the sub-chronic ketamine

  14. Selection for adaptation to dietary shifts: towards sustainable breeding of carnivorous fish.

    Directory of Open Access Journals (Sweden)

    Richard Le Boucher

    Full Text Available Genetic adaptation to dietary environments is a key process in the evolution of natural populations and is of great interest in animal breeding. In fish farming, the use of fish meal and fish oil has been widely challenged, leading to the rapidly increasing use of plant-based products in feed. However, high substitution rates impair fish health and growth in carnivorous species. We demonstrated that survival rate, mean body weight and biomass can be improved in rainbow trout (Oncorhynchus mykiss after a single generation of selection for the ability to adapt to a totally plant-based diet (15.1%, 35.3% and 54.4%, respectively. Individual variability in the ability to adapt to major diet changes can be effectively used to promote fish welfare and a more sustainable aquaculture.

  15. National toxicology program chemical nomination and selection process

    Energy Technology Data Exchange (ETDEWEB)

    Selkirk, J.K. [National Institute of Environmental Health Sciences, Research Triangle Park, NC (United States)

    1990-12-31

    The National Toxicology Program (NTP) was organized to support national public health programs by initiating research designed to understand the physiological, metabolic, and genetic basis for chemical toxicity. The primary mandated responsibilities of NTP were in vivo and vitro toxicity testing of potentially hazardous chemicals; broadening the spectrum of toxicological information on known hazardous chemicals; validating current toxicological assay systems as well as developing new and innovative toxicity testing technology; and rapidly communicating test results to government agencies with regulatory responsibilities and to the medical and scientific communities. 2 figs.

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

    Science.gov (United States)

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

    2009-05-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

  18. Selective observation of Goos-H\\"anchen and Imbert-Federov shifts in partial reflection via optimized weak measurements in linear and elliptical polarization basis

    CERN Document Server

    Goswami, S; Pal, M; Nandi, A; Panigrahi, P K; Ghosh, N

    2015-01-01

    The spatial and the angular variants of the Goos-H\\"anchen (GH) and the Imbert-Federov (IF) beam shifts contribute in a complex interrelated way to the resultant beam shift in partial reflection at planar dielectric interfaces. Here, we show that the angular GH and the two variants of the IF effects can be decoupled, amplified and separately observed by weak value amplification and subsequent conversion of spatial$\\leftrightarrow$angular nature of the beam shifts using appropriate pre and post selection of polarization states. We experimentally demonstrate such decoupling and illustrate various other intriguing manifestations of weak measurements by employing optimized pre and post selections (based on the eigen polarization states of the shifts) elliptical and / or linear polarization basis. The demonstrated ability to amplify, controllably decouple or combine the beam shifts via weak measurements may prove to be valuable for understanding the different physical contributions of the effects and for their app...

  19. Testing for natural selection in human exonic splicing regulators associated with evolutionary rate shifts.

    Science.gov (United States)

    Ramalho, Rodrigo F; Gelfman, Sahar; de Souza, Jorge E; Ast, Gil; de Souza, Sandro J; Meyer, Diogo

    2013-04-01

    Despite evidence that at the interspecific scale, exonic splicing silencers (ESSs) are under negative selection in constitutive exons, little is known about the effects of slightly deleterious polymorphisms on these splicing regulators. Through the application of a modified version of the McDonald-Kreitman test, we compared the normalized proportions of human polymorphisms and human/rhesus substitutions affecting exonic splicing regulators (ESRs) on sequences of constitutive and alternative exons. Our results show a depletion of substitutions and an enrichment of SNPs associated with ESS gain in constitutive exons. Moreover, we show that this evolutionary pattern is also present in a set of ESRs previously involved in the transition from constitutive to skipped exons in the mammalian lineage. The similarity between these two sets of ESRs suggests that the transition from constitutive to skipped exons in mammals is more frequently associated with the inhibition than with the promotion of splicing signals. This is in accordance with the hypothesis of a constitutive origin of exon skipping and corroborates previous findings about the antagonistic role of certain exonic splicing enhancers. PMID:23529588

  20. Ozone treatment of conditioned wastewater selects antibiotic resistance genes, opportunistic bacteria, and induce strong population shifts.

    Science.gov (United States)

    Alexander, Johannes; Knopp, Gregor; Dötsch, Andreas; Wieland, Arne; Schwartz, Thomas

    2016-07-15

    An ozone treatment system was investigated to analyze its impact on clinically relevant antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). A concentration of 0.9±0.1g ozone per 1g DOC was used to treat conventional clarified wastewater. PCR, qPCR analyses, Illumina 16S Amplicon Sequencing, and PCR-DGGE revealed diverse patterns of resistances and susceptibilities of opportunistic bacteria and accumulations of some ARGs after ozone treatment. Molecular marker genes for enterococci indicated a high susceptibility to ozone. Although they were reduced by almost 99%, they were still present in the bacterial population after ozone treatment. In contrast to this, Pseudomonas aeruginosa displayed only minor changes in abundance after ozone treatment. This indicated different mechanisms of microorganisms to cope with the bactericidal effects of ozone. The investigated ARGs demonstrated an even more diverse pattern. After ozone treatment, the erythromycin resistance gene (ermB) was reduced by 2 orders of magnitude, but simultaneously, the abundance of two other clinically relevant ARGs increased within the surviving wastewater population (vanA, blaVIM). PCR-DGGE analysis and 16S-Amplicon-Sequencing confirmed a selection-like process in combination with a substantial diversity loss within the vital wastewater population after ozone treatment. Especially the PCR-DGGE results demonstrated the survival of GC-rich bacteria after ozone treatment. PMID:27058129

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

    International Nuclear Information System (INIS)

    The effects of heteroatoms Eh(Eh=O, S, Se, Te) on 13C chemical shifts in eleven isological series of R1-Eh-R2 unsaturated compounds are compared. A linear relation between 13C nuclei screening and tEh electronegativity is observed. An assumption is suggested that both likeness of the effects of 6A and 7A group elements on 13C chemical shifts of R1 and R2 substituents and their difference for elements of the 4A group are caused by unbonded interactions of the substituents with unshared electron pairs of heteroatoms

  2. General principles for selection of chemical process for its conducting under nuclear reactor irradiation

    International Nuclear Information System (INIS)

    Full text : Selection of temperature regime the initial chemicals and its radiation chemical conversation products have to be the stable at the temperatures 300-500 degrees Celsium. The presence of high intensity slow neutrons restrict the number of chemical compounds, that must be irradiated due to its radioactive capture and formation the radioactive isotopes

  3. A Schematic Method for Sustainable Material Selection of Toxic Chemicals in Design and Manufacturing

    OpenAIRE

    Yuan, Chris Yingchun; David Dornfeld

    2010-01-01

    Toxic chemicals used in product design and manufacturing are grave concerns due to their toxic impact on human health. Implementing sustainable material selection strategies on toxic chemicals can substantially improve the sustainability of products in both design and manufacturing processes. In this paper, a schematic method is presented for characterizing and benchmarking the human health impact of toxic chemicals, as a visual aid to facilitate decision-making in the material selection proc...

  4. Shifts in controls on the temporal coherence of throughfall chemical flux in Acadia National Park, Maine, USA

    Science.gov (United States)

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

    2013-01-01

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

  5. Highly Selective Hg (II Ion Detection Based on Linear Blue-Shift of the Maximum Absorption Wavelength of Silver Nanoparticles

    Directory of Open Access Journals (Sweden)

    Li Ping Wu

    2012-01-01

    Full Text Available A new method of detecting Hg (II ion with silver nanoparticles (AgNPs is developed in this contribution. When Hg (II ions were added into AgNPs solution, the solution displayed rapid color change and blue shift of the maximum absorption wavelength (Δλ, which was in proportion to the Hg (II ion concentration over the range of 2.0 × 10−7–6.0 × 10−6 mol/L, with detection limit (3σ of 6.6 × 10−9 mol/L. Under the same experimental conditions, other metal ions did not interfere. Thus, we propose a rapid, simple and highly selective method for detecting Hg (II ion.

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

    OpenAIRE

    Mizyuk, Volodymyr; Shibanov, Volodymyr

    2011-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Ivanir, Hadar; Goldbourt, Amir

    2014-07-01

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

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

    Science.gov (United States)

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

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

  12. Mechanisms of selectivity loss during tungsten CVD (chemical vapor deposition)

    Energy Technology Data Exchange (ETDEWEB)

    Creighton, J.R.

    1990-01-01

    The tungsten subfluoride mechanism as well as other proposed mechanisms of selectivity loss are reviewed. To further demonstrate the viability of the tungsten subfluoride mechanism, we have extended the measurement of the tungsten subfluoride production rate down to 450{degree}C. We also report results from some preliminary experiments designed to identify the selectivity loss mechanism when elemental silicon is available for reaction. Comments regarding the origins of the insulator effect and selectivity loss for silane reduction are offered. 23 refs., 2 figs.

  13. Sustainable Material Selection of Toxic Chemicals in Design and Manufacturing From Human Health Impact Perspective

    OpenAIRE

    Yuan, Chris; Dornfeld, David

    2009-01-01

    Toxic chemicals used in product design and manufacturing are grave concerns due to their significant impact on human health. Sustainable material selections are needed by industry to reduce the overall impact of toxic chemicals in both design and manufacturing. In this paper, we integrate the human health impact assessment into standard material selection process for developing a sustainable material selection metric for decision support in design and manufacturing. A schematic method is pres...

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

    Science.gov (United States)

    Sieh, Daniel; Kubiak, Clifford P

    2016-07-18

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

  15. Physico-Chemical Studies of the Pvc K+ - Selective Membrane

    Directory of Open Access Journals (Sweden)

    Ana COROIAN

    2002-12-01

    Full Text Available A plasticized ion-selective membrane based on PVC matrix which tricrezylphosphate (TCP and containing K+ - ionophores (dibenzo-18-crown-6 and decyl-18-crown-6 was used to obtain a potentiometric potassium sensor. The potassium selective membranes were characterized in terms of their electrochemical and physical properties, surface morphology and structural parameters. The a.c. impedance, UV/VIS analysis of the membranes was also studied.

  16. Selection and Evaluation of Chemical Indicators for Waste Stream Identification

    Science.gov (United States)

    DeVita, W. M.; Hall, J.

    2015-12-01

    Human and animal wastes pose a threat to the quality of groundwater, surface water and drinking water. This is especially of concern for private and public water supplies in agricultural areas of Wisconsin where land spreading of livestock waste occurs on thin soils overlaying fractured bedrock. Current microbial source tracking (MST) methods for source identification requires the use of polymerase chain reaction (PCR) techniques. Due to cost, these tests are often not an option for homeowners, municipalities or state agencies with limited resources. The Water and Environmental Analysis Laboratory sought to develop chemical methods to provide lower cost processes to determine sources of fecal waste using fecal sterols, pharmaceuticals (human and veterinary) and human care/use products in ground and surface waters using solid phase extraction combined with triple quadrupole mass spectrometry. The two separate techniques allow for the detection of fecal sterol and other chemical markers in the sub part per billion-range. Fecal sterol ratios from published sources were used to evaluate drinking water samples and wastewater from onsite waste treatment systems and municipal wastewater treatment plants. Pharmaceuticals and personal care products indicative of human waste included: acetaminophen, caffeine, carbamazepine, cotinine, paraxanthine, sulfamethoxazole, and the artificial sweeteners; acesulfame, saccharin, and sucralose. The bovine antibiotic sulfamethazine was also targeted. Well water samples with suspected fecal contamination were analyzed for fecal sterols and PPCPs. Results were compared to traditional MST results from the Wisconsin State Laboratory of Hygiene. Chemical indicators were found in 6 of 11 drinking water samples, and 5 of 11 were in support of MST results. Lack of detection of chemical indicators in samples contaminated with fecal waste supports the need for confirmatory methods and advancement of chemical indicator detection technologies.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-10-15

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

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

    Czech Academy of Sciences Publication Activity Database

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

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

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

    Science.gov (United States)

    Truflandier, Lionel A; Autschbach, Jochen

    2010-03-17

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

  20. Selective Chemical-Lithographic Reaction Techniques Using Radiation Technology for Biological Application

    International Nuclear Information System (INIS)

    This report, titled 'selective Chemical-Lithographic Reaction Techniques Using Radiation Technology for Biological Application' contains a research summary, 1) development of selective reaction technology using irradiation of electron beams, 2) preparation of functional surfaces using selective radiation technology on carbon-based nanomaterials, and 3) development of bio-applicable biochips using combinatorial surface modification

  1. CO2 SELECTIVE CERAMIC MEMBRANE FOR WATER-GAS-SHIFT REACTION WITH CONCOMITANT RECOVERY OF CO2

    Energy Technology Data Exchange (ETDEWEB)

    Paul K.T. Liu

    2005-07-15

    A high temperature membrane reactor (MR) has been developed to enhance the water-gas-shift (WGS) reaction efficiency with concomitant CO{sub 2} removal for sequestration. This improved WGS-MR with CO{sub 2} recovery capability is ideally suitable for integration into the Integrated Gasification Combined-Cycle (IGCC) power generation system. Two different CO{sub 2}-affinity materials were selected in this study. The Mg-Al-CO{sub 3}-layered double hydroxide (LDH) was investigated as an adsorbent or a membrane for CO{sub 2} separation. The adsorption isotherm and intraparticle diffusivity for the LDH-based adsorbent were experimentally determined, and suitable for low temperature shift (LTS) of WGS. The LDH-based membranes were synthesized using our commercial ceramic membranes as substrate. These experimental membranes were characterized comprehensively in terms of their morphology, and CO{sub 2} permeance and selectivity to demonstrate the technical feasibility. In parallel, an alternative material-base membrane, carbonaceous membrane developed by us, was characterized, which also demonstrated enhanced CO{sub 2} selectivity at the LTS-WGS condition. With optimization on membrane defect reduction, these two types of membrane could be used commercially as CO{sub 2}-affinity membranes for the proposed application. Based upon the unique CO{sub 2} affinity of the LDHs at the LTS/WGS environment, we developed an innovative membrane reactor, Hybrid Adsorption and Membrane Reactor (HAMR), to achieve {approx}100% CO conversion, produce a high purity hydrogen product and deliver a concentrated CO{sub 2} stream for disposal. A mathematical model was developed to simulate this unique one -step process. Finally a benchtop reactor was employed to generate experimental data, which were consistent with the prediction from the HAMR mathematical model. In summary, the project objective, enhancing WGS efficiency for hydrogen production with concomitant CO{sub 2} removal for

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-08-15

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

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

    International Nuclear Information System (INIS)

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

  4. 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.

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

    Indian Academy of Sciences (India)

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

    2014-05-01

    Uranium L3 X-ray absorption edge was measured in various compounds containing uranium in U4+, U5+ and U6+ oxidation states. The measurements have been carried out at the Energy Dispersive EXAFS beamline (BL-08) at INDUS-2 synchrotron radiation source at RRCAT, Indore. Energy shifts of ∼ 2–3 eV were observed for U L3 edge in the U-compounds compared to their value in elemental U. The different chemical shifts observed for the compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on U cation in the above compounds.

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

    International Nuclear Information System (INIS)

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

  7. Chemical tools selectively target components of the PKA system

    Directory of Open Access Journals (Sweden)

    Drewianka Stephan

    2009-02-01

    Full Text Available Abstract Background In the eukaryotic cell the cAMP-dependent protein kinase (PKA is a key enzyme in signal transduction and represents the main target of the second messenger cAMP. Here we describe the design, synthesis and characterisation of specifically tailored cAMP analogs which can be utilised as a tool for affinity enrichment and purification as well as for proteomics based analyses of cAMP binding proteins. Results Two sets of chemical binders were developed based on the phosphorothioate derivatives of cAMP, Sp-cAMPS and Rp-cAMPS acting as cAMP-agonists and -antagonists, respectively. These compounds were tested via direct surface plasmon resonance (SPR analyses for their binding properties to PKA R-subunits and holoenzyme. Furthermore, these analogs were used in an affinity purification approach to analyse their binding and elution properties for the enrichment and improvement of cAMP binding proteins exemplified by the PKA R-subunits. As determined by SPR, all tested Sp-analogs provide valuable tools for affinity chromatography. However, Sp-8-AEA-cAMPS displayed (i superior enrichment properties while maintaining low unspecific binding to other proteins in crude cell lysates, (ii allowing mild elution conditions and (iii providing the capability to efficiently purify all four isoforms of active PKA R-subunit in milligram quantities within 8 h. In a chemical proteomics approach both sets of binders, Rp- and Sp-cAMPS derivatives, can be employed. Whereas Sp-8-AEA-cAMPS preferentially binds free R-subunit, Rp-AHDAA-cAMPS, displaying antagonist properties, not only binds to the free PKA R-subunits but also to the intact PKA holoenzyme both from recombinant and endogenous sources. Conclusion In summary, all tested cAMP analogs were useful for their respective application as an affinity reagent which can enhance purification of cAMP binding proteins. Sp-8-AEA-cAMPS was considered the most efficient analog since Sp-8-AHA-cAMPS and Sp-2-AHA

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

    International Nuclear Information System (INIS)

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

  9. Selective vapor detection of an integrated chemical sensor array

    Science.gov (United States)

    Jung, Youngmo; Kim, Young Jun; Choi, Jaebin; Lim, Chaehyun; Shin, Beom Ju; Moon, Hi Gyu; Lee, Taikjin; Kim, Jae Hun; Seo, Minah; Kang, Chong Yun; Jun, Seong Chan; Lee, Seok; Kim, Chulki

    2015-07-01

    Graphene is a promising material for vapor sensor applications because of its potential to be functionalized for specific chemical gases. In this work, we present a graphene gas sensor that uses single-stranded DNA (ssDNA) molecules as its sensing agent. We investigate the characteristics of graphene field effect transistors (FETs) coated with different ssDNAs. The sensitivity and recovery rate for a specific gas are modified according to the differences in the DNA molecules' Guanine (G) and Cytosine (C) content. ssDNA-functionalized devices show a higher recovery rate compared to bare graphene devices. Pattern analysis of a 2-by-2 sensor array composed of graphene devices functionalized with different-sequence ssDNA enables identification of NH3, NO2, CO, SO2 using Principle Component Analysis (PCA).

  10. Effect of prolonged chemical challenges on selected properties of silorane

    DEFF Research Database (Denmark)

    de Jesus, Vivian CBR; Martinelli, Natan Luiz; Pascotto, Renata Corrêa;

    Objectives: The purpose of this study was to investigate the effect of prolonged chemical challenges on water sorption, solubility, and roughness of a silorane-based material when compared to methacrylate-based composites. Methods: Initial roughness and mass were registered for specimens (n=24...... phosphoric acid, 75% ethanol or distilled water for 7, 14, 21, and 180 days, when new measurements were performed. Subsequently, specimens were dehydrated until a constant mass was obtained. Water sorption and solubility were calculated after 180 days of immersion in the different solutions. Data were...... differences in water sorption and solubility were detected amongst the investigated composites (p<0.001). The silorane-based composite demonstrated low water sorption (with similar values to Filtek Z250 and Filtek Z350XT) and low solubility (with similar values to Filtek Z250) after prolonged immersion in the...

  11. Dynamic model for selective metabolic activation in chemical carcinogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Selkirk, J.K.; MacLeod, M.C.

    1980-01-01

    Theoretical calculations predict the relative ease of formation of carbonium ions from 7,8-dihydro-7,8-dihydroxybenzo(a)pyrene-9,10-oxide or from either of the 2 symmetrical bay regions of B(e)P, and suggest their attraction to cellular nucleophiles. When both isomers were metabolized by hamster embryo fibroblasts (HEF) and the products analyzed, the results showed that the probable reason for benzo(e)pyrene's lack of carcinogenicity was its metabolic preference to attack the molecule away from the bay-region area. Particularly striking was the absence of any evidence for the formation of a significant amount of B(e)P-9,10-dihydrodiol. This suggests a metabolic basis for the relative lack of carcinogenic and mutagenic activity of B(e)P. The reason for this is not clear but may be due to physical or chemical factors such as membrane solubility or stereochemical requirements of the active site of the enzyme. The bay-region theory of PAH carcinogenesis predicts that carbonium ion formation from 9,10-dihydro-9,10-dihydroxybenzo(e)pyrene-11, 12-oxide, if formed, would be energetically favorable. Thus, the inability of HEF and microcomes to form B(e)P-9,10-dihydrodiol, the precursor of its potentially highly reactive diol-epoxide, would explain the relative inertness of B(e)P in several biological systems. As the subtle biochemical interactions of the various carcinogen intermediates become clarified, it becomes apparent that susceptibility and resistance to malignant transformation are based on a complex set of both chemical and physical parameters. It is becoming clear that metabolism kinetics, membrane interaction, and the role of nuclear metabolism help dictate the passage of the carcinogen and its reactive intermediates into and through the metabolic machinery of the cell. (ERB)

  12. Chemical constituents of selected Sudanese medicinal and aromatic plants

    International Nuclear Information System (INIS)

    Sudanese medicinal and aromatic plants (Alternanthra repens, Ambrosia maritima, Citrus paradisi, Croton zambesicus, Lepidium sativum, Morettia phillaena, Nauclea latifolia, Plectranthus barbatus, Pluchea dioscorides, and Sphaeranthus suaveolens) were analyzed for their chemical composition, mineral contents and secondary constituents. The concentration of manganese, copper, iron, nickel, lead, zinc and potassium in plant samples was performed using x-ray fluorescence spectrometry. The trace elements found in the smallest amount of the investigated plant species are lead, nickel and copper, while high concentration was detected for potassium, iron and manganese. Mn was accumulated with high level in Alternanthra repens species. Potassium was abundant in S. suaveolens and Ambrosia maritima. The values of concentration obtained for all studied elements were compared with published values of reference material, trace elements in Hay (powder) by International Atomic Energy Agency. Phyto chemical analysis of investigated plants was performed for constituents: Flavonoids, saponins, tannins, alkaloids, amino acids and sugars. The methanolic extracts of P.barbatus, C.paradisi, A.repens, N.latifolia, L. sativum and C. zambesicus are found to contain alkaloids. Results of TLC analysis were shown as Rf values for saponins, bitter principles, essential oils, flavonoids and alkaloids. Quantification of flavonoids and tannins showed that flavonoid content was highest in case of Alternanthera repens and Sphaeranthus suavertens, whereas the highest tannin content was in case of Nauclea latifolia and Sphaearanthus suavertens. The results suggest that the user of traditional Sudanese crude drugs should be warned of potential danger of heavy metal poisoning because their concentrations seem to be higher than maximum values allowed by health agencies in several countries. This study has provided some biochemical basis for the ethno medical use of extracts from different candidate plant

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

    Science.gov (United States)

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

    2015-11-01

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

  14. Selecting Sagittarius: Identification and Chemical Characterization of the Sagittarius Stream

    CERN Document Server

    Hyde, E A; Zucker, D B; Ibata, R; Siebert, A; Lewis, G F; Penarrubia, J; Irwin, M; Gilmore, G; Lane, R R; Koch, A; Conn, A R; Diakogiannis, F I; Martell, S

    2015-01-01

    Wrapping around the Milky Way, the Sagittarius stream is the dominant substructure in the halo. Our statistical selection method has allowed us to identify 106 highly likely members of the Sagittarius stream. Spectroscopic analysis of metallicity and kinematics of all members provides us with a new mapping of the Sagittarius stream. We find correspondence between the velocity distribution of stream stars and those computed for a triaxial model of the Milky Way dark matter halo. The Sagittarius trailing arm exhibits a metallicity gradient, ranging from $-0.59$ dex to $-0.97$ dex over 142$^{\\circ}$. This is consistent with the scenario of tidal disruption from a progenitor dwarf galaxy that possessed an internal metallicity gradient. We note high metallicity dispersion in the leading arm, causing a lack of detectable gradient and possibly indicating orbital phase mixing. We additionally report on a potential detection of the Sextans dwarf spheroidal in our data.

  15. Antimicrobial, antioxidant activities and chemical composition of selected Thai spices

    Directory of Open Access Journals (Sweden)

    Juraithip Wungsintaweekul

    2010-12-01

    Full Text Available Nine volatile oils and six methanol extracts from Ocimum americanum, O. basilicum, O. sanctum, Citrus hystrix,Alpinia galanga, Curcuma zedoaria, Kaempferia parviflora and Zingiber cassumunar were assessed for antimicrobial andantioxidant activities. The volatile oils and extracts were investigated against eight bacteria and three fungi. The resultsillustrated that O. americanum volatile oil exhibited broad spectrum activity against tested bacteria with the MICs ranging1.4-3.6 mg/ml and Candida spp. with the MICs ranging from 0.5-0.6 mg/ml. The O. sanctum volatile oil showed a considerableactivity against only Candida spp. with the MICs ranging from 0.8-1.4 mg/ml. Interestingly, growth of Mycobacteriumphlei was inhibited by the volatiles of O. americanum, C. hystrix peel, and C. zedoaria with MIC of 1.7, 3.5 and 1.2 mg/ml,respectively. For antioxidant activity evaluation, the methanol extracts of C. hystrix (leaf and peel and K. parviflora hadpotent antioxidant activity by the radical-scavenging DPPH method with IC50 of 24.6, 66.3 and 61.5 mg/ml, respectively.GC-MS analysis revealed the typical chemical profiles of the volatile oils. The major component showed the characteristicsof the volatile oils and was probably responsible for the antimicrobial effect.

  16. Non-Precious Bimetallic Catalysts for Selective Dehydrogenation of an Organic Chemical Hydride System

    KAUST Repository

    Shaikh Ali, Anaam

    2015-07-06

    Methylcyclohexane (MCH)-Toluene (TOL) chemical hydride cycles as a hydrogen carrier system is successful with the selective dehydrogenation reaction of MCH to TOL, which has been achieved only using precious Pt-based catalysts. Herein, we report improved selectivity using non-precious metal nickel-based bimetallic catalysts, where the second metal occupies the unselective step sites.

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

    Science.gov (United States)

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

    2016-07-18

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-12-15

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

    Roč. 17, č. 38 (2015), s. 24944-24955. ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA14-03564S Institutional support: RVO:61388963 Keywords : NMR chemical shifts * transition metal complexes * relativistic effects * method calibration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.493, year: 2014 http://pubs.rsc.org/en/content/articlepdf/2015/cp/c5cp04214c

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

    OpenAIRE

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

    1993-01-01

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

  2. Mass spectrometry analysis of polychlorinated biphenyls: chemical ionization and selected ion chemical ionization using methane as a reagent gas

    OpenAIRE

    RAYMOND E. MARCH; MILA D. LAUSEVIC; TATJANA M. VASILJEVIC

    2000-01-01

    In the present paper a quadrupole ion trap mass spectrometer, coupled with a gas chromatograph, was used to compare the electron impact ionization (EI) and chemical ionization (Cl) technique, in terms of their selectivity in polychlorinated biphenyls (PCBs) quantitative analysis. The experiments were carried out with a modified Varian SATURN III quadrupole ion-storage mass spectrometer equipped with Varian waveform generator, coupled with a gas chromatograph with DB-5 capillary column. The di...

