Sample records for chemical shifts scs

  1. Experimental and theoretical study of substituent effect on 13C NMR chemical shifts of 5-arylidene-2,4-thiazolidinediones

    NASA Astrophysics Data System (ADS)

    Rančić, Milica P.; Trišović, Nemanja P.; Milčić, Miloš K.; Ajaj, Ismail A.; Marinković, Aleksandar D.

    2013-10-01

    The electronic structure of 5-arylidene-2,4-thiazolidinediones has been studied by using experimental and theoretical methodology. The theoretical calculations of the investigated 5-arylidene-2,4-thiazolidinediones have been performed by the use of quantum chemical methods. The calculated 13C NMR chemical shifts and NBO atomic charges provide an insight into the influence of such a structure on the transmission of electronic substituent effects. Linear free energy relationships (LFERs) have been further applied to their 13C NMR chemical shifts. The correlation analyses for the substituent-induced chemical shifts (SCS) have been performed with σ using SSP (single substituent parameter), field (σF) and resonance (σR) parameters using DSP (dual substituent parameter), as well as the Yukawa-Tsuno model. The presented correlations account satisfactorily for the polar and resonance substituent effects operative at Cβ, and C7 carbons, while reverse substituent effect was found for Cα. The comparison of correlation results for the investigated molecules with those obtained for seven structurally related styrene series has indicated that specific cross-interaction of phenyl substituent and groups attached at Cβ carbon causes increased sensitivity of SCS Cβ to the resonance effect with increasing of electron-accepting capabilities of the group present at Cβ.

  2. Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

    PubMed

    Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

    2014-02-11

    An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

  3. The influence of shear-velocity heterogeneity on ScS2/ScS amplitude ratios and estimates of Q in the mantle

    NASA Astrophysics Data System (ADS)

    Chaves, Carlos A. M.; Ritsema, Jeroen

    2016-08-01

    Regional waveforms of deep-focus Tonga-Fiji earthquakes indicate anomalous traveltime differences (ScS2-ScS) and amplitude ratios (ScS2/ScS) of the phases ScS and ScS2. The correlation between the ScS2-ScS delay time and the ScS2/ScS amplitude ratio suggests that shear wave apparent Q in the mantle below the Tonga-Fiji region is highest when shear wave velocities are lowest. This observation is unexpected if temperature variations were responsible for the seismic anomalies. Using spectral element method waveform simulations for four tomographic models, we demonstrate that focusing and scattering of shear waves by long-wavelength 3-D heterogeneity in the mantle may overwhelm the signal from intrinsic attenuation in long-period ScS2/ScS amplitude ratios. The tomographic models reproduce the trends in recorded ScS2-ScS difference times and ScS2/ScS amplitude ratios. Although they cannot be ruled out, variations in shear wave attenuation (i.e., the quality factor Q) are not necessary to explain the data.

  4. The influence of shear-velocity heterogeneity on ScS2/ScS amplitude ratios and estimates of Q in the mantle

    NASA Astrophysics Data System (ADS)

    Ritsema, J.; Chaves, C. A. M.

    2016-12-01

    Regional waveforms of deep-focus Tonga-Fiji earthquakes indicate anomalous traveltime differences (ScS2-ScS) and amplitude ratios (ScS2/ScS) of the phases ScS and ScS2. The correlation between the ScS2-ScS delay time and the ScS2/ScS amplitude ratio suggests that shear-wave apparent Q in the mantle below the Tonga-Fiji region is highest when shear-wave velocities are lowest. This observation is unexpected if temperature variations were responsible for the seismic anomalies. Using spectral-element-method waveform simulations for four tomographic models we demonstrate that focusing and scattering of shear waves by long-wavelength 3D heterogeneity in the mantle may overwhelm the signal from intrinsic attenuation in long-period ScS2/ScS amplitude ratios. The tomographic models reproduce the variability in recorded ScS2-ScS difference times and ScS2/ScS amplitude ratios. Variations in shear-wave attenuation (i.e., the quality factor Q) are not necessary to explain the data. An explanation for slow shear wave propagation without intrinsic attenuation does not require a creative solution from mineral physics.