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

    International Nuclear Information System (INIS)

    Objective: To investigate the reproducibility and influencing factors of relative quantification of phosphorus metabolites with two-dimensional chemical shift imaging (2D CSI) in rabbit liver. Methods: Using 2D CSI MRS, 500 ml phosphate (NaH2PO4) solution phantom with 0.05 mol/L concentration and one healthy rabbit were scanned 30 times respectively in one day and rescanned 30 times in the next day, and the stability of MR scanner and reproducibility of within-run and between-days in the same individual were analyzed. Each of thirty rabbits was scanned and rescanned one time respectively in different days, and the reproducibility of between-days in one group was analyzed. The data were statistically analyzed with t tests. Results: (1) Phosphate solution phantom had a good reproducibility of within-run with the coefficient variation (CV) of 4.92% and 5.12% respectively in different two days. No significant change of phosphorus metabolites was detected in between-days, which was 16.68±0.82 and 16.56± 0.85 respectively (t=0.665, P>0.05). (2) The CV of metabolites in one healthy rabbit ranged from 8.04% to 34.13%. Among the metabolites, β-ATP had the best reproducibility with the CV less than 10%. PME was 0.88±0.28 and 0.88±0.30, PDE was 4.35±0.66 and 4.35±0.66, Pi was 0.95±0.30 and 0.97±0.28, α-ATP was 5.58±0.60 and 5.61±0.61, β-ATP was 2.70±0.22 and 2.71± 0.22, γ-ATP was 2.20±0.63 and 2.18±0.44 respectively, no significant changes of metabolites were detected in between-days (P>0.05). (3) The CV of metabolites in 30 healthy rabbits ranged from 8.48% to 36.21%. Among the metabolites, β-ATP had the best reproducibility with CV less than 10%. PME was 0.84±0.30 and 0.79±0.28, PDE was 4.29±0.72 and 3.94±0.84, Pi was 0.91±0.28 and 0.92± 0.31, α-ATP was 5.65±0.66 and 5.36±0.60, β-ATP was 2.71±0.23 and 2.66±0.25, γ-ATP was 2.07±0.29 and 1.99±0.37 respectively, no significant changes of metabolites were detected in between-days (P>0

  4. Chemically Selective Coated Quartz Crystal Microbalance (QCM) Array for Detection of Volatile Organic Chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Bohuszewicz, T.V.; Frye-Mason, G.C.; Martin, S.J.; Osbourn, G.C. Bartholomew, J.W.; Schneider, T.W.; Spates, J.J.

    1998-11-04

    Liquid flow cells have been fabricated to prepare an array of QCMS operating simultaneously for detection and identification of VOCS in water. TWO signals, a tlequency response and a damping voltage response, were obtained per resonator. A blank QCM was used as a reference to account for changes in liquid density and viscosity. Nine different polymer coatings applied using a spin coat technique have been examined for VOC response under liquid flow conditions. A matrix of three classes of VOCS were examined for each coating with four chemicals in each class. The three classes of VOCS are polar, nonpolar and chlorinated. A pattern recognition technique, called visually empirical region of influence (VERI), was used to cluster the responses in n-dimensional space. Chemicals within a class varying by only one methyl group (e.g., toluene and xylene) are easily discriminated using only two different coatings with three different QCM responses. All chemicak were easily separated and detected with a total of 5 films and 6 responses with >99% accuracy.

  5. Targeted energy transfer between a Rotor and a Morse oscillator: A model for selective chemical dissociation

    OpenAIRE

    Memboeuf, Antony; Aubry, Serge

    2005-01-01

    Standard Kramers theory of chemical reactions involves a coupling with a Langevin thermal bath which intrinsically forbids the possible existence of Discrete Breathers (DBs) (i.e. local modes). However, it is now known that in complex systems, that energy may focus for long time as Discrete Breathers (local mode). In very special systems, targeted energy transfer may occur subsequently to another selected site and induces an ultraselective chemical reaction operating at low temperature. The d...

  6. Chemical interaction of Ce-Fe mixed oxides for methane selective oxidation

    Institute of Scientific and Technical Information of China (English)

    祝星; 杜云鹏; 王华; 魏永刚; 李孔斋; 孙令玥

    2014-01-01

    Chemical interaction of Ce-Fe mixed oxides was investigated in methane selective oxidation via methane temperature pro-grammed reduction and methane isothermal reaction tests over Ce-Fe oxygen carriers. In methane temperature programmed reduction test, Ce-Fe oxide behaved complete oxidation at the lower temperature and selective oxidation at higher temperatures. Ce-Fe mixed oxides with the Fe content in the range of 0.1-0.5 was able to produce syngas with high selectivity in high-temperature range (800-900 °C), and a higher Fe amount over 0.5 seemed to depress the CO formation. In isothermal reaction, complete oxidation oc-curred at beginning following with selective oxidation later. Ce1-xFexO2-δ oxygen carriers (x≤0.5) were proved to be suitable for the selective oxidation of methane. Ce-Fe mixed oxides had the well-pleasing reducibility with high oxygen releasing rate and CO selec-tivity due to the interaction between Ce and Fe species. Strong chemical interaction of Ce-Fe mixed oxides originated from both Fe* activated CeO2 and Ce3+ activated iron oxides (FeOm), and those chemical interaction greatly enhanced the oxygen mobility and se-lectivity.

  7. Selected bibliography for the extraction of uranium from seawater: chemical process and plant design feasibility study

    Energy Technology Data Exchange (ETDEWEB)

    Binney, S.E.; Polkinghorne, S.T.; Jante, R.R.; Rodman, M.R.; Chen, A.C.T.; Gordon, L.I.

    1979-02-01

    A selected annotated bibliography of 521 references was prepared as a part of a feasibility study of the extraction of uranium from seawater. For the most part, these references are related to the chemical processes whereby the uranium is removed from the seawater. A companion docment contains a similar bibliography of 471 references related to oceanographic and uranium extraction plant siting considerations, although some of the references are in common. The bibliography was prepared by computer retrieval from Chemical Abstracts, Nuclear Science Abstracts, Energy Data Base, NTIS, and Oceanic Abstracts. References are listed by author, country of author, and selected keywords.

  8. Selected bibliography for the extraction of uranium from seawater: chemical process and plant design feasibility study

    International Nuclear Information System (INIS)

    A selected annotated bibliography of 521 references was prepared as a part of a feasibility study of the extraction of uranium from seawater. For the most part, these references are related to the chemical processes whereby the uranium is removed from the seawater. A companion docment contains a similar bibliography of 471 references related to oceanographic and uranium extraction plant siting considerations, although some of the references are in common. The bibliography was prepared by computer retrieval from Chemical Abstracts, Nuclear Science Abstracts, Energy Data Base, NTIS, and Oceanic Abstracts. References are listed by author, country of author, and selected keywords

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

    Science.gov (United States)

    Rosner, D. E.; Nagarajan, R.

    1985-01-01

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

  10. Analysis of abused drugs by selected ion monitoring: quantitative comparison of electron impact and chemical ionization

    International Nuclear Information System (INIS)

    A comparison was made of the relative sensitivities of electron impact and chemical ionization when used for selected ion monitoring analysis of commonly abused drugs. For most of the drugs examined chemical ionization using ammonia as the reactant gas gave the largest single m/e ion current response per unit weight of sample. However, if maximum sensitivity is desired it is important to evaluate electron impact and chemical ionization with respect to both maximum response and degree of interference from background and endogenous materials

  11. Efficient and selective chemical transformations under flow conditions: The combination of supported catalysts and supercritical fluids

    OpenAIRE

    M. Isabel Burguete; Eduardo García-Verdugo; Luis, Santiago V.

    2011-01-01

    This paper reviews the current trends in the combined use of supported catalytic systems, either on solid supports or in liquid phases and supercritical fluids (scFs), to develop selective and enantioselective chemical transformations under continuous and semi-continuous flow conditions. The results presented have been selected to highlight how the combined use of those two elements can contribute to: (i) Significant improvements in productivity as a result of the enhanced diffusion of substr...

  12. Selection for chemical trait remixing in an invasive weed after reassociation with a coevolved specialist

    OpenAIRE

    Zangerl, A. R.; Stanley, M. C.; Berenbaum, M R

    2008-01-01

    The interaction between Depressaria pastinacella (parsnip webworm) and wild parsnip (Pastinaca sativa), in its native Europe and in its longstanding nonindigenous range in the midwestern United States, is characterized by chemical phenotype matching, ostensibly mediated by reciprocal selective responses. The first appearance of D. pastinacella on P. sativa in New Zealand in 2004 provided an opportunity to quantify selective impacts of a coevolved herbivore and calibrate rates of phytochemical...

  13. 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.

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  16. Pharmaceuticals and other organic chemicals in selected north-central and northwestern Arkansas streams

    Science.gov (United States)

    Haggard, B.E.; Galloway, J.M.; Green, W.R.; Meyer, M.T.

    2006-01-01

    Recently, our attention has focused on the low level detection of many antibiotics, pharmaceuticals, and other organic chemicals in water resources. The limited studies available suggest that urban or rural streams receiving wastewater effluent are more susceptible to contamination. The purpose of this study was to evaluate the occurrence of antibiotics, pharmaceuticals, and other organic chemicals at 18 sites on seven selected streams in Arkansas, USA, during March, April, and August 2004. Water samples were collected upstream and downstream from the influence of effluent discharges in northwestern Arkansas and at one site on a relatively undeveloped stream in north-central Arkansas. At least one antibiotic, pharmaceutical, or other organic chemical was detected at all sites, except at Spavinaw Creek near Mayesville, Arkansas. The greatest number of detections was observed at Mud Creek downstream from an effluent discharge, including 31 pharmaceuticals and other organic chemicals. The detection of these chemicals occurred in higher frequency at sites downstream from effluent discharges compared to those sites upstream from effluent discharges; total chemical concentration was also greater downstream. Wastewater effluent discharge increased the concentrations of detergent metabolites, fire retardants, fragrances and flavors, and steroids in these streams. Antibiotics and associated degradation products were only found at two streams downstream from effluent discharges. Overall, 42 of the 108 chemicals targeted in this study were found in water samples from at least one site, and the most frequently detected organic chemicals included caffeine, phenol, para-cresol, and acetyl hexamethyl tetrahydro naphthalene (AHTN). ?? ASA, CSSA, SSSA.

  17. Chemical deactivation of Cu-SSZ-13 ammonia selective catalytic reduction (NH3-SCR) systems

    NARCIS (Netherlands)

    Lezcano-Gonzalez, I.; Deka, U.; van der Bij, H. E.; Paalanen, P.; Arstad, B.; Weckhuysen, B. M.; Beale, A. M.

    2014-01-01

    The chemical deactivation of Cu-SSZ-13 Ammonia Selective Catalytic Reduction (NH3-SCR) catalysts by Pt, Zn, Ca and P has been systematically investigated using a range of analytical techniques in order to study the influence on both the zeolitic framework and the active Cu2+ ions. The results obtain

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-15

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

  20. 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)

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

    Science.gov (United States)

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

    2016-04-01

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

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

    International Nuclear Information System (INIS)

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

  3. 1H and 13C NMR Chemical Shift Assignments and Conformational Analysis for the Two Diastereomers of the Vitamin K Epoxide Reductase Inhibitor Brodifacoum

    International Nuclear Information System (INIS)

    Proton and 13C NMR chemical shift assignments and 1H-1H scalar couplings for the two diastereomers of the vitamin K epoxide reductase (VKOR) inhibitor brodifacoum have been determined from acetone solutions containing both diastereomers. Data were obtained from homo- and heteronuclear correlation spectra acquired at 1H frequencies of 750 and 900 MHz over a 268-303 K temperature range. Conformations inferred from scalar coupling and 1-D NOE measurements exhibit large differences between the diastereomers. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  4. 129Xe-NMR of xenon adsorbed on zeolites: determination of the dimensions of the void space from the chemical shift δ(129Xe)

    International Nuclear Information System (INIS)

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

  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 s...

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

    Institute of Scientific and Technical Information of China (English)

    WANG Zhen; ZHANG Jing

    2011-01-01

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

  7. Magnetic moments in chemically ordered mass-selected CoPt and FePt clusters

    International Nuclear Information System (INIS)

    By combining high photon flux and chemical selectivity, X-ray absorption spectroscopy and X-ray magnetic circular dichroism (XMCD) have been used to study the magnetism of CoPt and FePt clusters before and after their transition to the chemically ordered L10-like phase. Compared to the bulk, we find larger magnetic spin and orbital moments of Fe, Co and Pt atoms in nanoalloys. - Highlights: • Study of magnetism on well-defined CoPt and FePt clusters embedded in carbon matrix • X-ray magnetic circular dichroism (XMCD) at each specific Fe, Co and Pt edges, before and after annealing to induce transition to the chemically L10-like phase. • Quantitative values of the spin and orbital magnetic moments of Co (resp. Fe) and Pt after the chemical ordering transition. • Specific nanoalloy effects

  8. Insights on FXR selective modulation. Speculation on bile acid chemical space in the discovery of potent and selective agonists

    Science.gov (United States)

    Sepe, Valentina; Festa, Carmen; Renga, Barbara; Carino, Adriana; Cipriani, Sabrina; Finamore, Claudia; Masullo, Dario; del Gaudio, Federica; Monti, Maria Chiara; Fiorucci, Stefano; Zampella, Angela

    2016-01-01

    Bile acids are the endogenous modulators of the nuclear receptor FXR and the membrane receptor GPBAR1. FXR represents a promising pharmacological target for the treatment of cholestatic liver disorders. Currently available semisynthetic bile acid derivatives cover the same chemical space of bile acids and therefore they are poorly selective toward BA receptors, increasing patient risk for adverse side effects. In this report, we have investigated around the structure of CDCA describing the synthesis and the in vitro and in vivo pharmacological characterization of a novel family of compounds modified on the steroidal tetracyclic core and on the side chain. Pharmacological characterization resulted in the identification of several potent and selective FXR agonists. These novel agents might add utility in the treatment of cholestatic disorders by potentially mitigating side effects linked to unwanted activation of GPBAR1. PMID:26740187

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

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Kenneth F.

    2006-07-26

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

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

    Science.gov (United States)

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

    2013-05-01

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

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

    Science.gov (United States)

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

    2012-12-01

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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    OpenAIRE

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

    2009-01-01

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

  14. Investigation of microcantilever array with ordered nanoporous coatings for selective chemical detection.

    Energy Technology Data Exchange (ETDEWEB)

    Allendorf, Mark D.; Thornberg, Steven Michael (Sandia National Laboratories, Albuquerque, NM); Lee, J. -H. (Georgia Institute of Technology, Atlanta, GA); Robinson, Alex Lockwood (Sandia National Laboratories, Albuquerque, NM); Hesketh, Peter J. (Georgia Institute of Technology, Atlanta, GA); Greathouse, Jeffery A. (Sandia National Laboratories, Albuquerque, NM); Houk, Ronald J. T.

    2010-03-01

    In this paper we demonstrate the potential for novel nanoporous framework materials (NFM) such as metal-organic frameworks (MOFs) to provide selectivity and sensitivity to a broad range of analytes including explosives, nerve agents, and volatile organic compounds (VOCs). NFM are highly ordered, crystalline materials with considerable synthetic flexibility resulting from the presence of both organic and inorganic components within their structure. Detection of chemical weapons of mass destruction (CWMD), explosives, toxic industrial chemicals (TICs), and volatile organic compounds (VOCs) using micro-electro-mechanical-systems (MEMS) devices, such as microcantilevers and surface acoustic wave sensors, requires the use of recognition layers to impart selectivity. Traditional organic polymers are dense, impeding analyte uptake and slowing sensor response. The nanoporosity and ultrahigh surface areas of NFM enhance transport into and out of the NFM layer, improving response times, and their ordered structure enables structural tuning to impart selectivity. Here we describe experiments and modeling aimed at creating NFM layers tailored to the detection of water vapor, explosives, CWMD, and VOCs, and their integration with the surfaces of MEMS devices. Force field models show that a high degree of chemical selectivity is feasible. For example, using a suite of MOFs it should be possible to select for explosives vs. CWMD, VM vs. GA (nerve agents), and anthracene vs. naphthalene (VOCs). We will also demonstrate the integration of various NFM with the surfaces of MEMS devices and describe new synthetic methods developed to improve the quality of VFM coatings. Finally, MOF-coated MEMS devices show how temperature changes can be tuned to improve response times, selectivity, and sensitivity.

  15. Selection for chemical trait remixing in an invasive weed after reassociation with a coevolved specialist.

    Science.gov (United States)

    Zangerl, A R; Stanley, M C; Berenbaum, M R

    2008-03-25

    The interaction between Depressaria pastinacella (parsnip webworm) and wild parsnip (Pastinaca sativa), in its native Europe and in its longstanding nonindigenous range in the midwestern United States, is characterized by chemical phenotype matching, ostensibly mediated by reciprocal selective responses. The first appearance of D. pastinacella on P. sativa in New Zealand in 2004 provided an opportunity to quantify selective impacts of a coevolved herbivore and calibrate rates of phytochemical response in its host plant. Webworms in 2006 reduced seed production up to 75% in New Zealand populations, and in 2007 infestations increased in severity in all populations except one. Most New Zealand populations fall into a furanocoumarin phenotype cluster distinct from European and U.S. phenotypes, although one heavily attacked population clusters with two U.S. populations and one European population long associated with webworms. Multivariate selection analysis substituting realized fitness (with webworms present) for potential fitness (absent webworms) as the dependent variable revealed that reassociation with a coevolved specialist in a nonindigenous area profoundly altered the selection regime, favoring trait remixing and rapid chemical changes in parsnip populations, as predicted by the geographic mosaic theory. That uninfested populations of New Zealand parsnips contain higher amounts of octyl acetate, a floral volatile used by webworms for orientation, suggests that plants that escape from specialized enemies may also experience selection to increase kairomones, as well as to reduce allomones. PMID:18238901

  16. Selecting the optimal anti-aliasing filter for multichannel biosignal acquisition intended for inter-signal phase shift analysis.

    Science.gov (United States)

    Keresnyei, Róbert; Megyeri, Péter; Zidarics, Zoltán; Hejjel, László

    2015-01-01

    The availability of microcomputer-based portable devices facilitates the high-volume multichannel biosignal acquisition and the analysis of their instantaneous oscillations and inter-signal temporal correlations. These new, non-invasively obtained parameters can have considerable prognostic or diagnostic roles. The present study investigates the inherent signal delay of the obligatory anti-aliasing filters. One cycle of each of the 8 electrocardiogram (ECG) and 4 photoplethysmogram signals from healthy volunteers or artificially synthesised series were passed through 100-80-60-40-20 Hz 2-4-6-8th order Bessel and Butterworth filters digitally synthesized by bilinear transformation, that resulted in a negligible error in signal delay compared to the mathematical model of the impulse- and step responses of the filters. The investigated filters have as diverse a signal delay as 2-46 ms depending on the filter parameters and the signal slew rate, which is difficult to predict in biological systems and thus difficult to compensate for. Its magnitude can be comparable to the examined phase shifts, deteriorating the accuracy of the measurement. As a conclusion, identical or very similar anti-aliasing filters with lower orders and higher corner frequencies, oversampling, and digital low pass filtering are recommended for biosignal acquisition intended for inter-signal phase shift analysis. PMID:25514627

  17. Selecting the optimal anti-aliasing filter for multichannel biosignal acquisition intended for inter-signal phase shift analysis

    International Nuclear Information System (INIS)

    The availability of microcomputer-based portable devices facilitates the high-volume multichannel biosignal acquisition and the analysis of their instantaneous oscillations and inter-signal temporal correlations. These new, non-invasively obtained parameters can have considerable prognostic or diagnostic roles. The present study investigates the inherent signal delay of the obligatory anti-aliasing filters. One cycle of each of the 8 electrocardiogram (ECG) and 4 photoplethysmogram signals from healthy volunteers or artificially synthesised series were passed through 100–80–60–40–20 Hz 2–4–6–8th order Bessel and Butterworth filters digitally synthesized by bilinear transformation, that resulted in a negligible error in signal delay compared to the mathematical model of the impulse- and step responses of the filters. The investigated filters have as diverse a signal delay as 2–46 ms depending on the filter parameters and the signal slew rate, which is difficult to predict in biological systems and thus difficult to compensate for. Its magnitude can be comparable to the examined phase shifts, deteriorating the accuracy of the measurement. As a conclusion, identical or very similar anti-aliasing filters with lower orders and higher corner frequencies, oversampling, and digital low pass filtering are recommended for biosignal acquisition intended for inter-signal phase shift analysis. (note)

  18. Solvent selection causes remarkable shifts of the ``Ouzo region'' for poly(lactide-co-glycolide) nanoparticles prepared by nanoprecipitation

    Science.gov (United States)

    Beck-Broichsitter, Moritz; Nicolas, Julien; Couvreur, Patrick

    2015-05-01

    Polymer nanoparticles (NPs) offer versatile novel biological features of interest for drug delivery applications. ``Ouzo diagrams'' allowed for a systematic manufacture of specified colloidal formulations by the widely used nanoprecipitation process. Surprisingly, despite the well-documented relevance of the applied organic solvent for nanoprecipitation, its effect on the actual status of the ``Ouzo region'' was so far not studied. Herein, investigations were undertaken to account for the potential impact of the solvent type on the ``Ouzo diagrams'' for poly(lactide-co-glycolide) (PLGA) and tetrahydrofuran (THF), 1,4-dioxane, acetone and dimethyl sulfoxide (DMSO). The ``Ouzo region'' shifted considerably to higher polymer fractions upon solvent change (rank order: THF documented relevance of the applied organic solvent for nanoprecipitation, its effect on the actual status of the ``Ouzo region'' was so far not studied. Herein, investigations were undertaken to account for the potential impact of the solvent type on the ``Ouzo diagrams'' for poly(lactide-co-glycolide) (PLGA) and tetrahydrofuran (THF), 1,4-dioxane, acetone and dimethyl sulfoxide (DMSO). The ``Ouzo region'' shifted considerably to higher polymer fractions upon solvent change (rank order: THF Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01695a

  19. Selective pharmacological blockade of the 5-HT7 receptor attenuates light and 8-OH-DPAT induced phase shifts of mouse circadian wheel running activity

    Directory of Open Access Journals (Sweden)

    Jonathan eShelton

    2015-01-01

    Full Text Available Recent reports have illustrated a reciprocal relationship between circadian rhythm disruption and mood disorders. The 5-HT7 receptor may provide a crucial link between the two sides of this equation since the receptor plays a critical role in sleep, depression, and circadian rhythm regulation. To further define the role of the 5-HT7 receptor as a potential pharmacotherapy to correct circadian rhythm disruptions, the current study utilized the selective 5-HT7 antagonist JNJ-18038683 (10 mg/kg in three different circadian paradigms. While JNJ-18038683 was ineffective at phase shifting the onset of wheel running activity in mice when administered at different circadian time (CT points across the circadian cycle, pretreatment with JNJ-18038683 blocked non-photic phase advance (CT6 induced by the 5-HT1A/7 receptor agonist 8-OH-DPAT (3 mg/kg. Since light induced phase shifts in mammals are partially mediated via the modulation of the serotonergic system, we determined if JNJ-18038683 altered phase shifts induced by a light pulse at times known to phase delay (CT15 or advance (CT22 wheel running activity in free running mice. Light exposure resulted in a robust shift in the onset of activity in vehicle treated animals at both times tested. Administration of JNJ-18038683 significantly attenuated the light-induced phase delay and completely blocked the phase advance. The current study demonstrates that pharmacological blockade of the 5-HT7 receptor by JNJ-18038683 blunts both non-photic and photic phase shifts of circadian wheel running activity in mice. These findings highlight the importance of the 5-HT7 receptor in modulating circadian rhythms. Due to the opposite modulating effects of light resetting between diurnal and nocturnal species, pharmacotherapy targeting the 5-HT7 receptor in conjunction with bright light therapy may prove therapeutically beneficial by correcting the desynchronization of internal rhythms observed in depressed individuals.

  20. Pesticides, selected elements, and other chemicals in adult total diet samples October 1979-September 1980

    International Nuclear Information System (INIS)

    The US Food and Drug Administration (FDA) conducts Total Diet Studies to determine the dietary intake of selected pesticides, industrial chemicals, and elements (including radionuclides). These studies involve the retail purchase and analysis of foods representative of the diets of infants, toddlers, and adults. The individual food items are separated into a number of food groups, each of which is analyzed as a composite. This report summarizes the results for adult Total Diet samples collected in 20 cities between October 1979 and September 1980. The average concentration, range of concentrations, and calculated average daily intake of each chemical found are presented by food group. The average daily intakes of the chemicals are similar to those found in the several preceding years and are within acceptable limits. The results for samples collected during the same period that represent the diets of infants and toddlers are reported separately

  1. A Comprehensive Framework for Surfactant Selection and Design for Emulsion Based Chemical Product Design

    DEFF Research Database (Denmark)

    Mattei, Michele; Kontogeorgis, Georgios; Gani, Rafiqul

    2014-01-01

    developmentof a methodology and relevant tools in order to spare time and resources in the design of emulsion-based chemical products, so that the products can reach the market faster and at a reduced cost. Theunderstanding and modeling of the characteristic behavior of emulsions and their peculiar...... ingredientsis consequently necessary to tackle this problem with computer-aided methods and tools. A compre-hensive framework for the selection and design of surfactants, the main responsible for the formationand the stability of emulsions, is presented here together with the modeling of the cloud point, a key...... thetype of emulsion expected (through the hydrophilic–lipophilic balance), and its stability (through thehydrophilic–lipophilic deviation), forming a robust chemical product design tool. The application of thisframework is highlighted for the design of some emulsion based chemical products....

  2. Selective Chemical Labeling of Proteins with Small Fluorescent Molecules Based on Metal-Chelation Methodology

    OpenAIRE

    Nobuaki Soh

    2008-01-01

    Site-specific chemical labeling utilizing small fluorescent molecules is a powerful and attractive technique for in vivo and in vitro analysis of cellular proteins, which can circumvent some problems in genetic encoding labeling by large fluorescent proteins. In particular, affinity labeling based on metal-chelation, advantageous due to the high selectivity/simplicity and the small tag-size, is promising, as well as enzymatic covalent labeling, thereby a variety of novel methods have been stu...

  3. Selective light induced chemical vapour deposition of titanium dioxide thin films

    OpenAIRE

    Wagner, Estelle; Hoffmann, Patrik

    2005-01-01

    Light Induced Chemical Vapour Deposition (LICVD) of titanium dioxide thin films is studied in this work. It is shown that this technique enables to deposit locally and selectively a chosen crystalline phase with a precise controlled thickness at low substrate temperature, allowing even the use of polymer substrates. A home made LICVD reactor was set up, consisting of a main chamber in which the substrate was placed on a temperature controlled plate and could be irradiated perpendicularly thro...

  4. Selective light induced chemical vapour deposition of titanium dioxide thin films

    OpenAIRE

    Wagner, Estelle

    2003-01-01

    Light Induced Chemical Vapour Deposition (LICVD) of titanium dioxide thin films is studied in this work. It is shown that this technique enables to deposit locally and selectively a chosen crystalline phase with a precise controlled thickness at low substrate temperature, allowing even the use of polymer substrates. A home made LICVD reactor was set up, consisting of a main chamber in which the substrate was placed on a temperature controlled plate and could be irradiated perpendicularly thro...

  5. Revisiting benzene cluster cations for the chemical ionization of dimethyl sulfide and select volatile organic compounds

    Science.gov (United States)

    Kim, Michelle J.; Zoerb, Matthew C.; Campbell, Nicole R.; Zimmermann, Kathryn J.; Blomquist, Byron W.; Huebert, Barry J.; Bertram, Timothy H.

    2016-04-01

    Benzene cluster cations were revisited as a sensitive and selective reagent ion for the chemical ionization of dimethyl sulfide (DMS) and a select group of volatile organic compounds (VOCs). Laboratory characterization was performed using both a new set of compounds (i.e., DMS, β-caryophyllene) as well as previously studied VOCs (i.e., isoprene, α-pinene). Using a field deployable chemical-ionization time-of-flight mass spectrometer (CI-ToFMS), benzene cluster cations demonstrated high sensitivity (> 1 ncps ppt-1) to DMS, isoprene, and α-pinene standards. Parallel measurements conducted using a chemical-ionization quadrupole mass spectrometer, with a much weaker electric field, demonstrated that ion-molecule reactions likely proceed through a combination of ligand-switching and direct charge transfer mechanisms. Laboratory tests suggest that benzene cluster cations may be suitable for the selective ionization of sesquiterpenes, where minimal fragmentation (validated against an atmospheric pressure ionization mass spectrometer, where measurements from the two instruments were highly correlated (R2 > 0.95, 10 s averages) over a wide range of sampling conditions.

  6. 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

  7. Combination of TRAIL with Bortezomib Shifted Apoptotic Signaling from DR4 to DR5 Death Receptor by Selective Internalization and Degradation of DR4

    OpenAIRE

    Bychkov, Maxim L.; Gasparian, Marine E.; Dolgikh, Dmitry A; Kirpichnikov, Mikhail P.

    2014-01-01

    TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) mediates apoptosis in cancer cells through death receptors DR4 and DR5 preferring often one receptor over another in the cells expressing both receptors. Receptor selective mutant variants of TRAIL and agonistic antibodies against DR4 and DR5 are highly promising anticancer agents. Here using DR5 specific mutant variant of TRAIL - DR5-B we have demonstrated for the first time that the sensitivity of cancer cells can be shifted fr...

  8. Chemically modified nucleic acid aptamers for in vitro selections: evolving evolution.

    Science.gov (United States)

    Kusser, W

    2000-03-01

    Combinatorial library selections through the systematic evolution of ligands by exponential enrichment (SELEX) technique identify so-called nucleic acid aptamers that bind with high-affinity and specificity to a wide range of selected molecules. However, the modest chemical functionality of nucleic acids poses some limits on their versatility as binders and catalysts, and, furthermore, the sensitivity of pure RNA- and DNA-based aptamers to nucleases restricts their use as therapeutic and diagnostic agents. Here we review synthetic chemistries for modifying nucleotides that have been developed to enhance the affinity of aptamers for targets and to increase their stability in biological fluids. Implementation of in vitro selections with modified nucleotides promises to be an elegant technique for the creation of ligands with novel physical and chemical properties and is anticipated to have a significant impact on biotechnology, diagnostics and drug development. The current molecular designs and applications of modified nucleotides for in vitro selections are reviewed, along with a discussion of future developments expected to further the utility of this approach in both practical and theoretical terms. PMID:10943570

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for non-relativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton and xenon dimers and free atoms. Relativistic...... corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the 4-component Dirac-Coulomb Hamiltonian using Dyall’s acv4z basis sets. The relativistic corrections to the nuclear magnetic...... shieldings and chemical shifts are combined with non-relativistic CCSD(T) calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr and the AQZP basis set for Xe. For the dimers also zero-point vibrational corrections obtained at the CCSD...

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  11. 1H chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter

    International Nuclear Information System (INIS)

    MR spectroscopy results in a mild case of guanidinoacetate methyltransferase (GAMT) deficiency are presented. The approach differs from previous MRS studies in the acquisition of a chemical shift imaging spectral map showing gray and white matter with the corresponding spectra in one overview. MR spectroscopy revealed guanidinoacetate (GAA) in the absence of creatine. New is that GAA signals are more prominent in gray matter than in white. In the prevailing view, that enzyme deficiency is localized in liver and pancreas and that all GAA is transported into the brain from the blood and the cerebrospinal fluid, this would be compatible with a more limited uptake and/or better clearance of GAA from the white matter compared to the grey matter. (orig.)

  12. H-1-, C-13-, and N-15-NMR chemical shifts for selected glucosides and ribosides of aromatic cytokinins

    Czech Academy of Sciences Publication Activity Database

    Vícha, J.; Maloň, Michal; Veselá, P.; Humpa, O.; Strnad, Miroslav; Marek, R.

    2010-01-01

    Roč. 48, č. 4 (2010), s. 318-322. ISSN 0749-1581 R&D Projects: GA ČR GA301/08/1649 Institutional research plan: CEZ:AV0Z50380511 Keywords : NMR * H-1 * C-13 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.247, year: 2010

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2015-09-21

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

  15. 31P-MR spectroscopy of all regions of the human heart at 1.5 T with acquisition-weighted chemical shift imaging

    International Nuclear Information System (INIS)

    Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac 31P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders 31P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.)

  16. Trace isotope analysis using resonance ionization mass spectrometry based on isotope selection with doppler shift of laser ablated atoms

    International Nuclear Information System (INIS)

    We have proposed a novel isotope selective Resonance Ionization Mass Spectroscopy (RIMS) concept, which can avoid the Doppler broadening on solid sample direct measurement based on laser ablation technique. We have succeeded in experimentally demonstrating the principle of our RIMS concept. Through comparison between the simulated and experimental results, we have validated the simulation model. It would be concluded from these results that we could achieve the isotope selectivity defined as the ratio of 41Ca to 40Ca sensitivity to be 4.5x1010 by adopting the multi-step excitation scheme in the present method. As future works, we will try to experimentally perform the multi-step excitation scheme and improve the detection efficiency by modifying the ion extraction configuration. (author)

  17. A napthelene-pyrazol conjugate: Al(III) ion-selective blue shifting chemosensor applicable as biomarker in aqueous solution.

    Science.gov (United States)

    Mukherjee, Manjira; Pal, Siddhartha; Lohar, Somenath; Sen, Buddhadeb; Sen, Supriti; Banerjee, Samya; Banerjee, Snehasis; Chattopadhyay, Pabitra

    2014-10-01

    A newly synthesized and crystalographically characterized napthelene–pyrazol conjugate, 1-[(5-phenyl-1H-pyrazole-3-ylimino)-methyl]-naphthalen-2-ol (HL) behaves as an Al(III) ion-selective chemosensor through internal charge transfer (ICT)-chelation-enhanced fluorescence (CHEF) processes in 100 mM HEPES buffer (water–DMSO 5:1, v/v) at biological pH with almost no interference of other competitive ions. This mechanism is readily studied from electronic, fluorimetric and (1)H NMR titration. The probe (HL) behaved as a highly selective fluorescent sensor for Al(III) ions as low as 31.78 nM within a very short response time (15–20 s). The sensor (HL), which has no cytotoxicity, is also efficient in detecting the distribution of Al(III) ions in HeLa cells via image development under fluorescence microscope. PMID:25075382

  18. Development of a physical and chemical property database for ten US EPA-selected oils

    International Nuclear Information System (INIS)

    In the event of an oil spill, data on the physical properties and chemical composition of crude oils and hydrocarbons must be known to allow experts to use environmental fate simulations. The complexity and expense of making the required measurements had rendered this data largely unavailable. A database of several physical and chemical properties of crude oils and petroleum products was developed by Environment Canada. A project called Development of a Composition Database for Selected Multicomponent Oils was initiated in 2002 with funding from the United States Environmental Protection Agency (US EPA) and Environment Canada. In this cooperative project, the research laboratory of the Emergencies Science and Technology Division of Environment Canada characterized ten typical crude oils and refined products identified by the US EPA. Measurements of physical properties included API gravity, density, sulphur content, water content, flash point, pour point, viscosity, surface and interfacial tension, adhesion, the equation for predicting evaporation, emulsion formation, and simulated boiling point distribution. The chemical composition of the oils selected included hydrocarbon groups, volatile organic compounds (including BTEX and other alkyl-benzene compounds), n-alkane distribution, distribution of alkylated polyaromatic hydrocarbon (PAH) homologues and other EPA priority PAHs, and biomarkers. The results obtained were integrated into the existing Environment Canada oil properties database and are made available to the public. This data will be used to support oil spill modelling for application to environmental problems caused by oil spills. 38 refs., 18 tabs., 2 figs

  19. Chemically Modulated Carbon Nitride Nanosheets for Highly Selective Electrochemiluminescent Detection of Multiple Metal-ions.

    Science.gov (United States)

    Zhou, Zhixin; Shang, Qiuwei; Shen, Yanfei; Zhang, Linqun; Zhang, Yuye; Lv, Yanqin; Li, Ying; Liu, Songqin; Zhang, Yuanjian

    2016-06-01

    Chemical structures of two-dimensional (2D) nanosheet can effectively control the properties thus guiding their applications. Herein, we demonstrate that carbon nitride nanosheets (CNNS) with tunable chemical structures can be obtained by exfoliating facile accessible bulk carbon nitride (CN) of different polymerization degree. Interestingly, the electrochemiluminescence (ECL) properties of as-prepared CNNS were significantly modulated. As a result, unusual changes for different CNNS in quenching of ECL because of inner filter effect/electron transfer and enhancement of ECL owing to catalytic effect were observed by adding different metal ions. On the basis of this, by using various CNNS, highly selective ECL sensors for rapid detecting multiple metal-ions such as Cu(2+), Ni(2+), and Cd(2+) were successfully developed without any labeling and masking reagents. Multiple competitive mechanisms were further revealed to account for such enhanced selectivity in the proposed ECL sensors. The strategy of preparing CNNS with tunable chemical structures that facilely modulated the optical properties would open a vista to explore 2D carbon-rich materials for developing a wide range of applications such as sensors with enhanced performances. PMID:27187874

  20. Selective and Sensitive Sensing of Flame Retardant Chemicals Through Phage Display Discovered Recognition Peptide.

    Science.gov (United States)

    Jin, Hyo-Eon; Zueger, Chris; Chung, Woo-Jae; Wong, Winnie; Lee, Byung Yang; Lee, Seung-Wuk

    2015-11-11

    We report a highly selective and sensitive biosensor for the detection of an environmentally toxic molecule, decabrominated diphenyl ether (DBDE), one of the most common congeners of the polybrominated frame retardants (polybrominated diphenyl ether (PBDE)), using newly discovered DBDE peptide receptors integrated with carbon nanotube field-effect transistors (CNT-FET). The specific DBDE peptide receptor was identified using a high-throughput screening process of phage library display. The resulting binding peptide carries an interesting consensus binding pocket with two Trp-His/Asn-Trp repeats, which binds to the DBDE in a multivalent manner. We integrated the novel DBDE binding peptide onto the CNT-FET using polydiacetylene coating materials linked through cysteine-maleimide click chemistry. The resulting biosensor could detect the desired DBDE selectively with a 1 fM detection limit. Our combined approaches of selective receptor discovery, material nanocoating through click chemistry, and integration onto a sensitive CNT-FET electronic sensor for desired target chemicals will pave the way toward the rapid development of portable and easy-to-use biosensors for desired chemicals to protect our health and environment. PMID:26455834

  1. Efficient and selective chemical transformations under flow conditions: The combination of supported catalysts and supercritical fluids

    Directory of Open Access Journals (Sweden)

    M. Isabel Burguete

    2011-09-01

    Full Text Available This paper reviews the current trends in the combined use of supported catalytic systems, either on solid supports or in liquid phases and supercritical fluids (scFs, to develop selective and enantioselective chemical transformations under continuous and semi-continuous flow conditions. The results presented have been selected to highlight how the combined use of those two elements can contribute to: (i Significant improvements in productivity as a result of the enhanced diffusion of substrates and reagents through the interfaces favored by the scF phase; (ii the long term stability of the catalytic systems, which also contributes to the improvement of the final productivity, as the use of an appropriate immobilization strategy facilitates catalyst isolation and reuse; (iii the development of highly efficient selective or, when applicable, enantioselective chemical transformations. Although the examples reported in the literature and considered in this review are currently confined to a limited number of fields, a significant development in this area can be envisaged for the near future due to the clear advantages of these systems over the conventional ones.

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

    International Nuclear Information System (INIS)

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

  3. Diffusion, Thermal Properties and Chemical Compatibilities of Select MAX Phases with Materials For Advanced Nuclear Systems

    Energy Technology Data Exchange (ETDEWEB)

    Barsoum, Michel [Drexel Univ., Philadelphia, PA (United States); Bentzel, Grady [Drexel Univ., Philadelphia, PA (United States); Tallman, Darin J. [Drexel Univ., Philadelphia, PA (United States); Sindelar, Robert [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Garcia-Diaz, Brenda [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Hoffman, Elizabeth [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-04-04

    The demands of Gen IV nuclear power plants for long service life under neutron irradiation at high temperature are severe. Advanced materials that would withstand high temperatures (up to 1000+ ºC) to high doses in a neutron field would be ideal for reactor internal structures and would add to the long service life and reliability of the reactors. The objective of this work is to investigate the chemical compatibility of select MAX with potential materials that are important for nuclear energy, as well as to measure the thermal transport properties as a function of neutron irradiation. The chemical counterparts chosen for this work are: pyrolytic carbon, SiC, U, Pd, FLiBe, Pb-Bi and Na, the latter 3 in the molten state. The thermal conductivities and heat capacities of non-irradiated MAX phases will be measured.

  4. Chemical Water Quality Assessment in Selected Location in Jos, Plateau State, Nigeria

    Directory of Open Access Journals (Sweden)

    G.G. Jidauna

    2014-05-01

    Full Text Available The study examined well water quality (chemical in Jos metropolis which it collected a total of twenty water samples that were taken for laboratory analysis. The stratified systematic random method was used in the selection of sample area/location. A total of (10 out of the existing (20 wards were systematically selected, while in each of the wards, two wells with one each from higher and lower elevations were randomly selected in which water samples were collected. The samples collected were analyses at UNICEF (WATSAN Laboratory Bauchi. USEPA method of water analysis was used to test for the chemical parameters. Pearson product moment correlation co-efficient was used test for the relationship between high and low elevation in the sample elements, as well as mean and standard deviation. The results indicates that pH, E.C, TDS, Pb, As and Cyanide appears within NSDWQMPL, while NO2, Cl, F, Mn, Mg, Ca, Cu, Zn, CaCo3 and Cr marginally falls within acceptable standard for drinking water quality maximum permitted limit. Consequently, NO3, SO4, Fe and CaCo3 in some parts of Jos metropolis fall outside acceptable standard of NSDWQMPL. Moreover, pH, E.C, TDS, Pb, NO2, NO3, Cl, F, Mn, Cr, As, Cu, Zn, showed that there is no significant relationship within the individual elements in regards to elevation (high and low in the study area whereas, SO4, Fe, Mg, Ca, CaCo 3 and CaCo3 showed that there is significant relationship in elevation (high and low among the individual sample elements. The study concludes that well water quality through chemical assessment in Jos metropolis is not fit for drinking. It recommends sensitizations campaign on the importance of clean water, sanitation, enforcement of existing laws and more research be undertaken to cover for seasonal variation, more elements and sample size.

  5. Non-selective chemical sensors in analytical chemistry: from ''electronic nose'' to ''electronic tongue''

    International Nuclear Information System (INIS)

    Development, recent historical background and analytical applications of promising sensor instruments based on sensor arrays with data processing by pattern recognition methods have been described. Attention is paid to the ''electronic tongue'' based on an array of original non-specific (non-selective) potentiometric chemical sensors. Application results for integral qualitative analysis of beverages and for quantitative analysis of biological liquids and solutions, containing heavy metals are reported. Discriminating abilities and precision obtained allow to consider ''electronic tongue'' as a perspective analytical tool. (orig.)

  6. Passive sampling of selected endocrine disrupting compounds using polar organic chemical integrative samplers

    International Nuclear Information System (INIS)

    Two types of polar organic chemical integrative samplers (pharmaceutical POCIS and pesticide POCIS) were examined for their sampling efficiency of selected endocrine disrupting compounds (EDCs). Laboratory-based calibration of POCISs was conducted by exposing them at high and low concentrations of 14 EDCs (4-alkyl-phenols, their ethoxylate oligomers, bisphenol A, selected estrogens and synthetic steroids) for different time periods. The kinetic studies showed an integrative uptake up to 28 days. The sampling rates for the individual compounds were obtained. The use of POCISs could result in an integrative approach to the quality status of the aquatic systems especially in the case of high variation of water concentrations of EDCs. The sampling efficiency of POCISs under various field conditions was assessed after their deployment in different aquatic environments. - Calibration and field performance of polar organic integrative samplers for monitoring EDCs in aquatic environments

  7. Interpenetrating Metal-Metalloporphyrin Framework for Selective CO2 Uptake and Chemical Transformation of CO2.

    Science.gov (United States)

    Gao, Wen-Yang; Tsai, Chen-Yen; Wojtas, Lukasz; Thiounn, Timmy; Lin, Chu-Chieh; Ma, Shengqian

    2016-08-01

    Herein we report a robust primitive cubic (pcu)-topology metal-metalloporphyrin framework (MMPF), MMPF-18, which was constructed from a ubiquitous secondary building unit of a tetranuclear zinc cluster, Zn4(μ4-O)(-COO)6, and a linear organic linker of 5,15-bis(4-carboxyphenyl)porphyrin (H2bcpp). The strong π-π stacking from porphyrins and the lengthy H2bcpp ligand affords a 4-fold-interpenetrating network along with reduced void spaces and confined narrow channels. Thereby, MMPF-18 presents segmented pores and high-density metalloporphyrin centers for selective CO2 uptake over CH4 and size-selective chemical transformation of CO2 with epoxides forming cyclic carbonates under ambient conditions. PMID:27337152

  8. Selective chemical vapor deposition of tungsten films on titanium-ion-irradiated silicon dioxide

    International Nuclear Information System (INIS)

    Selective area deposition of adherent tungsten (W) film on titanium (Ti)-ion-irradiated silicon dioxide (SiO2 is achieved. First, Ti-ion irradiation through a stencil mask is performed at 600 eV for 1.1 x 1016 atoms/cm2 in a reaction chamber. Next, ArF excimer laser (λ = 193 nm) chemical vapor deposition (CVD) with tungsten hexafluoride (WF6) and hydrogen (H2) is carried out for 40 seconds at 400 K. Finally, low-pressure (LP) CVD is carried out at 600 K and then W films are deposited selectively on the ion-irradiated SiO2. Without the laser CVD step, the ion-irradiation pattern disappears during LPCVD and no W film deposition occurs

  9. Highly Chemical and Regio-selective Catalytic Oxidation with a Novel Manganese Catalyst

    Institute of Scientific and Technical Information of China (English)

    刘斌; 陈怡; 余成志; 沈征武

    2003-01-01

    The chemical selectivity of a novel active manganese compound [Mn2IVμ-O)3(TMTACN)2] (PF6)2 (1) in catalytic oxidation reactions depended on the structure of substrates and 1 was able to catalyze the oxidation of toluene into benzaldehyde and/or benzoic acid under very mild conditions. The following results were obtained: (1) The selectivity of the oxidation depended on the electronic density of double bonds. Reactivity was absent when strong electron-witherawing groups were conjugated with double bonds. (2) Allylic oxidation reactions mostly take place when double bond is present inside a ring system, whilst epoxiclarion reactions occur when the alkene moiety is part of linear chain. (3) In ring systems, the methylene group was more likely to be oxidized than the methyl group on ailylic position. As expected, the C--H bonds at the bridgeheads were unreactive.The secondary hydroxyl groups are more easily to be oxidized than the primary hydroxyl groups.

  10. Antioxidant and chemical properties of essential oil extracted from blend of selected spices

    Institute of Scientific and Technical Information of China (English)

    Ochuko Lucky Erukainure; Funmi Olabisi Kayode; Olubanke Adetutu Adeyoju; Sunday Oluwaseun Adenekan; Godfrey Asieba; Atinuke Ajayi; Mosebolatan Victoria Adegbola; Bolanle Basirat Sarumi

    2015-01-01

    Objective:To investigate the chemical properties of essential oil extracted from blends of selected Nigerian spices as well as its antioxidant protective potentials against free radicalin vitro. Methods: Essential oil was extracted from selected spices blend consisting ofMonodora myristica, Myristica fragrans, Tetrapleura tetraptera, andAframomum sceptrum using a Clevenger type apparatus. Oil obtained was subjected to phytochemical and gas chromatography-mass spectrometer analysis as well as analyzed for antioxidant activity which covers for 1,1-diphenyl-2 picrylhydrazyl, nitric oxide scavenging activities and reducing property. Results: Gas chromatography-mass spectrometer analysis revealed over 50 compoundfs withα-phellandrene being the most predominant compound (27.32%), which was followed by (-)-β-bourbonene (15.78%) and 5-(1-methylethyl)-α-phellandrene (11.80%). Phytochemical analysis showed high flavonoid content and a lower phenolic content. The oil showed a dose like dependent effect on the1-diphenyl-2 picrylhydrazyl and nitric oxide scavenging activities, these activities increased with increasing concentration. The same was also observed for the reducing power properties of the oil. Conclusions: The antioxidant activities exhibited by the essential oilin vitro signify its protective potential against free radicals. The chemical constituents,α-phellandrene in particular and the studied phytochemicals may be responsible for these effects. However,in vivo study is needed to further authenticate this potency.

  11. Selective removal technology using chemical etching and excimer assistance in precision recycle of color filter

    Institute of Scientific and Technical Information of China (English)

    Pai shan PA

    2011-01-01

    Color filters are produced using semiconductor production techniques although problems with Iow yield remain to be addressed. This study presents a new means of selective removal using excimer irradiation, chemical etching, or electrochemical machining on the fifth generation TFT LCDs. The selective removal of microstructure layers from the color filter surface of an optoelectronic flat panel display, as well as complete removal of the ITO thin-films, RGB layer, or resin black matrix (BM) layer from the substrate is possible. Individual defective film layers can be removed, or all films down to the Cr layer or bare glass can be completely eliminated. Experimental results demonstrate that defective ITO thin-films, RGB layers, or the resin BM layer can now be recycled with a great precision. When the ITO or RGB layer proves difficult to remove, excimer light can be used to help with removal. During this recycling process, the use of 225 nm excimer irradiation before chemical etching, or electrochemical machining, makes removal of stubborn film residues easy, effectively improving the quality of recycled color filters and reducing fabrication cost.

  12. Speciation of heavy metals in garden soils. Evidences from selective and sequential chemical leaching

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Zhongqi; Lee, Leda; Dayan, Sara; Grinshtein, Michael [Brooklyn College of The City Univ. of New York, Brooklyn, NY (United States). Environmental Sciences Analytical Cnter; Shaw, Richard [USDA-NRCS NYC Soil Survey, Staten Island, NY (United States)

    2011-06-15

    Purpose: Gardening (especially food growing) in urban areas is becoming popular, but urban soils are often very contaminated for historical reasons. There is lack of sufficient information as to the bioavailability of soil heavy metals to plants and human in urban environments. This study examines the relative leachability of Cr, Ni, As, Cd, Zn, and Pb for soils with varying characteristics. The speciation and mobility of these metals can be qualitatively inferred from the leaching experiments. The goal is to use the data to shed some light on their bioavailability to plant and human, as well as the basis for soil remediation. Materials and methods: Selective and sequential chemical leaching methods were both used to evaluate the speciation of Cr, Ni, As, Cd, Zn, and Pb in soil samples collected from New York City residential and community gardens. The sequential leaching experiment followed a standard BCR four-step procedure, while selective leaching involved seven different chemical extractants. Results and discussion: The results from selective and sequential leaching methods are consistent. In general, very little of the heavy metals were found in the easily soluble or exchangeable fractions. Larger fractions of Cd and Zn can be leached out than other metals. Lead appears predominantly in the organic or carbonate fractions, of which {proportional_to} 30-60% is in the easily soluble organic fraction. Most As cannot be leached out by any of the extractants used, but it could have been complicated by the ineffective dissolution of oxides by ammonium hydroxylamine. Ni and Cr were mostly in the residual fractions but some released in the oxidizable fractions. Therefore, the leachability of metals follow the order Cd/Zn > Pb > Ni/Cr. Conclusions: Despite of the controversy and inaccuracy surrounding chemical leaching methods for the speciation of metals, chemical leaching data provide important, general, and easy-to-access information on the mobility of heavy metals

  13. Selection of reference soils for chemicals testing in the European Community

    International Nuclear Information System (INIS)

    Based on an multivariate statistical evaluation of binary and metric data relating to the soil cover of the European Community five regionally representative reference soils (EURO-Soils) have been identified for chemicals testing in the EC. The soil material sampled at representative localities in Italy, Greece, Great Britain, France and Germany was treated and prepared according to OECD Test Guideline 106 and analysed in detail. The homogenised specimens were subject to an EC-wide ring test to evaluate the feasibility of the modified guideline and to validate the physical-chemical amenability of the reference soils for sorption tests. The results proved the validity of the soils selected for assessing the potential behaviour of new chemicals in soil on the basis of a comparative evaluation of the individual test results obtained. In the light of this parametric assessment potential test soils were subsequently identified in the individual EC Member States which correspond as far as possible to the above reference soils in terms of both taxonomy and sorption-relevant properties. (orig.). 164 refs., 30 tabs., 24 figs

  14. Selective chemical degradation of kerogen from Nenjiang Formation of the southern Songliao Basin

    Institute of Scientific and Technical Information of China (English)

    XIONG; YongQiang; WANG; YongQuan; WANG; YanMei

    2007-01-01

    A sequential selective chemical degradation has been performed on the kerogen from the Nenjiang Formation of the southern Songliao Basin by using a series of mild chemical degradations (alkaline hydrolysis, cleavage of ether-bonds and sulfur-bonds, and ruthenium tetroxide (RuO4) oxidation). Subsequently, the GC-MS analyses are carried out on different degradation products. The results show that chemical degradations can release a great number of GC/MS-determinable biomarkers from insoluble kerogen, such as, alkaline hydrolysis products mainly comprise n-alkanes, fatty acids and alkanols; thiophene compounds are predominantly ether-bound to kerogen matrix; the products from the cleavage of sulfur-sulfur and sulfur-carbon bonds in the kerogen include fatty acids, alkanols and some n-alkanes with high carbon numbers; RuO4 oxidation products are predominantly monocarboxylic acids and α,ω-dicarboxylic acids. The distributions of main degradation products indicate that organic matter in this kerogen is predominantly derived from algae and bacteria, and that small amounts of high plant-derived organic matter are possibly combined into kerogen matrix at the late stage by sulfur bonds and other means. This study will provide an important approach for further discussing sources of organic matter in source rocks and their depositional paleoenvironments.

  15. Comparative Assessment of the Physico-Chemical and Bacteriological Qualities of Selected Streams in Louisiana

    Directory of Open Access Journals (Sweden)

    Paul B. Tchounwou

    2005-04-01

    Full Text Available The objective of this research was to compare the chemical/physical parameters and bacterial qualities of selected surface water streams in Louisiana, including a natural stream (control and an animal waste related stream. Samples were collected and analyzed for fecal coliforms. Fecal coliforms isolated from these samples were identified to the species level. Chemical analysis was performed following standard test protocols (LaMotte 2002. An analysis of biological oxygen demand (BOD, chemical oxygen demand (COD, total organic carbon (TOC, total dissolved solids (TDS, conductivity, pH, temperature, ammonia nitrogen, nitrate nitrogen, iron, copper, phosphate, potassium, sulfate, turbidity, zinc and bacterial levels was performed following standard test protocols as presented in Standard Methods for the Examination of Water and Wastewater [9]. Results of the comparisons of the various surface water streams showed that phosphate levels, according to Mitchell and Stapp, were considered good for Lake Claiborne (control and Bayou Dorcheat. The levels were found to be .001 mg/L and .007 mg/L respectively. Other streams associated with animal waste, had higher phosphate levels of 2.07 mg/L and 2.78 mg/L, respectively. Conductivity and total dissolved solids (TDS levels were the lowest in Lake Claiborne and highest in the Hill Farm Research Station stream. It can be concluded from the data that some bacterial levels and various nutrient levels can be affected in water resources due to non-point source pollution. Many of these levels will remain unaffected.