  5. New Properties of Drosophila scs and scs’ Insulators

    PubMed Central

    Kyrchanova, Olga; Leman, Dmitry; Parshikov, Alexander; Fedotova, Anna; Studitsky, Vasily; Maksimenko, Oksana; Georgiev, Pavel

    2013-01-01

    Insulators are defined as a class of regulatory elements that delimit independent transcriptional domains within eukaryotic genomes. The first insulators to be identified were scs and scs', which flank the domain including two heat shock 70 genes. Zw5 and BEAF bind to scs and scs', respectively, and are responsible for the interaction between these insulators. Using the regulatory regions of yellow and white reporter genes, we have found that the interaction between scs and scs' improves the enhancer-blocking activity of the weak scs' insulator. The sequences of scs and scs' insulators include the promoters of genes that are strongly active in S2 cells but not in the eyes, in which the enhancer-blocking activity of these insulators has been extensively examined. Only the promoter of the Cad87A gene located at the end of the scs insulator drives white expression in the eyes, and the white enhancer can slightly stimulate this promoter. The scs insulator contains polyadenylation signals that may be important for preventing transcription through the insulator. As shown previously, scs and scs' can insulate transcription of the white transgene from the enhancing effects of the surrounding genome, a phenomenon known as the chromosomal position effect (CPE). After analyzing many independent transgenic lines, we have concluded that transgenes carrying the scs insulator are rarely inserted into genomic regions that stimulate the white reporter expression in the eyes. PMID:23638134

  6. Substituent effect study on experimental ¹³C NMR chemical shifts of (3-(substituted phenyl)-cis-4,5-dihydroisoxazole-4,5-diyl)bis(methylene)diacetate derivatives.

    PubMed

    Kara, Yesim S

    2015-12-05

    Eleven novel (3-(substituted phenyl)-cis-4,5-dihydroisoxazole-4,5-diyl)bis(methylene) diacetate derivatives were synthesized in the present study. These dihydroisoxazole derivatives were characterized by IR, (1)H NMR, (13)C NMR and elemental analyses. Their (13)C NMR spectra were measured in Deuterochloroform (CDCl3). The correlation analysis for the substituent-induced chemical shift (SCS) with Hammett substituent constant (σ), inductive substituent constant (σI), different of resonance substituent constants (σR, σR(o)) and Swain-Lupton substituent parameters (F, R) were performed using SSP (single substituent parameter), and DSP (dual substituent parameter) methods, as well as single and multiple regression analysis. From the result of regression analysis, the effect of substituent on the (13)C NMR chemical shifts was explained. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Environmental concerns of supply chain sustainability (SCS)

    NASA Astrophysics Data System (ADS)

    Mokhtar, Mohd Faiz; Omar, Badrul; Nor, Nik Hisyamudin Muhd; Pauzi, Nur Fazlinda Mohd; Hasan, Sulaiman; Mohamed, W. A. Wan

    2017-04-01

    Environment concern is one important aspect for supply chain sustainability (SCS). Nowadays, company's activities give a lot of impact on the environment. Through these activities, there are other SCS issue of environment were identified. In this paper, the proposed SCS issue of environmental concern will be determined from Corporate Sustainability Report (CSR). Using a total weightage of 0.333 (after dividing into three aspects of sustainability), each proposed issues will be classified according to the company activities in order to determined weightage for each issue. Those weightages then will be used in developing of score metric for SCS in design phase. Result shows that the carbon footprint is the major concern for SCS of environment while environmental management system is a lowest concern for SCS environment.

  8. Chemical Vapor Deposited SiC (SCS-0) Fiber-Reinforced Strontium Aluminosilicate Glass-Ceramic Composites

    NASA Technical Reports Server (NTRS)

    Bansal, Narottam P.