  16. Personnel selection, training and certification in the U.S. Army Chemical Demilitarization Program

    International Nuclear Information System (INIS)

    This paper describes the major steps taken to assure the US Army, as well as state and federal officials, that the individuals slated to operate and maintain future chemical disposal facilities will be carefully screened, well-trained and certified to safely carry out their tasks. Careful personnel screening, total plant staff training, individual qualification and team certification protect plant personnel, the public and the environment. Experience has shown that the care taken in adequate screening of job applicants for highly technical and potentially hazardous work results in fewer incidents or accidents on the job. To ensure that each individual selected receives appropriate and necessary training, the US Army has constructed a five-building Chemical Demilitarization Training Facility (CDTF), which may set future standards in the hazardous waste disposal industry. The training center contains automated chemical agent material handling equipment, multiple furnace and pollution abatement system dynamic control room simulations and five laboratories for training agent analysis and monitoring personnel. A qualification and certification program marks the end of the training and verifies that plant employees are fully prepared to operate the disposal facility safely

  17. Selective wet chemical etching of metallic thin films designed by laser interference metallurgy (LIMET)

    Science.gov (United States)

    Catrin, Rodolphe; Gachot, Carsten; Marchand, Günter; Schmid, Ulrich; Mücklich, Frank

    2009-05-01

    The physical and chemical behaviour of materials is strongly correlated with their microstructure. Therefore, much effort is invested in the advanced microstructural design of metallic thin films. Laser Interference Metallurgy (LIMET) is used to locally tune the grain architecture of metallic thin films from the nanoto the microscale. This means a defined size and orientation of the grains with lateral periodicity, by interfering on the sample surface two or more laser beams of a high power nanosecond pulsed Nd:YAG laser. This technique enables the local nucleation and crystallization of amorphous or nanocrystalline metallic thin films, thus combining nano- and microcrystalline regions ordered in periodic line- or lattice-like arrangements in a composite architecture. After having locally modified the microstructure of e-beam evaporated Pt and Au thin films by laser irradiation a wet chemical etching procedure was induced in hot aqua regia. Doing so, a selective etching is achieved without using conventional lithography. Due to the laser-induced recrystallization in periodic structures, these microcrystalline zones of specific oriented grains show a higher resistance against the wet chemical etchant than the as-deposited, nanocrystalline areas, which are completely removed down to the substrate. Therefore, this procedure may have the potential to be an alternative, low cost approach to conventional lithographic techniques and provides a novel method for a straight-forward patterning of metallic thin films.

  18. Reactive chromophores for sensitive and selective detection of chemical warfare agents

    Science.gov (United States)

    Frye-Mason, Greg; Leuschen, Martin; la Grone, Marcus; Wald, Lara; Aker, Craig; Dock, Matt; Hancock, Lawrence F.; Fagan, Steve; Paul, Kateri

    2004-08-01

    A new sensor for highly toxic species including chemical warfare (CW) agents has been developed. This sensor is based on a unique CW indicating chromophore (CWIC) developed by Professor Tim Swager at MIT. The CWIC was designed to be sensitive to the reactivity that makes these chemicals so toxic. Since it requires the reactivity of the agent to be detected, the CWIC technology has shown remarkable selectivity for nerve agent surrogates and some other highly toxic species, thereby demonstrating the potential to provide low false alarm rate detection. Since the chromophore has mini-mal fluorescence prior to reaction with an electrophilic and toxic chemical, the sensor acts in a dark field fluorescence mode. This provides the sensor with exceptional sensitivity and a potential to detect priority analytes well below levels detected by current hand held sensors. Finally, it is based on a simple optical detection scheme that enables small and rugged sensors to be developed and produced at a low enough cost so they can be widely utilized.

  19. Separation of selected stable isotopes by liquid-phase thermal diffusion and by chemical exchange

    International Nuclear Information System (INIS)

    Useful applications of enriched stable nuclides are unduly restricted by high cost and limited availability. Recent research on liquid phase thermal diffusion (LTD) has resulted in practical processes for separating 34S, 35Cl, and 37Cl in significant quantities (100 to 500 g/yr) at costs much lower than those associated with the electromagnetic (Calutron) process. The separation of the isotopes of bromine by LTD is now in progress and 79Br is being produced in relatively simple equivalent at a rate on the order of 0.5 g/day. The results of recent measurements show that the isotopes of Zn can be separated by LTD of zinc alkyls. The isotopes of calcium can be separated by LTD and by chemical exchange. The LTD process is based on the use of aqueous Ca(NO3)2 as a working fluid. The chemical exchange method involves isotopically selective exchange between an aqueous phase containing a calcium salt and an organic phase containing calcium in the form of a complex with a macrocyclic ligand. The LTD method is suitable for high enrichments at low through-puts; whereas, the chemical exchange techniques is appropriate for lower enrichments at much higher production rates. Current research is directed toward reducing these concepts to practical processes

  20. Chemically Functionalized Arrays Comprising Micro and Nano-Electro-Mechanizal Systems for Reliable and Selective Characterization of Tank Waste

    Energy Technology Data Exchange (ETDEWEB)

    Michael J. Sepaniak

    2008-10-08

    Innovative technology of sensory and selective chemical monitoring of hazardous wastes present in storage tanks are of continued importance to the environment. This multifaceted research program exploits the unique characteristics of micro and nano-fabricated cantilever-based, micro-electro-mechanical systems (MEMES) and nano-electro-mechanical systems (NEMS) in chemical sensing.

  1. A novel reaction-based colorimetric and ratiometric fluorescent sensor for cyanide anion with a large emission shift and high selectivity.

    Science.gov (United States)

    Wang, Shaodan; Fei, Xiaoliang; Guo, Jing; Yang, Qingbiao; Li, Yaoxian; Song, Yan

    2016-02-01

    A hybrid carbazole-hemicyanine dye (Cac) has been developed as a novel colorimetric and ratiometric fluorescent sensor for cyanide detection. Upon treatment with cyanide, Cac displayed a remarkable fluorescence ratiometric response, with the emission wavelength displaying a very large emission shift (214 nm). The detection of cyanide was performed via the nucleophilic addition of cyanide anion to the indolium group of the sensor, which resulted in the blocking of the intramolecular charge transfer (ICT) process in the sensor, inducing a ratiometric fluorescence change and simultaneously an obvious color change. Furthermore, competitive anions did not showed any significant changes both in color and emission intensity ratio (I381/I595), indicating the high selectivity of the sensor to CN(-). PMID:26653444

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

    Science.gov (United States)

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

    2016-01-01

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

  3. Selective detection of heavy metal ions by self assembled chemical field effect transistors

    Energy Technology Data Exchange (ETDEWEB)

    Ruan, Hang, E-mail: hruan@nanosonic.com; Kang, Yuhong; Gladwin, Elizabeth; Claus, Richard O. [NanoSonic, Inc., 158 Wheatland Drive, Pembroke, Virginia 24136 (United States)

    2015-04-20

    Multiple layer-by-layer sensor material modifications were designed and implemented to achieve selectivity of semiconductor based chemical field effect transistors (ChemFETs) to particular heavy metal ions. The ChemFET sensors were fabricated and modified in three ways, with the intent to initially target first mercury and lead ions and then chromium ions, respectively. Sensor characterization was performed with the gate regions of the sensor elements exposed to different concentrations of target heavy metal ion solutions. A minimum detection level in the range of 0.1 ppm and a 10%–90% response time of less than 10 s were demonstrated. By combining layer-by-layer gold nanoparticles and lead ionophores, a sensor is produced that is sensitive and selective not only to chromium but also to Cr{sup 3+} and Cr{sup 6+}. This result supports the claim that high selectivity can be achieved by designing self-assembled bonding for lead, arsenic, chromium, cesium, mercury, and cadmium.

  4. Selective detection of heavy metal ions by self assembled chemical field effect transistors

    International Nuclear Information System (INIS)

    Multiple layer-by-layer sensor material modifications were designed and implemented to achieve selectivity of semiconductor based chemical field effect transistors (ChemFETs) to particular heavy metal ions. The ChemFET sensors were fabricated and modified in three ways, with the intent to initially target first mercury and lead ions and then chromium ions, respectively. Sensor characterization was performed with the gate regions of the sensor elements exposed to different concentrations of target heavy metal ion solutions. A minimum detection level in the range of 0.1 ppm and a 10%–90% response time of less than 10 s were demonstrated. By combining layer-by-layer gold nanoparticles and lead ionophores, a sensor is produced that is sensitive and selective not only to chromium but also to Cr3+ and Cr6+. This result supports the claim that high selectivity can be achieved by designing self-assembled bonding for lead, arsenic, chromium, cesium, mercury, and cadmium

  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. PMID:26845204

  6. Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

    Science.gov (United States)

    Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.

    2005-01-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221

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

    Science.gov (United States)

    Komatsu, Takanori; Kikuchi, Jun

    2013-09-17

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

  8. Hepatic steatosis assessment with {sup 1}H-spectroscopy and chemical shift imaging at 3.0 T before hepatic surgery: Reliable enough for making clinical decisions?

    Energy Technology Data Exchange (ETDEWEB)

    Koelblinger, Claus, E-mail: claus.koelblinger@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Krssak, Martin, E-mail: martin.krssak@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Maresch, Judith, E-mail: judith.maresch@meduniwien.ac.at [Department of Pathology, Medical University of Vienna (Austria); Wrba, Fritz, E-mail: fritz.wrba@meduniwien.ac.at [Department of Pathology, Medical University of Vienna (Austria); Kaczirek, Klaus, E-mail: klaus.kaczirek@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Gruenberger, Thomas, E-mail: thomas.gruenberger@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Tamandl, Dietmar, E-mail: dietmar.tamandl@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Ba-Ssalamah, Ahmed, E-mail: ahmed.ba-ssalamah@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Berger-Kulemann, Vanessa, E-mail: vanessa.berger-kulemann@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Weber, Michael, E-mail: michael.weber@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Schima, Wolfgang, E-mail: wolfgang.schima@khgh.at [Department of Radiology, KH Goettlicher Heiland and Herz-Jesu Krankenhaus, Dornbacher Strasse 20-28, 1170 Vienna (Austria)

    2012-11-15

    Purpose: To compare the accuracy of liver fat quantification using chemical shift imaging (CSI) and H1 MR-spectroscopy (MRS) at 3.0 T in patients undergoing liver resection. Methods: Totally 35 patients were included in this prospective IRB approved study. The histopathologically assessed liver fat was compared to the hepatic fat fractions calculated with CSI (with and without spleen correction) and MRS. Spearman's rank correlation and Fisher z-test were used for correlation analysis. Sensitivity and specificity regarding the detection of marked steatosis were calculated for the different modalities and compared using the McNemar test. Results: MRS (r = .85) and CSI with spleen correction (r = .85) showed a significantly better correlation (p = .03) with histology compared to CSI without spleen correction (r = .67). Sensitivity and specificity for the detection of marked steatosis was 100% (12/12) and 87% (20/23) for MRS and 92% (11/12) and 83% (19/23) for CSI with spleen correction (p > .12). Conclusion: For the assessment of hepatic steatosis both CSI with spleen correction and MRS at 3.0 T, show a good correlation with histology. CSI without spleen correction should not be used. Sensitivity and specificity for the detection of marked steatosis are high with both modalities. However, results that are scattered around the cut-off values are not reliable enough for clinical decisions.

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

    International Nuclear Information System (INIS)

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

  10. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-06-15

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

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

    Science.gov (United States)

    Pandey, Manoj Kumar; Nishiyama, Yusuke

    2015-12-01

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

  13. Shifting Attention

    Science.gov (United States)

    Ingram, Jenni

    2014-01-01

    This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…

  14. Selective growth of graphene in layer-by-layer via chemical vapor deposition

    Science.gov (United States)

    Park, Jaehyun; An, Hyosub; Choi, Dong-Chul; Hussain, Sajjad; Song, Wooseok; An, Ki-Seok; Lee, Won-Jun; Lee, Naesung; Lee, Wan-Gyu; Jung, Jongwan

    2016-07-01

    Selective and precise control of the layer number of graphene remains a critical issue for the practical applications of graphene. First, it is highly challenging to grow a continuous and uniform few-layer graphene since once the monolayer graphene fully covers a copper (Cu) surface, the growth of the second layer stops, resulting in mostly nonhomogeneous films. Second, from the selective adlayer growth point of view, there is no clear pathway for achieving this. We have developed the selective growth of a graphene adlayer in layer-by-layer via chemical vapor deposition (CVD) which makes it possible to stack graphene on a specific position. The key idea is to deposit a thin Cu layer (~40 nm thick) on pre-grown monolayer graphene and to apply additional growth. The thin Cu atop the graphene/Cu substrate acts as a catalyst to decompose methane (CH4) gas during the additional growth. The adlayer is grown selectively on the pre-grown graphene, and the thin Cu is removed through evaporation during CVD, eventually forming large-area and uniform double layer graphene. With this technology, highly uniform graphene films with precise thicknesses of 1 to 5 layers and graphene check patterns with 1 to 3 layers were successfully demonstrated. This method provides precise LBL growth for a uniform graphene film and a technique for the design of new graphene devices.Selective and precise control of the layer number of graphene remains a critical issue for the practical applications of graphene. First, it is highly challenging to grow a continuous and uniform few-layer graphene since once the monolayer graphene fully covers a copper (Cu) surface, the growth of the second layer stops, resulting in mostly nonhomogeneous films. Second, from the selective adlayer growth point of view, there is no clear pathway for achieving this. We have developed the selective growth of a graphene adlayer in layer-by-layer via chemical vapor deposition (CVD) which makes it possible to stack graphene

  15. Tribochemical interaction between nanoparticles and surfaces of selective layer during chemical mechanical polishing

    International Nuclear Information System (INIS)

    Nanoparticles have been widely used in polish slurries such as those in the chemical mechanical polishing (CMP) process. For understanding the mechanisms of CMP, an atomic force microscope (AFM) is used to characterize polished surfaces of selective layers, after a set of polishing experiments. To optimize the CMP polishing process, one needs to get information on the interaction between the nano-abrasive slurry nanoparticles and the surface of selective layer being polished. The slurry used in CMP process of the solid surfaces is slurry with large nanoparticle size colloidal silica sol nano-abrasives. Silica sol nano-abrasives with large nanoparticle are prepared and characterized by transmission electron microscopy, particles colloidal size, and Zeta potential in this paper. The movement of nanoparticles in liquid and the interaction between nanoparticles and solid surfaces coating with selective layer are very important to obtain an atomic alloy smooth surface in the CMP process. We investigate the nanoparticle adhesion and removal processes during CMP and post-CMP cleaning. The mechanical interaction between nanoparticles and the wafer surface was studied using a microcontact wear model. This model considers the nanoparticle effects between the polishing interfaces during load balancing. Experimental results on polishing and cleaning are compared with numerical analysis. This paper suggests that during post-CMP cleaning, a combined effort in chemical and mechanical interaction (tribochemical interactions) would be effective in removal of small nanoparticles during cleaning. For large nanoparticles, more mechanical forces would be more effective. CMP results show that the removal rate has been improved to 367 nm/min and root mean square (RMS) of roughness has been reduced from 4.4 to 0.80 nm. Also, the results show that the silica sol nano-abrasives about 100 nm are of higher stability (Zeta potential is −65 mV) and narrow distribution of nanoparticle

  16. Long-term effects of soil management practices on selected indicators of chemical soil quality

    Directory of Open Access Journals (Sweden)

    Alicja Pecio

    2016-06-01

    Full Text Available The study was conducted in scope of Catch-C project “Compatibility of agricultural management practices and types of farming in the EU to enhance climate change mitigation and soil health” (7FP, realized in 2012–2014 by the consortium of partners from 10 European countries (http://www.catch-c.eu. This work reports the effects of soil management practices – under different soil and climatic conditions – on the selected soil chemical quality indicators, based on the analysis of data extracted from literature on long term experiments (LTEs in Europe, as well as from LTEs held by the Catch-C consortium partners. The dataset related to soil chemical quality indicators consisted of 1044 records and referred to 59 long-term trials. The following indicators of chemical soil quality were analyzed: pH, N total content, N total stock, C:N ratio, N mineral content, P and K availability. They are the most frequently used indicators in the European literature on long-term experiments collected in the Catch-C project database. Soil organic carbon, however, the most important indicator was not presented here, due to it was covered by a separate study on indicators for climate change mitigation. The indicators were analyzed using their response ratio (RR to a management practice. For a given treatment (management practice, this ratio was calculated as the quotient between the indicator value obtained in the treatment, and the indicator value in the reference treatment. The examples were: rotation (with cereals, with legume crops, with tuber or root crops, with grassland vs. adequate monoculture, catch/cover crops vs. no catch/cover crops, no-tillage and no-inversion tillage vs. conventional tillage, mineral fertilization vs. no fertilization, organic fertilization (compost, farmyard manure, slurry vs. mineral fertilization at the same available nitrogen input, crop residue incorporation vs. removal. All tested practices influenced soil chemical quality

  17. Stirring competes with chemical induction in chiral selection of Langmuir monolayer domains

    Directory of Open Access Journals (Sweden)

    Petit-Garrido Nuria

    2013-08-01

    Full Text Available Chirality, the absence of mirror symmetry, can be equally invoked in relation to physical forces and chemical induction processes, yet a competition between these two types of influences is rarely reported. Here, we employ Langmuir monolayers of azobenzene surfactants as a prototypical self-assembled two-dimensional system in which chiral selection is controlled by the combined independent action of a chiral dopant and vortical stirring. The two effects can be arbitrarily coupled, either constructively or destructively, leading to a situation of perfect compensation. The induced enantiomorphic excess is measured in terms of the statistical imbalance of an ensemble of sub-millimeter monolayer domains, where achiral molecules self-assemble with a well-defined orientational chirality, which is unambiguously resolved using Brewster angle microscopy.

  18. Effect of selected spices on chemical and sensory markers in fortified rye-buckwheat cakes.

    Science.gov (United States)

    Przygodzka, Małgorzata; Zieliński, Henryk; Ciesarová, Zuzana; Kukurová, Kristina; Lamparski, Grzegorz

    2016-07-01

    The aim of this study was to find out the effect of selected spices on chemical and sensorial markers in cakes formulated on rye and light buckwheat flour fortified with spices. Among collection of spices, rye-buckwheat cakes fortified individually with cloves, nutmeg, allspice, cinnamon, vanilla, and spice mix revealed the highest sensory characteristics and overall quality. Cakes fortified with cloves, allspice, and spice mix showed the highest antioxidant capacity, total phenolics, rutin, and almost threefold higher available lysine contents. The reduced furosine content as well as free and total fluorescent intermediatory compounds were observed as compared to nonfortified cakes. The FAST index was significantly lowered in all cakes enriched with spices, especially with cloves, allspice, and mix. In contrast, browning index increased in compare to cakes without spices. It can be suggested that clove, allspice, vanilla, and spice mix should be used for production of safety and good quality cakes. PMID:27386114

  19. Chemical composition and antibacterial activity of selected essential oils and some of their main compounds.

    Science.gov (United States)

    Wanner, Juergen; Schmidt, Erich; Bail, Stefanie; Jirovetz, Leopold; Buchbauer, Gerhard; Gochev, Velizar; Girova, Tanya; Atanasova, Teodora; Stoyanova, Albena

    2010-09-01

    The chemical composition of essential oils of cabreuva (Myrocarpus fastigiatus Allemao, Fabaceae) from Brazil, cedarwood (Juniperus ashei, Cupressaceae) from Texas, Juniper berries (Juniperus communis L., Cupressaceae) and myrrh (Commiphora myrrha (Nees) Engl., Burseraceae) were analyzed using GC/FID and GC/MS. The antimicrobial activity of these essential oils and some of their main compounds were tested against eleven different strains of Gram-positive and Gram-negative bacteria by using agar diffusion and agar serial dilution methods. Animal and plant pathogens, food poisoning and spoilage bacteria were selected. The volatile oils exhibited considerable inhibitory effects against all tested organisms, except Pseudomonas, using both test methods. Higher activity was observed against Gram-positive strains in comparison with Gram-negative bacteria. Cabreuva oil from Brazil showed similar results, but in comparison with the other oils tested, only when higher concentrations of oil were used. PMID:20922991

  20. Comparison of Selected Methods for Individual Decontamination of Chemical Warfare Agents

    Directory of Open Access Journals (Sweden)

    Tomas Capoun

    2014-06-01

    Full Text Available This study addresses the individual decontamination of chemical warfare agents (CWA and other hazardous substances. The individual decontamination applies to contaminated body surfaces, protective clothing and objects immediately after contamination, performed individually or by mutual assistance using prescribed or improvised devices. The article evaluates the importance of individual decontamination, security level for Fire and Rescue Service Units of the Czech Republic (FRS CR and demonstrates some of the devices. The decontamination efficiency of selected methods (sorbent, glove and sponge, two-chamber foam device and wiping with alcohol was evaluated for protective clothing and painted steel plate contaminated with O-ethyl-S-(diisopropylaminoethyl-methylthiophosphonate (VX, sulfur mustard, o-cresol and acrylonitrile. The methods were assessed from an economic point of view and with regard to specific user parameters, such as the decontamination of surfaces or materials with poor accessibility and vertical surfaces, the need for a water rinse as well as toxic waste and its disposal.

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

    Institute of Scientific and Technical Information of China (English)

    许波; 李浩然; 王从敏; 许映杰; 韩世钧

    2005-01-01

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

  2. Determination of the Tautomeric Equilibria of Pyridoyl Benzoyl -Diketones in the Liquid and Solid State through the use of Deuterium Isotope Effects on 1H and 13C NMR Chemical Shifts and Spin Coupling Constants

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Borisov, Eugeny V.; Lindon, John C.

    2015-01-01

    The tautomeric equilibria for 2-pyridoyl-, 3-pyridoyl-, and 4-pyridoyl-benzoyl methane have been investigated using deuterium isotope effects on 1H and 13C chemical shifts both in the liquid and the solid state. Equilibria are established both in the liquid and the solid state. In addition, in th...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2000-07-01

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

  4. Optimization of chemical structure of Schottky-type selection diode for crossbar resistive memory.

    Science.gov (United States)

    Kim, Gun Hwan; Lee, Jong Ho; Jeon, Woojin; Song, Seul Ji; Seok, Jun Yeong; Yoon, Jung Ho; Yoon, Kyung Jean; Park, Tae Joo; Hwang, Cheol Seong

    2012-10-24

    The electrical performances of Pt/TiO(2)/Ti/Pt stacked Schottky-type diode (SD) was systematically examined, and this performance is dependent on the chemical structures of the each layer and their interfaces. The Ti layers containing a tolerable amount of oxygen showed metallic electrical conduction characteristics, which was confirmed by sheet resistance measurement with elevating the temperature, transmission line measurement (TLM), and Auger electron spectroscopy (AES) analysis. However, the chemical structure of SD stack and resulting electrical properties were crucially affected by the dissolved oxygen concentration in the Ti layers. The lower oxidation potential of the Ti layer with initially higher oxygen concentration suppressed the oxygen deficiency of the overlying TiO(2) layer induced by consumption of the oxygen from TiO(2) layer. This structure results in the lower reverse current of SDs without significant degradation of forward-state current. Conductive atomic force microscopy (CAFM) analysis showed the current conduction through the local conduction paths in the presented SDs, which guarantees a sufficient forward-current density as a selection device for highly integrated crossbar array resistive memory. PMID:22999222

  5. Comparison of Selected Soil Chemical Properties of Two Different Mangrove Forests in Sarawak

    Directory of Open Access Journals (Sweden)

    Empi Rambok

    2010-01-01

    Full Text Available Problem statement: Despite few studies of forest health and environmental conditions of mangrove forest in Sarawak, the data was not sufficient to facilitate baseline data and direct comparison of mangrove forest health obtained for different location of mangrove forest in Sarawak. On this regard, determination of contemporary mangrove soil condition was essential to addressing mangrove forest for forest health, carbon storage and environmental balance. The study attempts to obtained preliminary database of mangrove forest soil chemical properties and to compare the forest health from two different mangrove forest locations. Approach: Mangrove soil samples were taken from Miri and Limbang Division of Sarawak at 0-30 cm depth. Selected soil chemical properties were determined and data obtained were analyzed using Statistical Analysis System (SAS Version 9.2. Results: The soil acidity, total N, total P, CEC and humic acid of both locations were significantly different while in terms of total carbon and organic matter were similar. Conclusion: Regional diversity has significant effects the soil acidity, total N, total P, CEC and yield of the study areas. Data obtained can be useful for further study of carbon stock and nutrient content.

  6. Improving N(6)-methyladenosine site prediction with heuristic selection of nucleotide physical-chemical properties.

    Science.gov (United States)

    Zhang, Ming; Sun, Jia-Wei; Liu, Zi; Ren, Ming-Wu; Shen, Hong-Bin; Yu, Dong-Jun

    2016-09-01

    N(6)-methyladenosine (m(6)A) is one of the most common and abundant post-transcriptional RNA modifications found in viruses and most eukaryotes. m(6)A plays an essential role in many vital biological processes to regulate gene expression. Because of its widespread distribution across the genomes, the identification of m(6)A sites from RNA sequences is of significant importance for better understanding the regulatory mechanism of m(6)A. Although progress has been achieved in m(6)A site prediction, challenges remain. This article aims to further improve the performance of m(6)A site prediction by introducing a new heuristic nucleotide physical-chemical property selection (HPCS) algorithm. The proposed HPCS algorithm can effectively extract an optimized subset of nucleotide physical-chemical properties under the prescribed feature representation for encoding an RNA sequence into a feature vector. We demonstrate the efficacy of the proposed HPCS algorithm under different feature representations, including pseudo dinucleotide composition (PseDNC), auto-covariance (AC), and cross-covariance (CC). Based on the proposed HPCS algorithm, we implemented an m(6)A site predictor, called M6A-HPCS, which is freely available at http://csbio.njust.edu.cn/bioinf/M6A-HPCS. Experimental results over rigorous jackknife tests on benchmark datasets demonstrated that the proposed M6A-HPCS achieves higher success rates and outperforms existing state-of-the-art sequence-based m(6)A site predictors. PMID:27293216

  7. Use of toxicokinetics to support chemical evaluation: Informing high dose selection and study interpretation.

    Science.gov (United States)

    Creton, Stuart; Saghir, Shakil A; Bartels, Michael J; Billington, Richard; Bus, James S; Davies, Will; Dent, Matthew P; Hawksworth, Gabrielle M; Parry, Simon; Travis, Kim Z

    2012-03-01

    Toxicokinetic (TK) information can substantially enhance the value of the data generated from toxicity testing, and is an integral part of pharmaceutical safety assessment. It is less widely used in the chemical, agrochemical and consumer products industries, but recognition of its value is growing, as reflected by increased reference to the use of TK information in new and draft OECD test guidelines. To help promote increased consideration of the important role TK can play in chemical risk assessment, we have gathered practical examples from the peer-reviewed literature, as well as in-house industry data, that highlight opportunities for the use of TK in the selection of dose levels. Use of TK can help to ensure studies are designed to be of most relevance to assessing potential risk in humans, and avoid the use of excessively high doses that could result in unnecessary suffering in experimental animals. Greater emphasis on the potential contribution of TK in guiding study design and interpretation should be incorporated in regulatory data requirements and associated guidance. PMID:22198561

  8. Chemical tagging of the Ursa Major moving group: A northern selection of FGK stars

    CERN Document Server

    Tabernero, H M; Hernandez, J I Gonzalez; Eiff, M Ammler-von

    2014-01-01

    Stellar kinematic groups are kinematical coherent groups of stars which might share a common origin.These groups spread through the Galaxy over time due to tidal effects caused by Galactic rotation and disc heating.However, the chemical information survives these processes. The information provided by the analysis of chemical elements can reveal the origin of these kinematic groups. Here we investigate the origin of the stars that belong to the Ursa Major Moving Group. We present high-resolution spectroscopic observations obtained from three different spectrographs of kinematically selected FGK stars of the Ursa Major moving group. Stellar atmospheric parameters (Teff, log(g), xi, and [Fe/H]) were determined using our own automatic code (StePar) which makes use of the sensitivity of iron equivalent widths measured in the spectra. We critically compare the StePar results with other methods (Teff values derived using the infrared flux method and log(g) values based on Hipparcos parallaxes). We derived the chemi...

  9. Challenges and trends in the determination of selected chemical contaminants and allergens in food.

    Science.gov (United States)

    Krska, Rudolf; Becalski, Adam; Braekevelt, Eric; Koerner, Terry; Cao, Xu-Liang; Dabeka, Robert; Godefroy, Samuel; Lau, Ben; Moisey, John; Rawn, Dorothea F K; Scott, Peter M; Wang, Zhongwen; Forsyth, Don

    2012-01-01

    This article covers challenges and trends in the determination of some major food chemical contaminants and allergens, which-among others-are being monitored by Health Canada's Food Directorate and for which background levels in food and human exposure are being analyzed and calculated. Eleven different contaminants/contaminant groups and allergens have been selected for detailed discussion in this paper. They occur in foods as a result of: use as a food additive or ingredient; processing-induced reactions; food packaging migration; deliberate adulteration; and/or presence as a chemical contaminant or natural toxin in the environment. Examples include acrylamide as a food-processing-induced contaminant, bisphenol A as a food packaging-derived chemical, melamine and related compounds as food adulterants and persistent organic pollutants, and perchlorate as an environmental contaminant. Ochratoxin A, fumonisins, and paralytic shellfish poisoning toxins are examples of naturally occurring toxins whereas sulfites, peanuts, and milk exemplify common allergenic food additives/ingredients. To deal with the increasing number of sample matrices and analytes of interest, two analytical approaches have become increasingly prevalent. The first has been the development of rapid screening methods for a variety of analytes based on immunochemical techniques, utilizing ELISA or surface plasmon resonance technology. The second is the development of highly sophisticated multi-analyte methods based on liquid chromatography coupled with multiple-stage mass spectrometry for identification and simultaneous quantification of a wide range of contaminants, often with much less requirement for tedious cleanup procedures. Whereas rapid screening methods enable testing of large numbers of samples, the multi analyte mass spectrometric methods enable full quantification with confirmation of the analytes of interest. Both approaches are useful when gathering surveillance data to determine

  10. Chemically selective polymer substrate based direct isotope dilution alpha spectrometry of Pu

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Sumana, E-mail: sumana@barc.gov.in [Fuel Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085 (India); Pandey, Ashok K. [Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085 (India); Shah, R.V. [Fuel Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085 (India); Aggarwal, S.K., E-mail: skaggr2002@gmail.com [Fuel Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085 (India)

    2015-06-09

    Highlights: • Membrane based alpha spectrometry was developed for plutonium. • A thin bifunctional layer was grafted on a porous membrane. • UV method used for grafting is simple and highly reproducible. • This method does not require preconcentration and source preparation steps. • Isotope dilution was used to enhance analytical performance. - Abstract: Quantification of actinides in the complex environmental, biological, process and waste streams samples requires multiple steps like selective preconcentration and matrix elimination, solid source preparations generally by evaporation or electrodeposition, and finally alpha spectrometry. To minimize the sample manipulation steps, a membrane based isotope dilution alpha spectrometry method was developed for the determination of plutonium concentrations in the complex aqueous solutions. The advantages of this method are that it is Pu(IV) selective at 3 M HNO{sub 3}, high preconcentration factor can be achieved, and obviates the need of solid source preparation. For this, a thin phosphate–sulfate bifunctional polymer layer was anchored on the surface of microporous poly(ethersulfone) membrane by UV induced surface grafting. The thickness of the bifunctional layer on one surface of the poly(ethersulfone) membrane was optimized. The thickness, physical and chemical structures of the bifunctional layer were studied by secondary ionization mass spectrometry (SIMS), scanning electron microscopy (SEM) and SEM–EDS (energy-dispersive spectroscopy). The optimized membrane was used for preconcentration of Pu(IV) from aqueous solutions having 3–4 M HNO{sub 3}, followed by direct quantification of the preconcentrated Pu(IV) by isotope dilution alpha spectrometry using {sup 238}Pu spike. The chemical recovery efficiency of Pu(IV) was found to be 86 ± 3% below Pu(IV) loading capacity (1.08 μg in 2 × 1 cm{sup 2}) of the membrane sample. The experiments with single representative actinides indicated that Am

  11. Chemically selective polymer substrate based direct isotope dilution alpha spectrometry of Pu

    International Nuclear Information System (INIS)

    Highlights: • Membrane based alpha spectrometry was developed for plutonium. • A thin bifunctional layer was grafted on a porous membrane. • UV method used for grafting is simple and highly reproducible. • This method does not require preconcentration and source preparation steps. • Isotope dilution was used to enhance analytical performance. - Abstract: Quantification of actinides in the complex environmental, biological, process and waste streams samples requires multiple steps like selective preconcentration and matrix elimination, solid source preparations generally by evaporation or electrodeposition, and finally alpha spectrometry. To minimize the sample manipulation steps, a membrane based isotope dilution alpha spectrometry method was developed for the determination of plutonium concentrations in the complex aqueous solutions. The advantages of this method are that it is Pu(IV) selective at 3 M HNO3, high preconcentration factor can be achieved, and obviates the need of solid source preparation. For this, a thin phosphate–sulfate bifunctional polymer layer was anchored on the surface of microporous poly(ethersulfone) membrane by UV induced surface grafting. The thickness of the bifunctional layer on one surface of the poly(ethersulfone) membrane was optimized. The thickness, physical and chemical structures of the bifunctional layer were studied by secondary ionization mass spectrometry (SIMS), scanning electron microscopy (SEM) and SEM–EDS (energy-dispersive spectroscopy). The optimized membrane was used for preconcentration of Pu(IV) from aqueous solutions having 3–4 M HNO3, followed by direct quantification of the preconcentrated Pu(IV) by isotope dilution alpha spectrometry using 238Pu spike. The chemical recovery efficiency of Pu(IV) was found to be 86 ± 3% below Pu(IV) loading capacity (1.08 μg in 2 × 1 cm2) of the membrane sample. The experiments with single representative actinides indicated that Am(III) did not sorb to

  12. Structural Plasticity of Malaria Dihydroorotate Dehydrogenase Allows Selective Binding of Diverse Chemical Scaffolds

    International Nuclear Information System (INIS)

    Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.

  13. Phase diagram of selectively cross-linked block copolymers shows chemically microstructured gel

    Science.gov (United States)

    von der Heydt, Alice; Zippelius, Annette

    2015-02-01

    We study analytically the intricate phase behavior of cross-linked AB diblock copolymer melts, which can undergo two main phase transitions due to quenched random constraints. Gelation, i.e., spatially random localisation of polymers forming a system-spanning cluster, is driven by increasing the number parameter μ of irreversible, type-selective cross-links between random pairs of A blocks. Self-assembly into a periodic pattern of A/B-rich microdomains (microphase separation) is controlled by the AB incompatibility χ inversely proportional to temperature. Our model aims to capture the system's essential microscopic features, including an ensemble of random networks that reflects spatial correlations at the instant of cross-linking. We identify suitable order parameters and derive a free-energy functional in the spirit of Landau theory that allows us to trace a phase diagram in the plane of μ and χ. Selective cross-links promote microphase separation at higher critical temperatures than in uncross-linked diblock copolymer melts. Microphase separation in the liquid state facilitates gelation, giving rise to a novel gel state whose chemical composition density mirrors the periodic AB pattern.

  14. CHEMICALLY FABRICATED SILVER NANOPARTICLES ENHANCES THE ACTIVITY OF ANTIBIOTICS AGAINST SELECTED HUMAN BACTERIAL PATHOGENS

    Directory of Open Access Journals (Sweden)

    S. Thangapandiyan and P. Prema*

    2012-05-01

    Full Text Available Due to the outbreak of infectious diseases caused by different pathogenic bacteria and the development of antibiotic resistance, the pharmaceutical companies and the researchers are now searching for new unconventional antibacterial agents. Nanotechnology represents a modern and innovative approach to develop new formulations based on metallic nanoparticles with antimicrobial properties. The potential bioactivity of chemically fabricated silver nanoparticles has been extensively studied. However, the antibacterial activity of silver nanoparticles individually or in combination with different antibiotics has not been demonstrated. In the present investigations, the effect of silver nanoparticles on the antibacterial activity of different antibiotics was evaluated against selected human bacterial pathogens such as Staphylococcus aureus, Streptococcus epidermis, Escherichia coli, Pseudomonas aeruginosa, and Bacillus cereus by disc diffusion method. In the presence of sub - inhibitory concentration of silver nanoparticles (100µL/disc, the antibacterial activities of all antibiotics are increased from 1 mm to 10 mm. The maximum fold increase was noticed for vancomycin against Pseudomonas aeruginosa (66.67%, Escherichia coli (62.50%, and Staphylococcus aureus (46% followed by rifampicin against Bacillus cereus (66.67% and kanamycin against Streptococcus epidermis (25%. These results signify that the silver nanoparticles showed potential antibacterial action of ß-lactams, glycopeptides, aminoglycosides, sulphonamides suggesting a possible utilization of silver nanocompounds in combination therapy against selected pathogens used in the experiment.

  15. Chemically vapor-deposited ZrB2 as a selective solar absorber

    International Nuclear Information System (INIS)

    Coatings of ZrB2 and TiB2 for photothermal solar absorber applications were prepared using chemical vapor deposition (CVD) techniques. Oxidation tests suggest a maximum temperature limit for air exposure of 600 K for TiB2 and 800 K for ZrB2. Both materials exhibit innate spectral selectivity with an emittance at 375 K ranging from 0.06 to 0.09, a solar absorptance for ZrB2 ranging from 0.67 to 0.77 and a solar absorptance for TiB2 ranging from 0.46 to 0.59. ZrB2 has better solar selectivity and more desirable oxidation behavior than TiB2. A 0.071 μm antireflection coating of Si3N4 deposited onto the ZrB2 coating leads to an increase in absorptance from 0.77 to 0.93, while the emittance remains unchanged. (Auth.)

  16. Phase diagram of selectively cross-linked block copolymers shows chemically microstructured gel.

    Science.gov (United States)

    von der Heydt, Alice; Zippelius, Annette

    2015-02-01

    We study analytically the intricate phase behavior of cross-linked AB diblock copolymer melts, which can undergo two main phase transitions due to quenched random constraints. Gelation, i.e., spatially random localisation of polymers forming a system-spanning cluster, is driven by increasing the number parameter μ of irreversible, type-selective cross-links between random pairs of A blocks. Self-assembly into a periodic pattern of A/B-rich microdomains (microphase separation) is controlled by the AB incompatibility χ inversely proportional to temperature. Our model aims to capture the system's essential microscopic features, including an ensemble of random networks that reflects spatial correlations at the instant of cross-linking. We identify suitable order parameters and derive a free-energy functional in the spirit of Landau theory that allows us to trace a phase diagram in the plane of μ and χ. Selective cross-links promote microphase separation at higher critical temperatures than in uncross-linked diblock copolymer melts. Microphase separation in the liquid state facilitates gelation, giving rise to a novel gel state whose chemical composition density mirrors the periodic AB pattern. PMID:25662662

  17. SELECTION AND MEASUREMENT OF PHYSICAL PROPERTIES FOR CHARACTERIZATION OF CHEMICAL PROTECTIVE CLOTHING MATERIALS

    Science.gov (United States)

    Chemical protective clothing (CPC) must possess certain physical properties if it is to function as an effective barrier to chemicals. he physical characteristics of CPC materials has gone largely unstudied; most attention has been focussecd on chemical resistance. hysical proper...

  18. 13C chemical shift anisotropies for carbonate ions in cement minerals and the use of 13C, 27Al and 29Si MAS NMR in studies of Portland cement including limestone additions

    International Nuclear Information System (INIS)

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

  19. Reactibodies generated by kinetic selection couple chemical reactivity with favorable protein dynamics.

    Science.gov (United States)

    Smirnov, Ivan; Carletti, Eugénie; Kurkova, Inna; Nachon, Florian; Nicolet, Yvain; Mitkevich, Vladimir A; Débat, Hélène; Avalle, Bérangère; Belogurov, Alexey A; Kuznetsov, Nikita; Reshetnyak, Andrey; Masson, Patrick; Tonevitsky, Alexander G; Ponomarenko, Natalia; Makarov, Alexander A; Friboulet, Alain; Tramontano, Alfonso; Gabibov, Alexander

    2011-09-20

    Igs offer a versatile template for combinatorial and rational design approaches to the de novo creation of catalytically active proteins. We have used a covalent capture selection strategy to identify biocatalysts from within a human semisynthetic antibody variable fragment library that uses a nucleophilic mechanism. Specific phosphonylation at a single tyrosine within the variable light-chain framework was confirmed in a recombinant IgG construct. High-resolution crystallographic structures of unmodified and phosphonylated Fabs display a 15-Å-deep two-chamber cavity at the interface of variable light (V(L)) and variable heavy (V(H)) fragments having a nucleophilic tyrosine at the base of the site. The depth and structure of the pocket are atypical of antibodies in general but can be compared qualitatively with the catalytic site of cholinesterases. A structurally disordered heavy chain complementary determining region 3 loop, constituting a wall of the cleft, is stabilized after covalent modification by hydrogen bonding to the phosphonate tropinol moiety. These features and presteady state kinetics analysis indicate that an induced fit mechanism operates in this reaction. Mutations of residues located in this stabilized loop do not interfere with direct contacts to the organophosphate ligand but can interrogate second shell interactions, because the H3 loop has a conformation adjusted for binding. Kinetic and thermodynamic parameters along with computational docking support the active site model, including plasticity and simple catalytic components. Although relatively uncomplicated, this catalytic machinery displays both stereo- and chemical selectivity. The organophosphate pesticide paraoxon is hydrolyzed by covalent catalysis with rate-limiting dephosphorylation. This reactibody is, therefore, a kinetically selected protein template that has enzyme-like catalytic attributes. PMID:21896761

  20. {sup 31}P-MR spectroscopy of all regions of the human heart at 1.5 T with acquisition-weighted chemical shift imaging; P-MR-Spektroskopie aller Wandabschnitte des menschlichen Herzens bei 1,5 T mit akquisitionsgewichteter Chemical-shift-Bildgebung

    Energy Technology Data Exchange (ETDEWEB)

    Koestler, H.; Beer, M.; Buchner, S.; Sandstede, J.; Pabst, T.; Kenn, W.; Hahn, D. [Wuerzburg Univ. (Germany). Abt. fuer Roentgendiagnostik; Landschuetz, W.; Kienlin, M. von [Wuerzburg Univ. (Germany). Physikalisches Inst.; Neubauer, S. [Dept. of Cardiovascular Medicine, John Radcliffe Hospital, Oxford (United Kingdom)

    2001-12-01

    Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac {sup 31}P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders {sup 31}P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.) [German] Ziel: Ziel der Arbeit war es zu untersuchen, ob die akquisitionsgewichtete Chemical-shift-Bildgebung (AW-CSI) die Bestimmung von PCr und ATP in der Seiten- und Hinterwand des menschlichen Herzens an einem klinischen 1,5 T MR-Tomographen erlaubt. Methoden: 12 gesunde Probanden wurden jeweils mit einer chemical shift imaging (CSI) und einer AW-CSI-Sequenz untersucht. Die Sequenzen unterschieden sich lediglich in der Anzahl der Wiederholungen der einzelnen

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

    International Nuclear Information System (INIS)

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

  2. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

    Science.gov (United States)

    Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi

    2016-05-17

    Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in

  3. Effect of Grain Size on Selected Physico-Chemical Properties of Clay

    Directory of Open Access Journals (Sweden)

    Osumanu H. Ahmed

    2009-01-01

    Full Text Available Problem statement: Mixture of the right proportion of expanding and non-expanding clays to improve plasticity (moldability of clays used in the pot industry of Malaysia is yet to be well investigated. In addition, little is known about the choice of the right clay size to eliminate or reduce the content of undesirable compounds such as Fe2O3, Al2O3 to improve the strength of pots and roofing tiles in the country. The objective of this study was to investigate how selected physico-chemical properties of pottery clay relate to grain size of Nyalau series ((Typic Paleudults. Approach: Soil samples were refined into 25, 20 and 63 µm using size grading method. The mineralogical composition of the samples was determined using X-Ray Diffraction (XRD. The chemical composition of the samples was also determined using standard procedures. Firing was done at 800°C in a muffle furnace and the cracks of the samples recorded. Results: The clay particles with sizes 20 and 25 µm were higher in LOI and total C than that those of 63 µm regardless of grain size, the clay investigated had quartz (SiO2, illite-montmorillonite, Anatase ((TiO2 and kaolinite. Grading affected the concentrations of Fe, Al and Si as clays with particle sizes 20 and 25 µm had higher contents of the aforementioned elements compared with those of 63 µm. The clay with particles 63 µm had the best strength and this was so because the clay particles had the lowest amount of Fe, Al and Si. Conclusion: The strength of Malaysian pots could be improved upon proper grading of the clay particles.

  4. Chemical Constituents and Combined Larvicidal Effects of Selected Essential Oils against Anopheles cracens (Diptera: Culicidae

    Directory of Open Access Journals (Sweden)

    Jitrawadee Intirach

    2012-01-01

    Full Text Available A preliminary study on larvicidal activity against laboratory-colonized Anopheles cracens mosquitos revealed that five of ten plant oils at concentration of 100 ppm showed 95–100% larval mortality. The essential oils of five plants, including Piper sarmentosum, Foeniculum vulgare, Curcuma longa, Myristica fragrans, and Zanthoxylum piperitum, were then selected for chemical analysis, dose-response larvicidal experiments, and combination-based bioassays. Chemical compositions analyzed by gas chromatography coupled to mass spectrometry demonstrated that the main component in the oil derived from P. sarmentosum, F. vulgare, C. longa, M. fragrans, and Z. piperitum was croweacin (71.01%, anethole (63.00%, ar-turmerone (30.19%, safrole (46.60%, and 1,8-cineole (21.27%, respectively. For larvicidal bioassay, all five essential oils exerted promising efficacy in a dose-dependent manner and different performances on A. cracens after 24 hours of exposure. The strongest larvicidal potential was established from P. sarmentosum, followed by F. vulgare, C. longa, M. fragrans, and Z. piperitum, with LC50 values of 16.03, 32.77, 33.61, 40.00, and 63.17 ppm, respectively. Binary mixtures between P. sarmentosum, the most effective oil, and the others at the highest ratio were proved to be highly efficacious with a cotoxicity coefficient value greater than 100, indicating synergistic activity. Results of mixed formulations of different essential oils generating synergistic effects may prove helpful in developing effective, economical, and ecofriendly larvicides, as favorable alternatives for mosquito management.

  5. Effect of irradiation on total chemical profiles of ten selected local herbs

    International Nuclear Information System (INIS)

    As utilisation of medicinal herbs in food and bio industry increases, mass production and the supply of high quality herbs are required. Restriction on the use of fumigants and preservatives on herbs demands safe hygienic technologies such as irradiation. The stability of the active components of ten local herbs after irradiation was studied. The herbs selected were Hempedu Bumi, Mas Cotek, Tongkat Ali, Kacip Fatimah, Misai Kucing, Dukung Anak, Jarum Tujuh Bilah, Kesom, Pegaga and Sambung Nyawa. The herbs were dried, powdered and irradiated at different doses of gamma radiation (0, 1, 3, 5, 10, 15 and 25 kGy) at room temperature prior to extraction. The herbs were then extracted either in methanol or chloroform and freeze dried. About 10.0 mg of each extract (in triplicates) were weighed into an Eppendorf vial and solubilised in 700 μl CD3OD using sonication in an ultrasound bath to obtain a clear solution. This solution was then transferred to a NMR vial and a 1H-NMR spectrum was acquired according to standard Total Quality Profile (TQP) protocol. The results of the statistical analysis showed clearly that all irradiated plant samples did not exhibit any significant pattern of differences. Using SIMCA analysis, we found that there is no statistical basis for separation of control, 1, 5, 10, 15 and 25 kGy irradiated samples on a 95 % confidence limit. TQP analysis for the ten selected herbal plant shows that irradiation up to 25 kGy did not cause significant changes to the total chemical profiles and thus the integrity of the herbal material in the analysed plants. (author)

  6. A Molecular and Chemical Perspective in Defining Melatonin Receptor Subtype Selectivity

    Directory of Open Access Journals (Sweden)

    Yung Hou Wong

    2013-09-01

    Full Text Available Melatonin is primarily synthesized and secreted by the pineal gland during darkness in a normal diurnal cycle. In addition to its intrinsic antioxidant property, the neurohormone has renowned regulatory roles in the control of circadian rhythm and exerts its physiological actions primarily by interacting with the G protein-coupled MT1 and MT2 transmembrane receptors. The two melatonin receptor subtypes display identical ligand binding characteristics and mediate a myriad of signaling pathways, including adenylyl cyclase inhibition, phospholipase C stimulation and the regulation of other effector molecules. Both MT1 and MT2 receptors are widely expressed in the central nervous system as well as many peripheral tissues, but each receptor subtype can be linked to specific functional responses at the target tissue. Given the broad therapeutic implications of melatonin receptors in chronobiology, immunomodulation, endocrine regulation, reproductive functions and cancer development, drug discovery and development programs have been directed at identifying chemical molecules that bind to the two melatonin receptor subtypes. However, all of the melatoninergics in the market act on both subtypes of melatonin receptors without significant selectivity. To facilitate the design and development of novel therapeutic agents, it is necessary to understand the intrinsic differences between MT1 and MT2 that determine ligand binding, functional efficacy, and signaling specificity. This review summarizes our current knowledge in differentiating MT1 and MT2 receptors and their signaling capacities. The use of homology modeling in the mapping of the ligand-binding pocket will be described. Identification of conserved and distinct residues will be tremendously useful in the design of highly selective ligands.

  7. 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.

  8. Is flower selection influenced by chemical imprinting to larval food provisions in the generalist bee Osmia bicornis (Megachilidae)?

    OpenAIRE

    Dobson, Heidi; Ayasse, Manfred; O'Neal, Katherine; Jacka, Jesse

    2012-01-01

    To investigate whether flower selection in polylectic solitary bees is modulated by chemical imprinting to nest provisions, larvae of Osmia bicornis (L.) were reared on either Brassica napus L. (Brassicaceae) or Onobrychis viciifolia Scop. (Fabaceae). Flower preferences by adults were evaluated in multiple-choice behavioral tests based on visit number and duration, and flowers selected in the first three visits; data were compared to control bees from the wild. Females reared on B. napus show...

  9. Acoustic Aposematism and Evasive Action in Select Chemically Defended Arctiine (Lepidoptera: Erebidae) Species: Nonchalant or Not?

    Science.gov (United States)

    Dowdy, Nicolas J; Conner, William E

    2016-01-01

    Tiger moths (Erebidae: Arctiinae) have experienced intense selective pressure from echolocating, insectivorous bats for over 65 million years. One outcome has been the evolution of acoustic signals that advertise the presence of toxins sequestered from the moths' larval host plants, i.e. acoustic aposematism. Little is known about the effectiveness of tiger moth anti-bat sounds in their natural environments. We used multiple infrared cameras to reconstruct bat-moth interactions in three-dimensional (3-D) space to examine how functional sound-producing organs called tymbals affect predation of two chemically defended tiger moth species: Pygarctia roseicapitis (Arctiini) and Cisthene martini (Lithosiini). P. roseicapitis and C. martini with intact tymbals were 1.8 and 1.6 times less likely to be captured by bats relative to those rendered silent. 3-D flight path and acoustic analyses indicated that bats actively avoided capturing sound-producing moths. Clicking behavior differed between the two tiger moth species, with P. roseicapitis responding in an earlier phase of bat attack. Evasive flight behavior in response to bat attacks was markedly different between the two tiger moth species. P. roseicapitis frequently paired evasive dives with aposematic sound production. C. martini were considerably more nonchalant and employed evasion in fewer interactions. Our results show that acoustic aposematism is effective at deterring bat predation in a natural context and that this strategy is likely to be the ancestral function of tymbal organs within the Arctiinae. PMID:27096408

  10. Chemical characterization of selected high copper dental amalgams using XPS and XRD techniques

    Energy Technology Data Exchange (ETDEWEB)

    Talik, E. [A. Chelkowski Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland)]. E-mail: talik@us.edu.pl; Babiarz-Zdyb, R. [A. Chelkowski Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland); Dziedzic, A. [Medical University of Silesia, Department of Conservative Dentistry and Periodontology, Akademicki 17 Sqr., 41-209 Bytom (Poland)

    2005-08-02

    The study was carried out to analyze some dependencies between the composition of seven high copper dental amalgams and mercury release behavior, as well as oxygen reactivity of metallic elements. Chemical comparative analysis of selected dental amalgams was carried out using X-ray photoelectron spectroscopy (XPS) technique and X-ray diffraction (XRD) method. The X-ray powder diffraction measurements revealed two main phases for measured amalgams: {gamma}{sub 1}-(Ag{sub 2}Hg{sub 3}) and {eta}'-(Cu{sub 6}Sn{sub 5}). The amount of mercury obtained by the XPS method was lower than the value quoted in the manufacturer's literature, which suggested evaporation of mercury under the UHV conditions. A linear decrease of oxygen and carbon contamination with the growing amount of Cu and Ag was observed. The XPS analysis showed that a high Sn concentration caused less resistance to oxidation. Some of the amalgams contained some extra elements, such as Bi, In, and Zn. All samples contained lead in metallic state and oxides. The amount of Ag, Cu, Sn ingredients determines the main properties of high copper amalgams and plays an important role in mercury evaporation. High tin concentration combined with the presence of smaller amounts of silver and copper (high Sn/Ag ratio) may influence the increase of mercury vaporization.

  11. Chemical characterization of selected high copper dental amalgams using XPS and XRD techniques

    International Nuclear Information System (INIS)

    The study was carried out to analyze some dependencies between the composition of seven high copper dental amalgams and mercury release behavior, as well as oxygen reactivity of metallic elements. Chemical comparative analysis of selected dental amalgams was carried out using X-ray photoelectron spectroscopy (XPS) technique and X-ray diffraction (XRD) method. The X-ray powder diffraction measurements revealed two main phases for measured amalgams: γ1-(Ag2Hg3) and η'-(Cu6Sn5). The amount of mercury obtained by the XPS method was lower than the value quoted in the manufacturer's literature, which suggested evaporation of mercury under the UHV conditions. A linear decrease of oxygen and carbon contamination with the growing amount of Cu and Ag was observed. The XPS analysis showed that a high Sn concentration caused less resistance to oxidation. Some of the amalgams contained some extra elements, such as Bi, In, and Zn. All samples contained lead in metallic state and oxides. The amount of Ag, Cu, Sn ingredients determines the main properties of high copper amalgams and plays an important role in mercury evaporation. High tin concentration combined with the presence of smaller amounts of silver and copper (high Sn/Ag ratio) may influence the increase of mercury vaporization

  12. Physical and chemical conditions in methanol maser selected hot-cores and UCHII regions

    CERN Document Server

    Purcell, C R; Burton, M G; Walsh, A J; Minier, V; Cunningham, M R; Balasubramanyam, R

    2008-01-01

    We present the results of a targeted 3-mm spectral line survey towards the eighty-three 6.67 GHz methanol maser selected star forming clumps observed by Purcell et al. 2006. In addition to the previously reported measurements of HCO+ (1 - 0), H13CO+ (1 - 0), and CH3CN (5 - 4) & (6 -5), we used the Mopra antenna to detect emission lines of N2H+ (1 - 0), HCN (1 - 0) and HNC (1 - 0) towards 82/83 clumps (99 per cent), and CH3OH (2 - 1) towards 78/83 clumps (94 per cent). The molecular line data have been used to derive virial and LTE masses, rotational temperatures and chemical abundances in the clumps, and these properties have been compared between sub-samples associated with different indicators of evolution. The greatest differences are found between clumps associated with 8.6 GHz radio emission, indicating the presence of an Ultra-Compact HII region, and `isolated' masers (without associated radio emission), and between clumps exhibiting CH3CN emission and those without. In particular, thermal CH3OH is ...