    1997-01-01

    Unidirectional SrO Al2O3 2SiO2 glass-ceramic matrix composites reinforced with uncoated Chemical Vapor Deposited (CVD) SiC (SCS-0) fibers have been fabricated by hot-pressing under appropriate conditions using the glass-ceramic approach. Almost fully dense composites having a fiber volume fraction of 0.24 have been obtained. Monoclinic celsian, SrAl2Si2O8, was the only crystalline phase observed in the matrix by x-ray diffraction. No chemical reaction was observed between the fiber and the matrix after high temperature processing. In three-point flexure, the composite exhibited a first matrix cracking stress of approx. 231 +/- 20 MPa and an ultimate strength of 265 +/- 17 MPa. Examination of fracture surfaces revealed limited short length fiber pull-out. From fiber push-out, the fiber/matrix interfacial debonding and frictional strengths were evaluated to be approx. 17.5 +/- 2.7 MPa and 11.3 +/- 1.6 MPa, respectively. Some fibers were strongly bonded to the matrix and could not be pushed out. The micromechanical models were not useful in predicting values of the first matrix cracking stress as well as the ultimate strength of the composites.

  9. A Short History of Three Chemical Shifts

    ERIC Educational Resources Information Center

    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…

  10. (13)C NMR substituent-induced chemical shifts in 4-(substituted phenyl)-3-phenyl-1,2,4-oxadiazol-5(4H)-ones (thiones).

    PubMed

    Kara, Yesim Saniye

    2015-01-01

    In the present, study mostly novel ten 4-(substituted phenyl)-3-phenyl-1,2,4-oxadiazol-5(4H)-ones and ten 4-(substituted phenyl)-3-phenyl-1,2,4-oxadiazol-5(4H)-thiones were synthesized. These oxadiazole derivatives were characterized by IR, (1)H NMR, (13)C NMR and elemental analyses. Their (13)C NMR spectra were measured in Deuterochloroform (CDCl3). The correlation analysis for the substituent-induced chemical shift (SCS) with Hammett substituent constants (σ), Brown Okamoto substituent constants (σ(+), σ(-)), inductive substituent constants (σI) and different of resonance substituent constants (σR, σR(o)) were performed using SSP (single substituent parameter), DSP (dual substituent parameter) and DSP-NLR (dual substituent parameter-non-linear resonance) methods, as well as single and multiple regression analysis. Negative ρ values were found for all correlations (reverse substituent effect). The results of all statistical analyses, (13)C NMR chemical shift of CN, CO and CS carbon of oxadiazole rings have shown satisfactory correlation. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. The microstructures of SCS-6 and SCS-8 SiC reinforcing fibers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sattler, M.L.; Kinney, J.H.; Zywicz, E.

    The microstructures of SCS-6 and SCS-8 SiC fibers have been examined and analyzed using high resolution transmission electron microscopy (HRTEM), microdiffraction, parallel electron energy loss spectroscopy (PEELS), x-ray diffraction and x-ray spectroscopy. The results of the study confirm findings from earlier studies wherein the microstructure of the fibers have been described as consisting of {beta}-SiC grown upon a monofilament turbostratic carbon core. The present study, however, provides much more detail regarding this microstructure. For example, PEELS spectroscopy and x-ray microscopy indicate that the composition of the SiC varies smoothly from SiC plus free C near the carbon core to SiCmore » at the midradial boundary. The SiC stoichiometry is roughly preserved from the midradial boundary to the exterior interface. HRTEM, microdiffraction, and dark field images provide evidence that the excess carbon is amorphous free carbon which is most likely situated at the grain boundaries of the SiC. The x-ray microscopy results are also consistent with the presence of two phases near the core which consist of SiC and free carbon having density less than graphite (2.25 g/cc). This complex microstructure may explain the recent observations of nonplanar failure in composites fabricated with SCS fibers.« less

  12. Quantum-mechanics-derived 13Cα chemical shift server (CheShift) for protein structure validation

    PubMed Central

    Vila, Jorge A.; Arnautova, Yelena A.; Martin, Osvaldo A.; Scheraga, Harold A.

    2009-01-01

    A server (CheShift) has been developed to predict 13Cα chemical shifts of protein structures. It is based on the generation of 696,916 conformations as a function of the φ, ψ, ω, χ1 and χ2 torsional angles for all 20 naturally occurring amino acids. Their 13Cα chemical shifts were computed at the DFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regression formula, to reproduce the values obtained with a larger basis set. Analysis of the accuracy and sensitivity of the CheShift predictions, in terms of both the correlation coefficient R and the conformational-averaged rmsd between the observed and predicted 13Cα chemical shifts, was carried out for 3 sets of conformations: (i) 36 x-ray-derived protein structures solved at 2.3 Å or better resolution, for which sets of 13Cα chemical shifts were available; (ii) 15 pairs of x-ray and NMR-derived sets of protein conformations; and (iii) a set of decoys for 3 proteins showing an rmsd with respect to the x-ray structure from which they were derived of up to 3 Å. Comparative analysis carried out with 4 popular servers, namely SHIFTS, SHIFTX, SPARTA, and PROSHIFT, for these 3 sets of conformations demonstrated that CheShift is the most sensitive server with which to detect subtle differences between protein models and, hence, to validate protein structures determined by either x-ray or NMR methods, if the observed 13Cα chemical shifts are available. CheShift is available as a web server. PMID:19805131