  13. Chemo-selective high yield microwave assisted reaction turns cellulose to green chemicals.

    Science.gov (United States)

    Hassanzadeh, Salman; Aminlashgari, Nina; Hakkarainen, Minna

    2014-11-01

    Exceptionally high cellulose liquefaction yields, up to 87% as calculated from the amount of solid residue, were obtained under mild conditions by utilizing the synergistic effect of microwave radiation and acid catalysis. The effect of processing conditions on degradation products was fingerprinted by rapid laser desorption ionization-mass spectrometry (LDI-MS) method. The reaction was chemo-tunable, enabling production of glucose (Glc) or levulinic acid (LeA) at significantly high selectivity and yields, the relative molar yields being up to 50 and 69%, respectively. A turning point from pure depolymerization to glucose to further degradation to levulinic acid and formic acid was observed at approximately 50% liquefaction or above 140 °C. This was accompanied by the formation of small amounts of solid spherical carbonized residues. The reaction was monitored by multiple analytical techniques. The high yields were connected to the ability of the process to break the strong secondary interactions in cellulose. The developed method has great potential for future production of green platform chemicals. PMID:25129766

  14. Mass spectrometric study of selected precursors and degradation products of chemical warfare agents.

    Science.gov (United States)

    Papousková, Barbora; Bednár, Petr; Frysová, Iveta; Stýskala, Jakub; Hlavác, Jan; Barták, Petr; Ulrichová, Jitka; Jirkovský, Jaromír; Lemr, Karel

    2007-12-01

    Selected precursors and degradation products of chemical warfare agents namely N,N-dialkylaminoethane-2-ols, N,N-dialkylaminoethyl-2-chlorides and some of related N-quaternary salts were studied by means of electrospray ionization-multiple tandem mass spectrometry (ESI-MS(n)). Proposed structures were confirmed with accurate mass measurement. General fragmentation patterns of these compounds are discussed in detail and suggested processes are confirmed using deuterated standards. The typical processes are elimination of alkene, hydrogen chloride, or water, respectively. Besides, elimination of ethene from propyl chain under specific conditions was observed and unambiguously confirmed using exact mass measurement and labelled standard. The potential of mass spectrometry to distinguish the positional isomers occurring among the studied compounds is reviewed in detail using two different MS instruments (i.e. ion trap and hybrid quadrupole-time of flight (Q-TOF) analyzer). A new microcolumn liquid chromatography (microLC)/MS(n) method was designed for the cases where the resolution based solely on differences in fragmentation is not sufficient. Low retention of the derivatives on reversed phase (RP) was overcome by using addition of less typical ion pairing agent (1 mM/l, 3,5-dinitrobenzoic acid) to the mobile phase (mixture water : acetonitrile). PMID:18085550

  15. Acoustic Aposematism and Evasive Action in Select Chemically Defended Arctiine (Lepidoptera: Erebidae) Species: Nonchalant or Not?

    Science.gov (United States)

    Dowdy, Nicolas J.; Conner, William E.

    2016-01-01

    Tiger moths (Erebidae: Arctiinae) have experienced intense selective pressure from echolocating, insectivorous bats for over 65 million years. One outcome has been the evolution of acoustic signals that advertise the presence of toxins sequestered from the moths’ larval host plants, i.e. acoustic aposematism. Little is known about the effectiveness of tiger moth anti-bat sounds in their natural environments. We used multiple infrared cameras to reconstruct bat-moth interactions in three-dimensional (3-D) space to examine how functional sound-producing organs called tymbals affect predation of two chemically defended tiger moth species: Pygarctia roseicapitis (Arctiini) and Cisthene martini (Lithosiini). P. roseicapitis and C. martini with intact tymbals were 1.8 and 1.6 times less likely to be captured by bats relative to those rendered silent. 3-D flight path and acoustic analyses indicated that bats actively avoided capturing sound-producing moths. Clicking behavior differed between the two tiger moth species, with P. roseicapitis responding in an earlier phase of bat attack. Evasive flight behavior in response to bat attacks was markedly different between the two tiger moth species. P. roseicapitis frequently paired evasive dives with aposematic sound production. C. martini were considerably more nonchalant and employed evasion in fewer interactions. Our results show that acoustic aposematism is effective at deterring bat predation in a natural context and that this strategy is likely to be the ancestral function of tymbal organs within the Arctiinae. PMID:27096408

  16. Tough Shift

    DEFF Research Database (Denmark)

    Brewer, Robert S.; Verdezoto, Nervo; Holst, Thomas;

    2015-01-01

    people to change their behavior at home. Leveraging prior research on encouraging reductions in residential energy use through game play, we introduce ShareBuddy: a casual mobile game intended to encourage players not only to reduce, but also to shift their electricity use. We conducted two field studies...... integrating real-world resource use into a game....

  17. Fluid Shifts

    Science.gov (United States)

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    1989-01-01

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

  20. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  1. Combination of TRAIL with bortezomib shifted apoptotic signaling from DR4 to DR5 death receptor by selective internalization and degradation of DR4.

    Directory of Open Access Journals (Sweden)

    Maxim L Bychkov

    Full Text Available TRAIL (tumor necrosis factor-related apoptosis-inducing ligand mediates apoptosis in cancer cells through death receptors DR4 and DR5 preferring often one receptor over another in the cells expressing both receptors. Receptor selective mutant variants of TRAIL and agonistic antibodies against DR4 and DR5 are highly promising anticancer agents. Here using DR5 specific mutant variant of TRAIL--DR5-B we have demonstrated for the first time that the sensitivity of cancer cells can be shifted from one TRAIL death receptor to another during co-treatment with anticancer drugs. First we have studied the contribution of DR4 and DR5 in HCT116 p53+/+ and HCT116 p53-/- cells and demonstrated that in HCT116 p53+/+ cells the both death receptors are involved in TRAIL-induced cell death while in HCT116 p53-/- cells prevailed DR4 signaling. The expression of death (DR4 and DR5 as well as decoy (DcR1 and DcR2 receptors was upregulated in the both cell lines either by TRAIL or by bortezomib. However, combined treatment of cells with two drugs induced strong time-dependent and p53-independent internalization and further lysosomal degradation of DR4 receptor. Interestingly DR5-B variant of TRAIL which do not bind with DR4 receptor also induced elimination of DR4 from cell surface in combination with bortezomib indicating the ligand-independent mechanism of the receptor internalization. Eliminatory internalization of DR4 resulted in activation of DR5 receptor thus DR4-dependent HCT116 p53-/- cells became highly sensitive to DR5-B in time-dependent manner. Internalization and degradation of DR4 receptor depended on activation of caspases as well as of lysosomal activity as it was completely inhibited by Z-VAD-FMK, E-64 and Baf-A1. In light of our findings, it is important to explore carefully which of the death receptors is active, when sensitizing drugs are combined with agonistic antibodies to the death receptors or receptor selective variants of TRAIL to enhance

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-15

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

  3. Tree Resin Composition, Collection Behavior and Selective Filters Shape Chemical Profiles of Tropical Bees (Apidae: Meliponini)

    OpenAIRE

    Leonhardt, Sara D.; Schmitt, Thomas; Blüthgen, Nico

    2011-01-01

    The diversity of species is striking, but can be far exceeded by the chemical diversity of compounds collected, produced or used by them. Here, we relate the specificity of plant-consumer interactions to chemical diversity applying a comparative network analysis to both levels. Chemical diversity was explored for interactions between tropical stingless bees and plant resins, which bees collect for nest construction and to deter predators and microbes. Resins also function as an environmental ...

  4. Shifting densities

    OpenAIRE

    Mille, Matthieu

    2000-01-01

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

  5. Understanding Boron through Size-Selected Clusters: Structure, Chemical Bonding, and Fluxionality

    Energy Technology Data Exchange (ETDEWEB)

    Sergeeva, Alina P.; Popov, Ivan A.; Piazza, Zachary A.; Li, Wei-Li; Romanescu, Constantin; Wang, Lai S.; Boldyrev, Alexander I.

    2014-04-15

    /C analogy. It is believed that the electronic transmutation concept will be effective and valuable in aiding the design of new boride materials with predictable properties. The study of boron clusters with intermediate properties between those of individual atoms and bulk solids has given rise to a unique opportunity to broaden the frontier of boron chemistry. Understanding boron clusters has spurred experimentalists and theoreticians to find new boron-based nanomaterials, such as boron fullerenes, nanotubes, two-dimensional boron, and new compounds containing boron clusters as building blocks. Here, a brief and timely overview is presented addressing the recent progress made on boron clusters and the approaches used in the authors’ laboratories to determine the structure, stability, and chemical bonding of size-selected boron clusters by joint photoelectron spectroscopy and theoretical studies. Specifically, key findings on all-boron hydrocarbon analogues, metal-centered boron wheels, and electronic transmutation in boron clusters are summarized.

  6. Selective synthesis of large diameter, highly conductive and high density single-walled carbon nanotubes by a thiophene-assisted chemical vapor deposition method on transparent substrates

    Science.gov (United States)

    Li, Jinghua; Otsuka, Keigo; Zhang, Xiao; Maruyama, Shigeo; Liu, Jie

    2016-07-01

    Selective synthesis of single-walled carbon nanotubes (SWNTs) with controlled properties is an important research topic for SWNT studies. Here we report a thiophene-assisted chemical vapor deposition (CVD) method to directly grow highly conductive SWNT thin films on substrates, including transparent ones. By adding low concentration thiophene into the carbon feedstock (ethanol), the as-prepared carbon nanotubes demonstrate an obvious up-shift in the diameter distribution while the single-walled structure is still retained. In the proposed mechanism, the change in the diameter is sourced from the increase in the carbon yield induced by the sulfur-containing compound. Such SWNTs are found to possess high conductivity with 95% SWNTs demonstrating on/off ratios lower than 100 in transistors. More importantly, it is further demonstrated that this method can be used to directly synthesize dense SWNT networks on transparent substrates which can be utilized as transparent conductive films (TCFs) with very high transparency. Such TCFs can be applied to fabricate a light modulating window as a proof-of-concept. The present work provides important insights into the growth mechanism of SWNTs and great potential for the preparation of TCFs with high scalability, easy operation and low cost.Selective synthesis of single-walled carbon nanotubes (SWNTs) with controlled properties is an important research topic for SWNT studies. Here we report a thiophene-assisted chemical vapor deposition (CVD) method to directly grow highly conductive SWNT thin films on substrates, including transparent ones. By adding low concentration thiophene into the carbon feedstock (ethanol), the as-prepared carbon nanotubes demonstrate an obvious up-shift in the diameter distribution while the single-walled structure is still retained. In the proposed mechanism, the change in the diameter is sourced from the increase in the carbon yield induced by the sulfur-containing compound. Such SWNTs are found to

  7. Selective deposition of a crystalline Si film by a chemical sputtering process in a high pressure hydrogen plasma

    International Nuclear Information System (INIS)

    The selective deposition of Si films was demonstrated using a chemical sputtering process induced by a high pressure hydrogen plasma at 52.6 kPa (400 Torr). In this chemical sputtering process, the initial deposition rate (Rd) is dependent upon the substrate type. At the initial stage of Si film formation, Rd on glass substrates increased with elapsed time and reached to a constant value. In contrast, Rd on Si substrates remained constant during the deposition. The selective deposition of Si films can be achieved by adjusting the substrate temperature (Tsub) and hydrogen concentration (CH2) in the process atmosphere. For any given deposition time, it was found that an optimum CH2 exists for a given Tsub to realize the selective deposition of a Si film, and the optimum Tsub value tends to increase with decreasing CH2. According to electron diffraction patterns obtained from the samples, the selectively prepared Si films showed epitaxial-like growth, although the Si films contained many defects. It was revealed by Raman scattering spectroscopy that some of the defects in the Si films were platelet defects induced by excess hydrogen incorporated during Si film formation. Raman spectrum also suggested that Si related radicals (SiH2, SiH, Si) with high reactivity contribute to the Si film formation. Simple model was derived as the guideline for achieving the selective growth

  8. Down Select Report of Chemical Hydrogen Storage Materials, Catalysts, and Spent Fuel Regeneration Processes - May 2008

    Energy Technology Data Exchange (ETDEWEB)

    Ott, Kevin C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Linehan, Sue [Rohm and Haas, Philadelphia, PA (United States); Lipiecki, Frank [Rohm and Haas, Philadelphia, PA (United States); Christopher, Aardahl L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2008-05-12

    Chemical Hydrogen Storage Center of Excellence FY2008 Second Quarter Milestone Report: Technical report describing assessment of hydrogen storage materials and progress towards meeting DOE’s hydrogen storage targets.

  9. Removal of Selected Endocrine Disrupting Chemicals During On-Site Wastewater Treatment Using A Constructed Wetland

    Science.gov (United States)

    Significant research has shown that domestic and industrial wastewater can be a source of endocrine disrupting chemicals (EDCs) to the environment. Much of this research has focused on municipal and industrial centralized wastewater treatment plants. These plants have been show...

  10. Down Select Report of Chemical Hydrogen Storage Materials, Catalysts, and Spent Fuel Regeneration Processes

    International Nuclear Information System (INIS)

    The DOE Hydrogen Storage Program is focused on identifying and developing viable hydrogen storage systems for onboard vehicular applications. The program funds exploratory research directed at identifying new materials and concepts for storage of hydrogen having high gravimetric and volumetric capacities that have the potential to meet long term technical targets for onboard storage. Approaches currently being examined are reversible metal hydride storage materials, reversible hydrogen sorption systems, and chemical hydrogen storage systems. The latter approach concerns materials that release hydrogen in endothermic or exothermic chemical bond-breaking processes. To regenerate the spent fuels arising from hydrogen release from such materials, chemical processes must be employed. These chemical regeneration processes are envisioned to occur offboard the vehicle

  11. Down Select Report of Chemical Hydrogen Storage Materials, Catalysts, and Spent Fuel Regeneration Processes

    Energy Technology Data Exchange (ETDEWEB)

    Ott, Kevin; Linehan, Sue; Lipiecki, Frank; Aardahl, Christopher L.

    2008-08-24

    The DOE Hydrogen Storage Program is focused on identifying and developing viable hydrogen storage systems for onboard vehicular applications. The program funds exploratory research directed at identifying new materials and concepts for storage of hydrogen having high gravimetric and volumetric capacities that have the potential to meet long term technical targets for onboard storage. Approaches currently being examined are reversible metal hydride storage materials, reversible hydrogen sorption systems, and chemical hydrogen storage systems. The latter approach concerns materials that release hydrogen in endothermic or exothermic chemical bond-breaking processes. To regenerate the spent fuels arising from hydrogen release from such materials, chemical processes must be employed. These chemical regeneration processes are envisioned to occur offboard the vehicle.

  12. Improved sensor selectivity for chemical vapors using organic thin-film transistors

    OpenAIRE

    Royer, James Edward

    2012-01-01

    Organic thin-film transistors (OTFTs) offer unique methods for chemical vapor detection due to multiple device parameters which are influenced by reactive gases. The simplest conventional readout for OTFT sensors is the drain current; however, the drain current is dependent on changes in fundamental device characteristics such as mobility and/or threshold voltage. The chemical properties of the analyte determine whether the mobility or threshold voltage response is dominant for the OTFT. The ...

  13. Pesticides, selected elements, and other chemicals in infant and toddler total diet samples, October 1980-March 1982

    Energy Technology Data Exchange (ETDEWEB)

    Gartrell, M.J.; Craun, J.C.; Podrebarac, D.S.; Gunderson, E.L.

    The US Food and Drug Administration (FDA) conducts Total Diet Studies to determine the dietary intake of selected pesticides, industrial chemicals, and elements (including radionuclides). These studies involve the retail purchase and analysis of foods representative of the diets of infants, toddlers, and adults. The individual food items are separated into a number of food groups, each of which is analyzed as a composite. This report summarizes the results for infant and toddler Total Diet samples collected in 13 cities between October 1980 and March 1982. The average concentration, range of concentrations, and calculated average daily intake of each chemical found are presented by food group. The average daily intakes of the chemicals are similar to those found in the several preceding years and generally are within acceptable limits. The results for samples collected during the same period that represent the adult diet are reported separately.

  14. Assessing the binding affinity of a selected class of DPP4 inhibitors using chemical descriptor-based multiple linear regression

    OpenAIRE

    Jose Isagani Janairo; Gerardo Janairo; Frumencio Co; Derrick Ethelbhert Yu

    2011-01-01

    The activity of a selected class of DPP4 inhibitors was preliminarily assessed using chemical descriptors derived AM1 optimized geometries. Using multiple linear regression model, it was found that ?E0, LUMO energy, area, molecular weight and ?H0 are the significant descriptors that can adequately assess the binding affinity of the compounds. The derived multiple linear regression (MLR) model was validated using rigorous statistical analysis. The preliminary model suggests t...

  15. A Q-learning with Selective Generalization Capability and its Application to Layout Planning of Chemical Plants

    OpenAIRE

    Hirashima, Yoichi

    2009-01-01

    A design method for CMAC that has selective generalization (SG-CMAC) has been proposed. Also, a Q-learning system using SG-CMAC is proposed, and the proposed system is applied to allocation problem of chemical plant. In the computer simulations, the proposed method could obtain optimal solutions with feasible computational cost, and the learning performance was improved as compared to conventional methods.

  16. Importance of asparagine on the conformational stability and chemical reactivity of selected anti-inflammatory peptides

    Energy Technology Data Exchange (ETDEWEB)

    Soriano-Correa, Catalina, E-mail: csorico@comunidad.unam.mx [Química Computacional, Facultad de Estudios Superiores (FES)-Zaragoza, Universidad Nacional Autónoma de México (UNAM), Iztapalapa, C.P. 09230 México, D.F. (Mexico); Barrientos-Salcedo, Carolina [Laboratorio de Química Médica y Quimiogenómica, Facultad de Bioanálisis Campus Veracruz-Boca del Río, Universidad Veracruzana, C.P. 91700 Veracruz (Mexico); Campos-Fernández, Linda; Alvarado-Salazar, Andres [Química Computacional, Facultad de Estudios Superiores (FES)-Zaragoza, Universidad Nacional Autónoma de México (UNAM), Iztapalapa, C.P. 09230 México, D.F. (Mexico); Esquivel, Rodolfo O. [Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa (UAM-Iztapalapa), C.P. 09340 México, D.F. (Mexico)

    2015-08-18

    Highlights: • Asparagine plays an important role to anti-inflammatory effect of peptides. • The electron-donor substituent groups favor the formation of the hydrogen bonds, which contribute in the structural stability of peptides. • Chemical reactivity and the physicochemical features are crucial in the biological functions of peptides. - Abstract: Inflammatory response events are initiated by a complex series of molecular reactions that generate chemical intermediaries. The structure and properties of peptides and proteins are determined by the charge distribution of their side chains, which play an essential role in its electronic structure and physicochemical properties, hence on its biological functionality. The aim of this study was to analyze the effect of changing one central amino acid, such as substituting asparagine for aspartic acid, from Cys–Asn–Ser in aqueous solution, by assessing the conformational stability, physicochemical properties, chemical reactivity and their relationship with anti-inflammatory activity; employing quantum-chemical descriptors at the M06-2X/6-311+G(d,p) level. Our results suggest that asparagine plays a more critical role than aspartic acid in the structural stability, physicochemical features, and chemical reactivity of these tripeptides. Substituent groups in the side chain cause significant changes on the conformational stability and chemical reactivity, and consequently on their anti-inflammatory activity.

  17. Importance of asparagine on the conformational stability and chemical reactivity of selected anti-inflammatory peptides

    International Nuclear Information System (INIS)

    Highlights: • Asparagine plays an important role to anti-inflammatory effect of peptides. • The electron-donor substituent groups favor the formation of the hydrogen bonds, which contribute in the structural stability of peptides. • Chemical reactivity and the physicochemical features are crucial in the biological functions of peptides. - Abstract: Inflammatory response events are initiated by a complex series of molecular reactions that generate chemical intermediaries. The structure and properties of peptides and proteins are determined by the charge distribution of their side chains, which play an essential role in its electronic structure and physicochemical properties, hence on its biological functionality. The aim of this study was to analyze the effect of changing one central amino acid, such as substituting asparagine for aspartic acid, from Cys–Asn–Ser in aqueous solution, by assessing the conformational stability, physicochemical properties, chemical reactivity and their relationship with anti-inflammatory activity; employing quantum-chemical descriptors at the M06-2X/6-311+G(d,p) level. Our results suggest that asparagine plays a more critical role than aspartic acid in the structural stability, physicochemical features, and chemical reactivity of these tripeptides. Substituent groups in the side chain cause significant changes on the conformational stability and chemical reactivity, and consequently on their anti-inflammatory activity

  18. High-capacity, selective solid sequestrants for innovative chemical separation: Inorganic ion exchange approach

    International Nuclear Information System (INIS)

    The approach of this task is to develop high-capacity, selective solid inorganic ion exchangers for the recovery of cesium and strontium from nuclear alkaline and acid wastes. To achieve this goal, Pacific Northwest Laboratories (PNL) is collaborating with industry and university participants to develop high capacity, selective, solid ion exchangers for the removal of specific contaminants from nuclear waste streams

  19. Tree resin composition, collection behavior and selective filters shape chemical profiles of tropical bees (Apidae: Meliponini).

    Science.gov (United States)

    Leonhardt, Sara D; Schmitt, Thomas; Blüthgen, Nico

    2011-01-01

    The diversity of species is striking, but can be far exceeded by the chemical diversity of compounds collected, produced or used by them. Here, we relate the specificity of plant-consumer interactions to chemical diversity applying a comparative network analysis to both levels. Chemical diversity was explored for interactions between tropical stingless bees and plant resins, which bees collect for nest construction and to deter predators and microbes. Resins also function as an environmental source for terpenes that serve as appeasement allomones and protection against predators when accumulated on the bees' body surfaces. To unravel the origin of the bees' complex chemical profiles, we investigated resin collection and the processing of resin-derived terpenes. We therefore analyzed chemical networks of tree resins, foraging networks of resin collecting bees, and their acquired chemical networks. We revealed that 113 terpenes in nests of six bee species and 83 on their body surfaces comprised a subset of the 1,117 compounds found in resins from seven tree species. Sesquiterpenes were the most variable class of terpenes. Albeit widely present in tree resins, they were only found on the body surface of some species, but entirely lacking in others. Moreover, whereas the nest profile of Tetragonula melanocephala contained sesquiterpenes, its surface profile did not. Stingless bees showed a generalized collecting behavior among resin sources, and only a hitherto undescribed species-specific "filtering" of resin-derived terpenes can explain the variation in chemical profiles of nests and body surfaces from different species. The tight relationship between bees and tree resins of a large variety of species elucidates why the bees' surfaces contain a much higher chemodiversity than other hymenopterans. PMID:21858119

  20. Tree resin composition, collection behavior and selective filters shape chemical profiles of tropical bees (Apidae: Meliponini.

    Directory of Open Access Journals (Sweden)

    Sara D Leonhardt

    Full Text Available The diversity of species is striking, but can be far exceeded by the chemical diversity of compounds collected, produced or used by them. Here, we relate the specificity of plant-consumer interactions to chemical diversity applying a comparative network analysis to both levels. Chemical diversity was explored for interactions between tropical stingless bees and plant resins, which bees collect for nest construction and to deter predators and microbes. Resins also function as an environmental source for terpenes that serve as appeasement allomones and protection against predators when accumulated on the bees' body surfaces. To unravel the origin of the bees' complex chemical profiles, we investigated resin collection and the processing of resin-derived terpenes. We therefore analyzed chemical networks of tree resins, foraging networks of resin collecting bees, and their acquired chemical networks. We revealed that 113 terpenes in nests of six bee species and 83 on their body surfaces comprised a subset of the 1,117 compounds found in resins from seven tree species. Sesquiterpenes were the most variable class of terpenes. Albeit widely present in tree resins, they were only found on the body surface of some species, but entirely lacking in others. Moreover, whereas the nest profile of Tetragonula melanocephala contained sesquiterpenes, its surface profile did not. Stingless bees showed a generalized collecting behavior among resin sources, and only a hitherto undescribed species-specific "filtering" of resin-derived terpenes can explain the variation in chemical profiles of nests and body surfaces from different species. The tight relationship between bees and tree resins of a large variety of species elucidates why the bees' surfaces contain a much higher chemodiversity than other hymenopterans.

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

    Institute of Scientific and Technical Information of China (English)

    雷立存; 任庆云; 母建奎; 祁宇轩; 何丽; 刘斋

    2015-01-01

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

  2. Importance of asparagine on the conformational stability and chemical reactivity of selected anti-inflammatory peptides

    Science.gov (United States)

    Soriano-Correa, Catalina; Barrientos-Salcedo, Carolina; Campos-Fernández, Linda; Alvarado-Salazar, Andres; Esquivel, Rodolfo O.

    2015-08-01

    Inflammatory response events are initiated by a complex series of molecular reactions that generate chemical intermediaries. The structure and properties of peptides and proteins are determined by the charge distribution of their side chains, which play an essential role in its electronic structure and physicochemical properties, hence on its biological functionality. The aim of this study was to analyze the effect of changing one central amino acid, such as substituting asparagine for aspartic acid, from Cys-Asn-Ser in aqueous solution, by assessing the conformational stability, physicochemical properties, chemical reactivity and their relationship with anti-inflammatory activity; employing quantum-chemical descriptors at the M06-2X/6-311+G(d,p) level. Our results suggest that asparagine plays a more critical role than aspartic acid in the structural stability, physicochemical features, and chemical reactivity of these tripeptides. Substituent groups in the side chain cause significant changes on the conformational stability and chemical reactivity, and consequently on their anti-inflammatory activity.

  3. Familiarity and Understanding of Chemical Hazard Warning Signs Among Select College Students of De La Salle Lipa

    Directory of Open Access Journals (Sweden)

    Bernardo C. Lunar

    2014-10-01

    Full Text Available Laboratory classes have become crucial parts of teaching science subjects. Most of the laboratories in natural science fields widely use chemicals of different types and hazard levels. Using descriptive- evaluative method of research, the study was carried out to assess students’ familiarity and comprehension of chemical hazard warning signs. Data were collected from randomly selected 150 student respondents enrolled in Chemistry and Biology Laboratory Classes during the second semester of SY 2012- 2013. A structured questionnaire was used for the data collection. The collected data were analysed using simple quantitative analysis. The results of the study revealed that the majority of the respondents were familiar with hazard signs of laboratory chemicals. After getting information on their level of awareness about potential hazards of laboratory chemicals, the respondents were also requested to match chemicals properties with the corresponding labels or pictograms. The results indicate that familiarity and understanding of hazard warning signs is low among the students. It also surveyed the preferred labelling technique which revealed that majority favoured the use of both colors and signs. An action plan was drafted as an output of the study aimed at putting forward corrective measures to address the laboratory related problems identified in the study.

  4. Preparation of betulinic acid derivatives by chemical and biotransformation methods and determination of cytotoxicity against selected cancer cell lines.

    Science.gov (United States)

    Baratto, Leopoldo C; Porsani, Mariana V; Pimentel, Ida C; Pereira Netto, Adaucto B; Paschke, Reinhard; Oliveira, Brás H

    2013-10-01

    Several novel 2,4-dinitrophenylhydrazone betulinic acid derivatives have been prepared by chemical and biotransformation methods using fungi and carrot cells. Some compounds showed significant cytotoxicity and selectivity against some tumor cell lines. The most active, 3-[(2,4-dinitrophenyl)hydrazono]lup-(20R)-29-oxolupan-28-oic acid, showed IC50 values between 1.76 and 2.51 μM against five human cancer cell lines. The most selective, 3-hydroxy-20-[(2,4-dinitrophenyl)hydrazono]-29-norlupan-28-oic acid, was five to seven times more selective for cancer cells when compared to fibroblasts. Cell cycle analysis and apoptosis induction were studied for the most active derivatives. PMID:23973824

  5. Application of INAA to reveal the chemical evolution of selected volcanic eruptiva from Santorini, Greece

    International Nuclear Information System (INIS)

    The pumiceous products of the large-scale explosive eruptions at Santorini show a high grade of similarity in their optical appearance as well as in their chemical composition. The demand for a clear classification of these eruption products was raised from archaeological research, where pumice can be interpreted as a 'post-eruption' time marker. Elements that underwent significant changes because of geochemical processes and that could be indicative for a distinction of pumice produced by the five major explosive eruptions were looked for. INAA of 25 elements allows a clear classification and contributes new information to the chemical evolution of Santorini volcano. (author)

  6. Chemical Variation in a Dominant Tree Species: Population Divergence, Selection and Genetic Stability across Environments

    OpenAIRE

    Julianne M O'Reilly-Wapstra; Miller, Alison M.; Hamilton, Matthew G.; Dean Williams; Naomi Glancy-Dean; Potts, Brad M.

    2013-01-01

    Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E). We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs) in a dominant tree species, Eu...

  7. Chemical conditions in present and future ecosystems in Forsmark - implications for selected radionuclides in the safety assessment SR-Site

    Energy Technology Data Exchange (ETDEWEB)

    Troejbom, Mats (Mats Troejbom Konsult AB (Sweden)); Grolander, Sara (Facilia AB (Sweden))

    2010-12-15

    This report is a background report for the biosphere analysis of the SR-Site Safety Assessment. This work aims to describe the future development of the chemical conditions at Forsmark, based on the present chemical conditions at landscape level taking landscape development and climate cases into consideration. The results presented contribute to the overall understanding of the present and future chemistry in the Forsmark area, and specifically, to the understanding of the behaviour of some selected radionuclides in the surface system. The future development of the chemistry at the site is qualitatively discussed with focus on the interglacial within the next 10,000 years. The effects on the chemical environment of future climate cases as Global Warming and cold permafrost climates are also briefly discussed. The work is presented in two independent parts describing background radionuclide activities in the Forsmark area and the distribution and behaviour of a large number of stable elements in the landscape. In a concluding section, implications of the future chemical environment of a selection of radionuclides important in the Safety Assessment are discussed based on the knowledge of stable elements. The broad range of elements studied show that there are general and expected patterns for the distribution and behaviour in the landscape of different groups of elements. Mass balances reveal major sources and sinks, pool estimations show where elements are accumulated in the landscape and estimations of time-scales give indications of the potential future development. This general knowledge is transferred to radionuclides not measured in order to estimate their behaviour and distribution in the landscape. It could be concluded that the future development of the chemical environment in the Forsmark area might affect element specific parameters used in de radionuclide model in different directions depending on element. The alternative climate cases, Global Warming

  8. A parameter selection for Raman spectroscopy-based detection of chemical contaminants in food powders

    Science.gov (United States)

    Raman spectroscopy technique has proven to be a reliable method for detection of chemical contaminants in food ingredients and products. To detect each contaminant particle in a food sample, it is important to determine the effective depth of penetration of laser through the food sample and the corr...

  9. The Reduction of Microbial and Chemical Contaminants with Selected POU/POE Systems

    Science.gov (United States)

    Centralized drinking water treatment and distribution alone may not always be the most practical or cost-effective option. Also, some consumers seeking a proactive measure to reduce exposure to pathogens and chemicals not currently monitored or regulated might consider employing...

  10. SYSTEMATIC PROCESS TO SELECT CHEMICALS FOR NEW AND REVISED AMBIENT WATER QUALITY CRITERIA

    Science.gov (United States)

    The U.S. Environmental Protection Agency (EPA) publishes and periodically updates ambient water quality criteria (AWQC) for the protection of human health and aquatic life through its authority under Section 304(a) of the Clean Water Act. The number of toxic chemicals generated ...

  11. Comparison of chemical profiles of selected gaharu oils from peninsular Malaysia

    International Nuclear Information System (INIS)

    Gaharu (agar wood) is a fragrant wood that is usually derived from the diseased timber of the genus Aquilaria (Thymelaeceae) and often occurs as dark coloured patches or streaks in the tree. Due to its strong, unique scent and medicinal properties, gaharu oil is greatly valued as perfumery ingredient and incense. Gaharu may be classified into various grades; Grade A, B, C and D and they are often graded according to the physical properties, gaharu formation and its unique scent. The lower grades such as Grade C are often distilled to obtain gaharu oils. As part of an on-going research on the chemical profiling of some Malaysian gaharu oils and evaluation of their potential beneficial properties; gaharu oils obtained from different sources were analysed and compared by GC and GC-MS. Identification of the chemical components was based on comparison of calculated retention indices and mass spectral data with literature values. Examination of the oils showed some variations and differences in terms of GC profiles, concentration and chemical components. Majority of the essential oil profiles were complex and made up of sesquiterpenoids and their oxygenated derivatives. However, common occurrences of chemical compounds such as 3-phenyl-butanone, α-guaiene, β-agar ofuran, α-agar ofuran, agarospirol and jinkoh-eremol were detected. (author)

  12. Linear solvation energy relationships for toxicity of selected organic chemicals to Daphnia pulex and Daphnia magna

    Science.gov (United States)

    Passino, Dora R.M.; Hickey, James P.; Frank, Anthony M.

    1988-01-01

    In the Laurentian Great Lakes, more than 300 contaminants have been identified in fish, other biota, water, and sediment. Current hazard assessment of these chemicals by the National Fisheries Research Center-Great Lakes is based on their toxicity, occurrence in the environment, and source. Although scientists at the Center have tested over 70 chemicals with the crustacean Daphnia pulex, the number of experimental data needed to screen the huge array of chemicals in the Great Lakes exceeds the practical capabilities of conducting bioassays. This limitation can be partly circumvented, however, by using mathematical models based on quantitative structure-activity relationships (QSAR) to provide rapid, inexpensive estimates of toxicity. Many properties of chemicals, including toxicity, bioaccumulation and water solubility are well correlated and can be predicted by equations of the generalized linear solvation energy relationships (LSER). The equation we used to model solute toxicity is Toxicity = constant + mVI/100 + s (π* + dδ) + bβm + aαm where VI = intrinsic (Van der Waals) molar volume; π* = molecular dipolarity/polarizability; δ = polarizability 'correction term'; βm = solute hydrogen bond acceptor basicity; and αm = solute hydrogen bond donor acidity. The subscript m designates solute monomer values for α and β. We applied the LSER model to 48-h acute toxicity data (measured as immobilization) for six classes of chemicals detected in Great Lakes fish. The following regression was obtained for Daphnia pulex (concentration = μM): log EC50 = 4.86 - 4.35 VI/100; N = 38, r2 = 0.867, sd = 0.403 We also used the LSER modeling approach to analyze to a large published data set of 24-h acute toxicity for Daphnia magna; the following regression resulted, for eight classes of compounds (concentration = mM): log EC50 = 3.88 - 4.52 VI/100 - 1.62 π* + 1.66 βm - 0.916 αm; N = 62, r2 = 0.859, sd = 0.375 In addition we developed computer software that identifies

  13. 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.

  14. Resonance Raman spectroscopy with chemical state selectivity on histidine and acetamide using synchrotron radiation

    International Nuclear Information System (INIS)

    We report on ultraviolet resonance Raman scattering experiments carried out on two model substances: histidine and acetamide using a UV synchrotron radiation source. In the case of aqueous histidine solution each protonated state of histidine tautomers was selectively excited by tuning the incident wavelength and the vibrational state of each protonated state was studied. We also demonstrated that the local pH condition of histidine can be identified directly from the spectra above pH 9. In the case of acetamide, the resonance Raman bands of acetamide with a stronger hydrogen bond at the NH2 site and weaker hydrogen bond at the C=O site were selectively observed. These findings will extend the selectivity and sensitivity of RR spectroscopy that is helpful to understanding protein functionality. (author)

  15. Physico-Chemical Analysis of Selected Groundwater Samples of Inkollu Mandal, Prakasam District, Andhra Pradesh, India

    Directory of Open Access Journals (Sweden)

    G. Arun Kumar

    2015-04-01

    Full Text Available Physico-chemical parameters of groundwater quality based on Physic-chemical parameters at Inkollu mandal, Prakasam district, Andhra Pradesh, India have been taken up to evaluate its suitability for Drinking purpose. Nine ground water samples were collected from different places of Inkollu mandal of Prakasam district. The quality analysis has been made through the pH, EC, TDS, Total Hardness, Sodium, Potassium, Calcium, Magnesium, Chloride, Sulphate, Nitrate, Fluoride and Iron. By observing the results, it was shown that the parameters from the water samples were compared with WHO (World Health Organization and BIS (Bureau of Indian Standards, USPH (United state Public health for ground water .The results revealed that some parameters were in high concentration and quality of the potable water has deteriorated to a large extent at some sampling locations.

  16. Selective chemical binding enhances cesium tolerance in plants through inhibition of cesium uptake

    Science.gov (United States)

    Adams, Eri; Chaban, Vitaly; Khandelia, Himanshu; Shin, Ryoung

    2015-03-01

    High concentrations of cesium (Cs+) inhibit plant growth but the detailed mechanisms of Cs+ uptake, transport and response in plants are not well known. In order to identify small molecules with a capacity to enhance plant tolerance to Cs+, chemical library screening was performed using Arabidopsis. Of 10,000 chemicals tested, five compounds were confirmed as Cs+ tolerance enhancers. Further investigation and quantum mechanical modelling revealed that one of these compounds reduced Cs+ concentrations in plants and that the imidazole moiety of this compound bound specifically to Cs+. Analysis of the analogous compounds indicated that the structure of the identified compound is important for the effect to be conferred. Taken together, Cs+ tolerance enhancer isolated here renders plants tolerant to Cs+ by inhibiting Cs+ entry into roots via specific binding to the ion thus, for instance, providing a basis for phytostabilisation of radiocesium-contaminated farmland.

  17. Selective chemical binding enhances cesium tolerance in plants through inhibition of cesium uptake

    DEFF Research Database (Denmark)

    Adams, Eri; Chaban, Vitaly; Khandelia, Himanshu; Shin, Ryoung

    2015-01-01

    High concentrations of cesium (Cs(+)) inhibit plant growth but the detailed mechanisms of Cs(+) uptake, transport and response in plants are not well known. In order to identify small molecules with a capacity to enhance plant tolerance to Cs(+), chemical library screening was performed using...... Arabidopsis. Of 10,000 chemicals tested, five compounds were confirmed as Cs(+) tolerance enhancers. Further investigation and quantum mechanical modelling revealed that one of these compounds reduced Cs(+) concentrations in plants and that the imidazole moiety of this compound bound specifically to Cs......(+). Analysis of the analogous compounds indicated that the structure of the identified compound is important for the effect to be conferred. Taken together, Cs(+) tolerance enhancer isolated here renders plants tolerant to Cs(+) by inhibiting Cs(+) entry into roots via specific binding to the ion thus, for...

  18. A combined chemical + enzymatic method to remove selected aromatics from aqueous streams

    International Nuclear Information System (INIS)

    Aromatics are major pollutants found in aqueous environments and in sediments. While there are many chemical and biochemical processes to remove and/or destroy these contaminants, they have to be considered in light of the economics and the time-scales for treatment. We describe our initial work on a hybrid chemical + enzymatic technique to remove aromatics from aqueous stream. The aromatic is first converted to the corresponding phenol through classical Fenton type chemistry involving catalysis by Fe(II). The phenol is subsequently polymerized through an enzymatic mechanism, using horseradish peroxidase as the oxidative enzyme. The polymer is insoluble in water and can be easily recovered. In addition, such phenolic polymers are useful products with varied applications in coatings and resin technologies. Thus, the pollutants can be eventually converted to useful products

  19. Physico-chemical change and heat stability of extra virgin olive oils flavoured by selected Tunisian aromatic plants.

    Science.gov (United States)

    Ayadi, M A; Grati-Kamoun, N; Attia, H

    2009-10-01

    Objectives of this work were studying physico-chemical change and heat stability of olive oils flavoured by selected Tunisian aromatic plants. Flavoured olive oils were prepared by maceration of fresh plant materials (rosemary, lavender, sage, menthe, basil, lemon and thyme) with olive oil at a 5% w/w level for 15 days. A sensorial evaluation was applied to select more appreciate flavoured olive oils by consumers. An oxidative procedure was applied to test the stability of selected flavoured olive oils: oils samples were kept in glass bottles and heated at 60 and 130 degrees C during 55 days and 6h, respectively. The resistance to oxidation of these selected flavoured oils was compared to a control samples by measuring PV, K232 and K270 values and change in chlorophyll, carotenes and polyphénols contents. Obtained results show that addition of aromatic plants causes a slight increase in free acidity and viscosity of aromatised olive oils. L*, b* and a* values show that addition of thyme cause a great change in olive oil colours. Heat stability results shows that from selected aromatic plants, rosemary was effectiveness against oxidation followed by thyme and lemon. However, olive oil flavoured with basil exhibit a similar behaviour versus thermal oxidation then the natural olive oil. PMID:19635520

  20. Application of Photocured Polymer Ion Selective Membranes for Solid-State Chemical Sensors

    Directory of Open Access Journals (Sweden)

    Natalia Abramova

    2015-06-01

    Full Text Available Application of conducting polymers with additional functional groups for a solid contact formation and photocurable membranes as sensitive elements of solid-state chemical sensors is discussed. Problems associated with application of UV-curable polymers for sensors are analyzed. A method of sensor fabrication using copolymerized conductive layer and sensitive membrane is presented and the proof of concept is confirmed by two examples of solid-contact electrodes for Ca ions and pH.

  1. Application of Photocured Polymer Ion Selective Membranes for Solid-State Chemical Sensors

    OpenAIRE

    Natalia Abramova; Andrey Bratov

    2015-01-01

    Application of conducting polymers with additional functional groups for a solid contact formation and photocurable membranes as sensitive elements of solid-state chemical sensors is discussed. Problems associated with application of UV-curable polymers for sensors are analyzed. A method of sensor fabrication using copolymerized conductive layer and sensitive membrane is presented and the proof of concept is confirmed by two examples of solid-contact electrodes for Ca ions and pH.

  2. "A Note on New Product Project Selection Model: Empirical Analysis in Chemical Industry" (in Japanese)

    OpenAIRE

    Kenichi Kuwashima; Junichi Tomita

    2001-01-01

    By focusing its attention on one particular scoring method that is used to evaluate R&D projects, this paper seeks to specify empirically the factors that discriminate successful projects from failed projects in the Japanese chemical industry. Our statistical analysis revealed that when projects are evaluated in this industry, three factors, marketability, technology, and synergistic potential, tend to be valued by practitioners approximately in a 3:2:1 ratio. Although the project evaluations...

  3. Comparison of Selected Methods for Individual Decontamination of Chemical Warfare Agents

    OpenAIRE

    Tomas Capoun; Jana Krykorkova

    2014-01-01

    This study addresses the individual decontamination of chemical warfare agents (CWA) and other hazardous substances. The individual decontamination applies to contaminated body surfaces, protective clothing and objects immediately after contamination, performed individually or by mutual assistance using prescribed or improvised devices. The article evaluates the importance of individual decontamination, security level for Fire and Rescue Service Units of the Czech Republic (FRS CR) and demons...

  4. Chemical contaminants on DOE lands and selection of contaminant mixtures for subsurface science research

    Energy Technology Data Exchange (ETDEWEB)

    Riley, R.G.; Zachara, J.M. [Pacific Northwest Lab., Richland, WA (United States)

    1992-04-01

    This report identifies individual contaminants and contaminant mixtures that have been measured in the ground at 91 waste sites at 18 US Department of Energy (DOE) facilities within the weapons complex. The inventory of chemicals and mixtures was used to identify generic chemical mixtures to be used by DOE`s Subsurface Science Program in basic research on the subsurface geochemical and microbiological behavior of mixed contaminants (DOE 1990a and b). The generic mixtures contain specific radionuclides, metals, organic ligands, organic solvents, fuel hydrocarbons, and polychlorinated biphenyls (PCBs) in various binary and ternary combinations. The mixtures are representative of in-ground contaminant associations at DOE facilities that are likely to exhibit complex geochemical behavior as a result of intercontaminant reactions and/or microbiologic activity stimulated by organic substances. Use of the generic mixtures will focus research on important mixed contaminants that are likely to be long-term problems at DOE sites and that will require cleanup or remediation. The report provides information on the frequency of associations among different chemicals and compound classes at DOE waste sites that require remediation.

  5. Chemical contaminants on DOE lands and selection of contaminant mixtures for subsurface science research

    Energy Technology Data Exchange (ETDEWEB)

    Riley, R.G.; Zachara, J.M. (Pacific Northwest Lab., Richland, WA (United States))

    1992-04-01

    This report identifies individual contaminants and contaminant mixtures that have been measured in the ground at 91 waste sites at 18 US Department of Energy (DOE) facilities within the weapons complex. The inventory of chemicals and mixtures was used to identify generic chemical mixtures to be used by DOE's Subsurface Science Program in basic research on the subsurface geochemical and microbiological behavior of mixed contaminants (DOE 1990a and b). The generic mixtures contain specific radionuclides, metals, organic ligands, organic solvents, fuel hydrocarbons, and polychlorinated biphenyls (PCBs) in various binary and ternary combinations. The mixtures are representative of in-ground contaminant associations at DOE facilities that are likely to exhibit complex geochemical behavior as a result of intercontaminant reactions and/or microbiologic activity stimulated by organic substances. Use of the generic mixtures will focus research on important mixed contaminants that are likely to be long-term problems at DOE sites and that will require cleanup or remediation. The report provides information on the frequency of associations among different chemicals and compound classes at DOE waste sites that require remediation.

  6. A corona discharge atmospheric pressure chemical ionization source with selective NO(+) formation and its application for monoaromatic VOC detection.

    Science.gov (United States)

    Sabo, Martin; Matejčík, Štefan

    2013-11-21

    We have developed a new type of corona discharge (CD) for atmospheric pressure chemical ionization (APCI) for application in ion mobility spectrometry (IMS) as well as in mass spectrometry (MS). While the other CD-APCI sources are able to generate H3O(+)·(H2O)n as the major reactant ions in N2 or in zero air, the present CD-APCI source has the ability to generate up to 84% NO(+)·(H2O)n reactant ions in zero air. The change of the working gas from zero air to N2 allows us to change the major reactant ions from NO(+)·(H2O)n to H3O(+)·(H2O)n. In this paper we present the description of the new CD-APCI and discuss the processes associated with the NO(+) formation. The selective formation of NO(+)·(H2O)n reactant ions offers chemical ionization based on these ions which can be of great advantage for some classes of chemicals. We demonstrate here a significant increase in the sensitivity of the IMS-MS instrument for monoaromatic volatile organic compound (VOC) detection upon NO(+)·(H2O)n chemical ionization. PMID:24081306

  7. A dispersion model of transport media in radiotracer investigations on selected chemical installations

    International Nuclear Information System (INIS)

    Tracer investigations of media transport through chemical reactors play a significant role in the chemical technology. They provide the basis for the determination of some important process parameters, such as flow character of the transported medium, degree of utilisation of the reactor volume during chemical transitions of substrates or even indicate possible mechanisms of chemical reactions. Determination of the medium flow characteristics is closely connected with the mathematical description of the process - a mathematical model of transport. The method of assessment of radiotracers suitability for the investigation of distillation processes presented in this paper allows to determine, in a simple manner, the parameters of distillation characteristics of the radionuclides, the average distillation temperature, the range of distillation temperatures, a suitable radiochemical purity. These parameters precisely determine the behavior of tracers to be expected in a wide range of variable conditions of the distillation process. Applications of tracer tested in such a manner to the investigations of dynamics of media in the industrial rectification columns has resulted in obtaining a dependable evaluation of the performance of these columns in a wide range of changes of their operational parameters. Particular attention has been paid to dynamics of the liquid [phase on the column plate. A dispersion model of liquid flow with hold-up zones has been proposed for the description of the liquid phase transport in the plate - overall assembly.The model consists of a number of flow and stagnant zones, with mass transfer between them. Another example of practical application of results from radiotracer investigation is an analysis of of phase dynamics in the installations designed for the process of liquefaction of Polish coals by means of their catalytic hydrogenation. For the analysis of phase transport in a reaction vessel various mathematical models were applied with

  8. Selective epitaxy of gallium nitride and related materials by metal-organic chemical vapor depostion

    Science.gov (United States)

    Kapolnek, David Joseph

    1999-11-01

    Selective epitaxy has been applied to many semiconductor materials for a variety of applications. We have developed basic selective epitaxy processes for Gallium Nitride, an important wide band gap semiconductor. This work has revealed that in many respects, GaN behaves similarly to other semiconductors. This makes possible such applications as regrown FET contacts and other three-dimensional device structures. In addition, selective growth using relatively small mask openings results in highly anisotropic growth that is exploited for a number of other applications. GaN pyramids grown using circular mask openings are ideal structures for GaN electron field emission devices. Lateral epitaxial overgrowth grown with linear mask openings is an exciting process that has recently been used for both GaN dislocation reduction and for buried structures in GaN epitaxial films. The discovery of GaN LEO has resulted in an explosion of research and has been applied in commercial GaN laser diodes. The fundamentals of Gallium Nitride selective epitaxy and the most important applications are contained in this dissertation.

  9. Antibacterial activity and Chemical Composition of Essential Oils of Ten Aromatic Plants against selected Bacteria

    OpenAIRE

    Pooja Bharti; Sheema Bai; Leena Seasotiya; Anupma Malik; Sunita Dalal

    2012-01-01

    The antibacterial activity of essential oils from ten aromatic plants Thymus vulgaris, Melaleuca alternifolia, Zanthoxylum rhetsa, Coriandrum sativum, Nardostachys jatamansi, Eucalyptus globules, Cyperus scariosus, Cinnamomum cecidodaphne, Olea europea, Foeniculum vulgare have been determined against nine selected bacteria. Essential oils from Thymus vulgaris, Melaleuca alternifolia and Eucalyptus globulus were found to possess maximum antibacterial activity. The GC-MS analyses of these oils ...

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-01-15

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

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

    International Nuclear Information System (INIS)

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

  14. Selective epitaxial Si based layers and TiSi 2 deposition by integrated chemical vapor deposition

    Science.gov (United States)

    Regolini, J. L.; Margail, J.; Bodnar, S.; Maury, D.; Morin, C.

    1996-07-01

    High performance IC manufacturing requirements, such as large diameter wafer uniformity, reproducibility, throughput and reliability can be fulfilled by commercial integrated processing, single wafer cluster tools. This paper presents results obtained on an industrial cluster reactor for 200 mm wafers by combining epitaxial silicon related materials and selective deposition of TiSi 2. Low temperature epitaxial Si and SiGe alloys are studied for buried thin layers used in CMOS and HBT devices. The doping profile abruptness for B and P are within SIMS resolution limits. TheTiSi 2/Si selective deposition is also investigated, sequentially and in situ, as a technique for future salicidedS/D with a reduction in technological steps and interface contamination. Statistical electrical results obtained using 0.35 and 0.25 μm CMOS technologies in which the CVD silicide deposition is tested, are presented and compared with the standard salicide technique.

  15. Chemical-technological approach to the selection of ceramic materials with predetermined thermistor properties

    Energy Technology Data Exchange (ETDEWEB)

    Plewa, J.; Altenburg, H. [Fachhochschule Muenster, Steinfurt (Germany). SIMa and Supraleiter-Keramik-Kristalle; Brunner, M. [Fachhochschule Koeln (Germany). Elektronische Bauelemente; Shpotyuk, O.; Vakiv, M. [Scientific Research Co. ' ' Carat' ' , Lviv Scientific Research Inst. of Materials, Lviv (Ukraine)

    2002-07-01

    The selection possibilities of quaternary Cu-Ni-Co-Mn oxide system restricted by cubic spinels (CuMn{sub 2}O{sub 4}, MnCo{sub 2}O{sub 4} and NiMn{sub 2}O{sub 4}) for NTC thermistors application were discussed. Phase compositions, microstructural features and electrical properties of the investigated spinel-structured ceramics were studied in tight connection with technological regimes of their sintering. (orig.)

  16. Phase diagram of selectively cross-linked block copolymers shows chemically microstructured gel

    OpenAIRE

    von der Heydt, Alice; Zippelius, Annette

    2014-01-01

    We study analytically the intricate phase behavior of cross-linked $AB$ diblock copolymer melts, which can undergo two main phase transitions due to quenched random constraints: Gelation, i.e., spatially random localization of polymers forming a system-spanning cluster, is driven by increasing the number parameter $\\mu$ of irreversible, type-selective cross-links between random pairs of $A$ blocks. Self-assembly into a periodic pattern of $A$/$B$-rich microdomains (microphase separation) is c...

  17. A bootstrapping soft shrinkage approach for variable selection in chemical modeling.

    Science.gov (United States)

    Deng, Bai-Chuan; Yun, Yong-Huan; Cao, Dong-Sheng; Yin, Yu-Long; Wang, Wei-Ting; Lu, Hong-Mei; Luo, Qian-Yi; Liang, Yi-Zeng

    2016-02-18

    In this study, a new variable selection method called bootstrapping soft shrinkage (BOSS) method is developed. It is derived from the idea of weighted bootstrap sampling (WBS) and model population analysis (MPA). The weights of variables are determined based on the absolute values of regression coefficients. WBS is applied according to the weights to generate sub-models and MPA is used to analyze the sub-models to update weights for variables. The optimization procedure follows the rule of soft shrinkage, in which less important variables are not eliminated directly but are assigned smaller weights. The algorithm runs iteratively and terminates until the number of variables reaches one. The optimal variable set with the lowest root mean squared error of cross-validation (RMSECV) is selected. The method was tested on three groups of near infrared (NIR) spectroscopic datasets, i.e. corn datasets, diesel fuels datasets and soy datasets. Three high performing variable selection methods, i.e. Monte Carlo uninformative variable elimination (MCUVE), competitive adaptive reweighted sampling (CARS) and genetic algorithm partial least squares (GA-PLS) are used for comparison. The results show that BOSS is promising with improved prediction performance. The Matlab codes for implementing BOSS are freely available on the website: http://www.mathworks.com/matlabcentral/fileexchange/52770-boss. PMID:26826688

  18. K-targeted metabolomic analysis extends chemical subtraction to DESIGNER extracts: selective depletion of extracts of hops (Humulus lupulus).

    Science.gov (United States)

    Ramos Alvarenga, René F; Friesen, J Brent; Nikolić, Dejan; Simmler, Charlotte; Napolitano, José G; van Breemen, Richard; Lankin, David C; McAlpine, James B; Pauli, Guido F; Chen, Shao-Nong

    2014-12-26

    This study introduces a flexible and compound targeted approach to Deplete and Enrich Select Ingredients to Generate Normalized Extract Resources, generating DESIGNER extracts, by means of chemical subtraction or augmentation of metabolites. Targeting metabolites based on their liquid-liquid partition coefficients (K values), K targeting uses countercurrent separation methodology to remove single or multiple compounds from a chemically complex mixture, according to the following equation: DESIGNER extract = total extract ± target compound(s). Expanding the scope of the recently reported depletion of extracts by immunoaffinity or solid phase liquid chromatography, the present approach allows a more flexible, single- or multi-targeted removal of constituents from complex extracts such as botanicals. Chemical subtraction enables both chemical and biological characterization, including detection of synergism/antagonism by both the subtracted targets and the remaining metabolite mixture, as well as definition of the residual complexity of all fractions. The feasibility of the DESIGNER concept is shown by K-targeted subtraction of four bioactive prenylated phenols, isoxanthohumol (1), 8-prenylnaringenin (2), 6-prenylnaringenin (3), and xanthohumol (4), from a standardized hops (Humulus lupulus L.) extract using specific solvent systems. Conversely, adding K-targeted isolates allows enrichment of the original extract and hence provides an augmented DESIGNER material. Multiple countercurrent separation steps were used to purify each of the four compounds, and four DESIGNER extracts with varying depletions were prepared. The DESIGNER approach innovates the characterization of chemically complex extracts through integration of enabling technologies such as countercurrent separation, K-by-bioactivity, the residual complexity concepts, as well as quantitative analysis by (1)H NMR, LC-MS, and HiFSA-based NMR fingerprinting. PMID:25437744

  19. Distribution and relationships between selected chemical elements in green alga Enteromorpha sp. from the southern Baltic

    International Nuclear Information System (INIS)

    The concentrations of heavy metals (Cd, Cu, Ni, Pb, Zn and Mn) and macroelements (K, Na, Ca and Mg) were determined in green alga Enteromorpha sp. from the coastal zone of the southern Baltic including Gulf of Gdansk and Vistula Lagoon in 2000-2003. In order to estimate the degree of accumulation of each element by the green alga, concentration and discrimination factors (CFs) with respect to seawater were calculated. The results of factor analysis (FA) and ANOVA clearly indicate geographical differences between concentrations of chemical elements. Enteromorpha sp. from Vistula Lagoon and the southern Baltic exhibited higher levels of Mn and Ni, and Na and K, respectively. Anthropogenic impact of Cu, Pb and Zn, possibly originated from municipal sewage, was identified in alga samples collected in the Gulf of Gdansk, especially in the vicinity of Gdynia. From comparison our data with those published earlier results that Pb content in Enteromorpha sp. from the Gulf of Gdansk decreased within 1978-2003 reflecting reducing use of leaded petrol in Baltic countries in this period. The alga Enteromorpha sp. can be used for biomonitoring surveys of metal contaminants in coastal areas of the Baltic Sea. - Enteromorpha sp. can be used as efficient biomonitor for chemical elements in coastal areas of the Baltic Sea

  20. PHYSICO-CHEMICAL ANALYSIS OF SELECTED GROUND WATER SAMPLES OF RURAL AREAS OF JAIPUR, RAJASTHAN

    Directory of Open Access Journals (Sweden)

    Priyanka Dhingra

    2014-12-01

    Full Text Available The aim of present study was to assess the status of the groundwater in rural areas of Jaipur city. People on globe are under tremendous threat due to undesired changes in the physical, chemical and biological characteristics of air, water and soil. Due to increased population, urbanization, industrialization, use of fertilizers water is highly polluted with different harmful contaminants Natural water resources are being contaminated due to weathering of rocks and leaching of soil, mining processing etc. It is necessary that quality of drinking water should be checked at regular time interval to prevent various water born diseases. In present analysis physico-chemical parameter of drinking water viz. pH, hardness, TDS, residual chlorine, dissolved oxygen, electrical conductivity, Free CO2 have been analyzed. Drinking water quality of 8 villages of Amber District Jaipur, Rajasthan was analyzed to identify the nature and quality of water. The drinking water samples were collected in clean polythene one liter cans and subjected for analysis in laboratory. The main objective of the present paper is to aware people of concerned area about the water quality and concerned health hazards.

  1. Physical, chemical and mineralogical characteristics of some selected gardud soils of kordofan region

    International Nuclear Information System (INIS)

    Recently much of the attention is given to gardud soil as the main alternative for the depleted marginal sandy soils. A lack of exact knowledge regarding these soils are evident. For studying gardud soil four sites were chosen according to the annual rainfall. Two pits were excavated in each site to represent the concaved and convexed locations plus composite samples to cover the area between two pits. Morphological, physical, chemical and mineralogical investigations were made. The results showed that the gardud soils were relatively differed within and between sites due to the climate and the topography. The dominant clay minerals are kaolinite, montmorillonite and illte. The chemical and physical characteristics were poor. Some of the restrictions limiting the use of these soils such as erosion, hardness, fertility, stoniness, drought and acidity. According to the American system of soil classification, the soils studied were given the following classification: (1) Bardab soil: (A) Kanhablic rhodustalf-fine clay, kaolinite, isohyperthermic (concaved). (B) Kandic paleustalf-very fine clay, kaolinite, isohyperthermic (convexed). (2) Sodari: (A) Typic comborthid-coarse loamy, mixed hyperthermic (concave). (B) Typic comborthid-coarse loamy, mixed hyperthermic (convexed). (3) Nihud (Rahad Elsilk): (A) Rhodic paleustalf-fine loamy, kaolinite isohyperthermic (concaved). (B) Aridic paleustalf-fine loamy kaolinite isohyperthermic (convexed). (4) Umgamalla: (A) Ustic hapustalf-fine loamy kaolinite isohyperthermic (concaved). (B)Ustic hapustalf-fine loamy kaolinite isohyperthermic (convexed). (Author)

  2. Distribution and relationships between selected chemical elements in green alga Enteromorpha sp. from the southern Baltic

    Energy Technology Data Exchange (ETDEWEB)

    Zbikowski, Radoslaw [Department of Food Sciences, Medical University of Gdansk, al. Gen. J Hallera 107, PL 80-416 Gdansk (Poland); Institute of Oceanography, University of Gdansk, Av. Pilsudskiego 46, PL 81-378 Gdynia (Poland); Szefer, Piotr [Department of Food Sciences, Medical University of Gdansk, al. Gen. J Hallera 107, PL 80-416 Gdansk (Poland)]. E-mail: pszef@amg.gda.pl; Latala, Adam [Institute of Oceanography, University of Gdansk, Av. Pilsudskiego 46, PL 81-378 Gdynia (Poland)

    2006-10-15

    The concentrations of heavy metals (Cd, Cu, Ni, Pb, Zn and Mn) and macroelements (K, Na, Ca and Mg) were determined in green alga Enteromorpha sp. from the coastal zone of the southern Baltic including Gulf of Gdansk and Vistula Lagoon in 2000-2003. In order to estimate the degree of accumulation of each element by the green alga, concentration and discrimination factors (CFs) with respect to seawater were calculated. The results of factor analysis (FA) and ANOVA clearly indicate geographical differences between concentrations of chemical elements. Enteromorpha sp. from Vistula Lagoon and the southern Baltic exhibited higher levels of Mn and Ni, and Na and K, respectively. Anthropogenic impact of Cu, Pb and Zn, possibly originated from municipal sewage, was identified in alga samples collected in the Gulf of Gdansk, especially in the vicinity of Gdynia. From comparison our data with those published earlier results that Pb content in Enteromorpha sp. from the Gulf of Gdansk decreased within 1978-2003 reflecting reducing use of leaded petrol in Baltic countries in this period. The alga Enteromorpha sp. can be used for biomonitoring surveys of metal contaminants in coastal areas of the Baltic Sea. - Enteromorpha sp. can be used as efficient biomonitor for chemical elements in coastal areas of the Baltic Sea.

  3. Selection of potential cold water marine species for testing of oil dispersants, and chemically dispersed oil

    International Nuclear Information System (INIS)

    A study regarding marine species for toxicity testing for Alaska conditions was presented and the potential adverse impacts of a large marine oil spill in cold water were discussed with the objective to determine if the spill should be treated by the use of oil dispersants. Without dispersion, the oil can pollute marine epifauna and can deposit on beaches. The decision to apply dispersants to a marine oil spill requires knowledge of the toxicity of the undispersed oil to pelagic marine life occurring via natural dispersion as opposed to the toxicity of the oil-dispersant mixture. Most standard toxicity tests apply to warm water species. This paper discussed the need to have a standard test species relevant to Alaska waters for toxicity testing. In this study, toxicity testing was done according to the methods of the Chemical Response to Oil Spills : Ecological Effects Research Forum (CROSERF). The testing included capturing adult species in the winter and holding them until larval hatching. Toxicity testing was completed in a narrow time frame before hatching ceased. Many chemical samples were tested. Topsmelt, urchins, shellfish, mysids, copepods, pink salmon fry, and tidepool sculpin were considered by the author to be the most useful for certain types of toxicity testing. 29 refs

  4. Selective Laser Sintering And Melting Of Pristine Titanium And Titanium Ti6Al4V Alloy Powders And Selection Of Chemical Environment For Etching Of Such Materials

    Directory of Open Access Journals (Sweden)

    Dobrzański L.A.

    2015-09-01

    Full Text Available The aim of the investigations described in this article is to present a selective laser sintering and melting technology to fabricate metallic scaffolds made of pristine titanium and titanium Ti6Al4V alloy powders. Titanium scaffolds with different properties and structure were manufactured with this technique using appropriate conditions, notably laser power and laser beam size. The purpose of such elements is to replace the missing pieces of bones, mainly cranial and facial bones in the implantation treatment process. All the samples for the investigations were designed in CAD/CAM (3D MARCARM ENGINEERING AutoFab (Software for Manufacturing Applications software suitably integrated with an SLS/SLM system. Cube-shaped test samples dimensioned 10×10×10 mm were designed for the investigations using a hexagon-shaped base cell. The so designed 3D models were transferred to the machine software and the actual rapid manufacturing process was commenced. The samples produced according to the laser sintering technology were subjected to chemical processing consisting of etching the scaffolds’ surface in different chemical mediums. Etching was carried out to remove the loosely bound powder from the surface of scaffolds, which might detach from their surface during implantation treatment and travel elsewhere in an organism. The scaffolds created were subjected to micro- and spectroscopic examinations

  5. 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.

  6. Chemically selective NMR imaging of a 3-component (solid-solid-liquid) sedimenting system.

    Science.gov (United States)

    Beyea, Steven D; Altobelli, Stephen A; Mondy, Lisa A

    2003-04-01

    A novel magnetic resonance imaging (MRI) technique which resolves the separate components of the evolving vertical concentration profiles of 3-component non-colloidal suspensions is described. This method exploits the sensitivity of MRI to chemical differences between the three phases to directly image the fluid phase and one of the solid phases, with the third phase obtained by subtraction. 19F spin-echo imaging of a polytetrafluoroethylene (PTFE) oil was interlaced with 1H SPRITE imaging of low-density polyethylene (LDPE) particles. The third phase was comprised of borosilicate glass spheres, which were not visible while imaging the PTFE or LDPE phases. The method is demonstrated by performing measurements on 2-phase materials containing only the floating (LDPE) particles, with the results contrasted to the experimental behaviour of the individual phases in the full 3-phase system. All experiments were performed using nearly monodisperse particles, with initial suspension volume fractions, phi(i), of 0.1. PMID:12713970

  7. Chemical composition of selected seaweeds from the Indian Ocean, KwaZulu-Natal coast, South Africa.

    Science.gov (United States)

    Magura, Judie; Moodley, Roshila; Jonnalagadda, Sreekantha B

    2016-08-01

    The chemical composition of three edible seaweeds (Codium capitatum, Hypnea spicifera and Sargassum elegans) and two inedible seaweeds (Halimeda cuneata and Spyridia hypnoides) from the Indian Ocean along the KwaZulu-Natal East Coast, South Africa were investigated as a function of seasonal variation. The proximate compositions of the edible seaweeds were determined. In edible seaweeds, the moisture level ranged from 85.4 to 89.5%, protein from 6.1 to 11.8%, lipids from 7.5 to 13.1% and carbohydrates from 37.8 to 71.9%. Elemental concentrations in the five studied seaweeds varied significantly with season (P health effects due to low concentrations of toxic elements. However, due to high levels of As in S. elegans, its consumption should be moderated to reduce dietary exposure to this toxic element. PMID:27153179

  8. Selective charge doping of chemical vapor deposition-grown graphene by interface modification

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Shengnan, E-mail: wang.shengnan@lab.ntt.co.jp; Suzuki, Satoru; Furukawa, Kazuaki; Orofeo, Carlo M.; Takamura, Makoto; Hibino, Hiroki [NTT Basic Research Laboratories, NTT Corporation, Atsugi, Kanagawa 243-0198 (Japan)

    2013-12-16

    The doping and scattering effect of substrate on the electronic properties of chemical vapor deposition (CVD)-grown graphene are revealed. Wet etching the underlying SiO{sub 2} of graphene and depositing self-assembled monolayers (SAMs) of organosilane between graphene and SiO{sub 2} are used to modify various substrates for CVD graphene transistors. Comparing with the bare SiO{sub 2} substrate, the carrier mobility of CVD graphene on modified substrate is enhanced by almost 5-fold; consistently the residual carrier concentration is reduced down to 10{sup 11} cm{sup −2}. Moreover, scalable and reliable p- and n-type graphene and graphene p-n junction are achieved on various silane SAMs with different functional groups.

  9. Selective charge doping of chemical vapor deposition-grown graphene by interface modification

    International Nuclear Information System (INIS)

    The doping and scattering effect of substrate on the electronic properties of chemical vapor deposition (CVD)-grown graphene are revealed. Wet etching the underlying SiO2 of graphene and depositing self-assembled monolayers (SAMs) of organosilane between graphene and SiO2 are used to modify various substrates for CVD graphene transistors. Comparing with the bare SiO2 substrate, the carrier mobility of CVD graphene on modified substrate is enhanced by almost 5-fold; consistently the residual carrier concentration is reduced down to 1011 cm−2. Moreover, scalable and reliable p- and n-type graphene and graphene p-n junction are achieved on various silane SAMs with different functional groups

  10. Selective charge doping of chemical vapor deposition-grown graphene by interface modification

    Science.gov (United States)

    Wang, Shengnan; Suzuki, Satoru; Furukawa, Kazuaki; Orofeo, Carlo M.; Takamura, Makoto; Hibino, Hiroki

    2013-12-01

    The doping and scattering effect of substrate on the electronic properties of chemical vapor deposition (CVD)-grown graphene are revealed. Wet etching the underlying SiO2 of graphene and depositing self-assembled monolayers (SAMs) of organosilane between graphene and SiO2 are used to modify various substrates for CVD graphene transistors. Comparing with the bare SiO2 substrate, the carrier mobility of CVD graphene on modified substrate is enhanced by almost 5-fold; consistently the residual carrier concentration is reduced down to 1011 cm-2. Moreover, scalable and reliable p- and n-type graphene and graphene p-n junction are achieved on various silane SAMs with different functional groups.

  11. Bioactive assessment of selected marine red algae against leishmania major and chemical constituents of osmundea pinnatifida

    International Nuclear Information System (INIS)

    Present bioconversion studies were carried out to convert drifted seaweed biomass into bioactive organic compost. Chemical analysis of the collected seaweed biomass from the Karachi coast revealed 60.30 % organic matter. Aerobic composting method i.e., windrow composting technique was applied for the conversion of collected seaweed biomass into organic compost. Employing this technique almost 70% biomass was converted into organic compost. On analysis, the compost obtained by the above method showed 2.3% Nitrogen, 0.86% Phosphate and 1.8% Potassium. Results for the analysis of heavy metals showed Mercury 0.05 mg / kg, Arsenic BDL Cadmium 0.080 mg / kg and Copper 7.1 mg / kg. Results for the biological evaluation of seaweed compost showed 78% germabilty while the Biogold and cow dung showed 83 and 60% germabilty. (author)

  12. A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells

    OpenAIRE

    Vedadi, Masoud; Barsyte-Lovejoy, Dalia; Liu, Feng; Rival-Gervier, Sylvie; Allali-Hassani, Abdellah; Labrie, Viviane; Wigle, Tim J.; DiMaggio, Peter A.; Wasney, Gregory A.; Siarheyeva, Alena; Dong, Aiping; Tempel, Wolfram; Wang, Sun-Chong; Chen, Xin; Chau, Irene

    2011-01-01

    Protein lysine methyltransferases G9a and GLP modulate the transcriptional repression of a variety of genes via dimethylation of Lys9 on histone H3 (H3K9me2) as well as dimethylation of non-histone targets. Here we report the discovery of UNC0638, an inhibitor of G9a and GLP with excellent potency and selectivity over a wide range of epigenetic and non-epigenetic targets. UNC0638 treatment of a variety of cell lines resulted in lower global H3K9me2 levels, equivalent to levels observed for sm...

  13. Rapid response behavior, at room temperature, of a nanofiber-structured TiO2 sensor to selected simulant chemical-warfare agents.

    Science.gov (United States)

    Ma, Xingfa; Zhu, Tao; Xu, Huizhong; Li, Guang; Zheng, Junbao; Liu, Aiyun; Zhang, Jianqin; Du, Huatai

    2008-02-01

    A chemical prototype sensor was constructed based on nanofiber-structured TiO2 and highly sensitive quartz resonators. The gas-sensing behavior of this new sensor to selected simulant warfare agents was investigated at room temperature. Results showed rapid response and good reversibility of this sensor when used with high-purity nitrogen. This provides a simple approach to preparation of materials needed as chemical sensors for selected organic volatiles or warfare agents. PMID:18094961

  14. Selectivity of Chemoresistive Sensors Made of Chemically Functionalized Carbon Nanotube Random Networks for Volatile Organic Compounds (VOC

    Directory of Open Access Journals (Sweden)

    Jean-François Feller

    2014-01-01

    Full Text Available Different grades of chemically functionalized carbon nanotubes (CNT have been processed by spraying layer-by-layer (sLbL to obtain an array of chemoresistive transducers for volatile organic compound (VOC detection. The sLbL process led to random networks of CNT less conductive, but more sensitive to vapors than filtration under vacuum (bucky papers. Shorter CNT were also found to be more sensitive due to the less entangled and more easily disconnectable conducting networks they are making. Chemical functionalization of the CNT’ surface is changing their selectivity towards VOC, which makes it possible to easily discriminate methanol, chloroform and tetrahydrofuran (THF from toluene vapors after the assembly of CNT transducers into an array to make an e-nose. Interestingly, the amplitude of the CNT transducers’ responses can be enhanced by a factor of five (methanol to 100 (chloroform by dispersing them into a polymer matrix, such as poly(styrene (PS, poly(carbonate (PC or poly(methyl methacrylate (PMMA. COOH functionalization of CNT was found to penalize their dispersion in polymers and to decrease the sensors’ sensitivity. The resulting conductive polymer nanocomposites (CPCs not only allow for a more easy tuning of the sensors’ selectivity by changing the chemical nature of the matrix, but they also allow them to adjust their sensitivity by changing the average gap between CNT (acting on quantum tunneling in the CNT network. Quantum resistive sensors (QRSs appear promising for environmental monitoring and anticipated disease diagnostics that are both based on VOC analysis.

  15. How Do I Know? A Guide to the Selection of Personal Protective Equipment for Use in Responding to A Release of Chemical Warfare Agents

    Energy Technology Data Exchange (ETDEWEB)

    Foust, C.B.

    1999-05-01

    An incident involving chemical warfare agents requires a unique hazardous materials (HAZMAT) response. As with an HAZMAT event, federal regulations prescribe that responders must be protected from exposure to the chemical agents. But unlike other HAZMAT events, special considerations govern selection of personal protective equipment (PPE). PPE includes all clothing, respirators and monitoring devices used to respond to a chemical release. PPE can differ depending on whether responders are military or civilian personnel.

  16. Characteristics and chemical compositions of particulate matter collected at the selected metro stations of Shanghai, China

    International Nuclear Information System (INIS)

    A campaign was conducted to assess and compare the air quality at the different metro platforms at Shanghai City, focusing on particulate matter (PM) levels, chemical compositions, morphology and mineralogy, as well as species of iron. Our results indicated that the average PM2.5 concentrations for the three metro lines were 177.7 μg/m3, 105.7 μg/m3 and 82.5 μg/m3, respectively, and the average PM1 concentrations for the three lines were 122.3 μg/m3, 84.1 μg/m3 and 59.6 μg/m3, respectively. Fe, Mn, Cr, Cu, Sr, Ba and Pb concentrations in all of the sampling sites were significantly higher than that in the urban ambient air, implicating that these trace metals may be associated with the metro systems working. Individual airborne dusts were studied for morphology and mineralogy characteristics. The results revealed that the presence of most individual particles were with no definite shape and most of them were with a large metal content. Furthermore, Fe-rich particles had significantly higher abundance in the metro systems, which were more frequently encountered in the underground lines than the aboveground line. The 2D distribution map of an interested Fe-rich particle showed an uneven Fe distribution, implying that a hollow or core of other substance exists in the particle center during the formation process. Cluster analysis revealed that Fe-rich particles were possibly a mixture of Fe species. Fitting of X-ray absorption near-edge fine structure spectra (XANES) showed the main iron species within the particles collected from the three contrasting metro lines of Shanghai to be hematite, magnetite, iron-metal and mineral Fe. Hematite and mineral Fe were all found in three lines, while magnetite only existed in aboveground metro line. Iron-metal was determined in both the older and younger underground lines, based on the X-ray diffraction (XRD) analysis. As diverse Fe species have different physical–chemical characteristics and toxicity, the speciation of Fe

  17. Chemical treatment of Escherichia coli: 3. Selective extraction of a recombinant protein from cytoplasmic inclusion bodies in intact cells.

    Science.gov (United States)

    Falconer, R J; O'Neill, B K; Middelberg, A P

    1999-02-20

    In previous parts of this study we developed procedures for the high-efficiency chemical extraction of soluble and insoluble protein from intact Escherichia coli cells. Although high yields were obtained, extraction of recombinant protein directly from cytoplasmic inclusion bodies led to low product purity due to coextraction of soluble contaminants. In this work, a two-stage procedure for the selective extraction of recombinant protein at high efficiency and high purity is reported. In the first stage, inclusion-body stability is promoted by the addition of 15 mM 2-hydroxyethyldisulfide (2-HEDS), also known as oxidized beta-mercaptoethanol, to the permeabilization buffer (6 M urea + 3 mM ethylenediaminetetraacetate [EDTA]). 2-HEDS is an oxidizing agent believed to promote disulfide bond formation, rendering the inclusion body resistant to solubilization in 6 M urea. Contaminating proteins are separated from the inclusion-body fraction by centrifugation. In the second stage, disulfide bonds are readily eliminated by including reducing agent (20 mM dithiothreitol [DTT]) into the permeabilization buffer. Extraction using this selective two-stage process yielded an 81% (w/w) recovery of the recombinant protein Long-R3-IGF-I from inclusion bodies located in the cytoplasm of intact E. coli, at a purity of 46% (w/w). This was comparable to that achieved by conventional extraction (mechanical disruption followed by centrifugation and solubilization). A pilot-scale procedure was also demonstrated using a stirred reactor and diafiltration. This is the first reported study that achieves both high extraction efficiency and selectivity by the chemical treatment of cytoplasmic inclusion bodies in intact bacterial cells. PMID:9921154

  18. Controllable synthesis of silver and silver sulfide nanocrystals via selective cleavage of chemical bonds

    International Nuclear Information System (INIS)

    A one-step colloidal process has been adopted to prepare silver (Ag) and silver sulfide (Ag2S) nanocrystals, thus avoiding presynthesis of an organometallic precursor and the injection of a toxic phosphine agent. During the reaction, a layered intermediate compound is first formed, which then acts as a precursor, decomposing into the nanocrystals. The composition of the as-obtained products can be controlled by selective cleavage of S–C bonds or Ag–S bonds. Pure Ag2S nanocrystals can be obtained by directly heating silver acetate (Ag(OAc)) and n-dodecanethiol (DDT) at 200 ° C without any surfactant, and pure Ag nanocrystals can be synthesized successfully if the reaction temperature is reduced to 190 ° C and the amount of DDT is decreased to 1 ml in the presence of a non-coordinating organic solvent (1-octadecene, ODE). Otherwise, the mixture of Ag and Ag2S is obtained by directly heating Ag(OAc) in DDT by increasing the reaction temperature or in a mixture of DDT and ODE at 200 ° C. The formation mechanism has been discussed in detail in terms of selective S–C and Ag–S bond dissociation due to the nucleophilic attack of DDT and the lower bonding energy of Ag–S. Interestingly, some products can easily self-assemble into two- or three-dimensional (2D or 3D) highly ordered superlattice structures on a copper grid without any additional steps. The excess DDT plays a key role in the superlattice structure due to the bundling and interdigitation of the thiolate molecules adsorbed on the as-obtained nanocrystals. (paper)

  19. Liquidus temperature and chemical durability of selected glasses to immobilize rare earth oxides waste

    Energy Technology Data Exchange (ETDEWEB)

    Mohd Fadzil, Syazwani Binti; Hrma, Pavel R.; Schweiger, Michael J.; Riley, Brian J.

    2015-06-30

    Pyroprocessing is a reprocessing method for managing and reusing used nuclear fuel (UNF) by dissolving it in an electrorefiner with a molten alkali or alkaline earth chloride salt mixture while avoiding wet reprocessing. Pyroprocessing UNF with a LiCl-KCl eutectic salt releases the fission products from the fuel and generates a variety of metallic and salt-based species, including rare earth (RE) chlorides. If the RE-chlorides are converted to oxides, borosilicate glass is a prime candidate for their immobilization because of its durability and ability to dissolve almost any RE waste component into the matrix at high loadings. Crystallization that occurs in waste glasses as the waste loading increases may complicate glass processing and affect the product quality. This work compares three types of borosilicate glasses in terms of liquidus temperature (TL): the International Simple Glass designed by the International Working Group, sodium borosilicate glass developed by Korea Hydro and Nuclear Power, and the lanthanide aluminoborosilicate (LABS) glass established in the United States. The LABS glass allows the highest waste loadings (over 50 mass% RE2O3) while possessing an acceptable chemical durability.

  20. Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif

    International Nuclear Information System (INIS)

    The DNA i-motif is a quadruplex structure formed in tandem cytosine-rich sequences in slightly acidic conditions. Besides being considered as a building block of DNA nano-devices, it may also play potential roles in regulating chromosome stability and gene transcriptions. The stability of i-motif is crucial for these functions. In this work, we investigated the mechanical stability of a single i-motif formed in the human telomeric sequence 5'-(CCCTAA)3CCC, which revealed a novel pH and loading rate-dependent bimodal unfolding force distribution. Although the cause of the bimodal unfolding force species is not clear, we proposed a phenomenological model involving a direct unfolding favored at lower loading rate or higher pH value, which is subject to competition with another unfolding pathway through a mechanically stable intermediate state whose nature is yet to be determined. Overall, the unique mechano—chemical responses of i-motif-provide a new perspective to its stability, which may be useful to guide designing new i-motif-based DNA mechanical nano-devices