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

    PubMed

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

    2018-01-01

    Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

  14. Type I and II β-turns prediction using NMR chemical shifts.

    PubMed

    Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer

    2014-07-01

    A method for predicting type I and II β-turns using nuclear magnetic resonance (NMR) chemical shifts is proposed. Isolated β-turn chemical-shift data were collected from 1,798 protein chains. One-dimensional statistical analyses on chemical-shift data of three classes β-turn (type I, II, and VIII) showed different distributions at four positions, (i) to (i + 3). Considering the central two residues of type I β-turns, the mean values of Cο, Cα, H(N), and N(H) chemical shifts were generally (i + 1) > (i + 2). The mean values of Cβ and Hα chemical shifts were (i + 1) < (i + 2). The distributions of the central two residues in type II and VIII β-turns were also distinguishable by trends of chemical shift values. Two-dimensional cluster analyses on chemical-shift data show positional distributions more clearly. Based on these propensities of chemical shift classified as a function of position, rules were derived using scoring matrices for four consecutive residues to predict type I and II β-turns. The proposed method achieves an overall prediction accuracy of 83.2 and 84.2% with the Matthews correlation coefficient values of 0.317 and 0.632 for type I and II β-turns, indicating that its higher accuracy for type II turn prediction. The results show that it is feasible to use NMR chemical shifts to predict the β-turn types in proteins. The proposed method can be incorporated into other chemical-shift based protein secondary structure prediction methods.

  15. Spinal Cord Stimulation (SCS) and Functional Magnetic Resonance Imaging (fMRI): Modulation of Cortical Connectivity With Therapeutic SCS.

    PubMed

    Deogaonkar, Milind; Sharma, Mayur; Oluigbo, Chima; Nielson, Dylan M; Yang, Xiangyu; Vera-Portocarrero, Louis; Molnar, Gregory F; Abduljalil, Amir; Sederberg, Per B; Knopp, Michael; Rezai, Ali R

    2016-02-01

    The neurophysiological basis of pain relief due to spinal cord stimulation (SCS) and the related cortical processing of sensory information are not completely understood. The aim of this study was to use resting state functional magnetic resonance imaging (rs-fMRI) to detect changes in cortical networks and cortical processing related to the stimulator-induced pain relief. Ten patients with complex regional pain syndrome (CRPS) or neuropathic leg pain underwent thoracic epidural spinal cord stimulator implantation. Stimulation parameters associated with "optimal" pain reduction were evaluated prior to imaging studies. Rs-fMRI was obtained on a 3 Tesla, Philips Achieva MRI. Rs-fMRI was performed with stimulator off (300TRs) and stimulator at optimum (Opt, 300 TRs) pain relief settings. Seed-based analysis of the resting state functional connectivity was conducted using seeds in regions established as participating in pain networks or in the default mode network (DMN) in addition to the network analysis. NCUT (normalized cut) parcellation was used to generate 98 cortical and subcortical regions of interest in order to expand our analysis of changes in functional connections to the entire brain. We corrected for multiple comparisons by limiting the false discovery rate to 5%. Significant differences in resting state connectivity between SCS off and optimal state were seen between several regions related to pain perception, including the left frontal insula, right primary and secondary somatosensory cortices, as well as in regions involved in the DMN, such as the precuneus. In examining changes in connectivity across the entire brain, we found decreased connection strength between somatosensory and limbic areas and increased connection strength between somatosensory and DMN with optimal SCS resulting in pain relief. This suggests that pain relief from SCS may be reducing negative emotional processing associated with pain, allowing somatosensory areas to become more

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

    PubMed

    Berjanskii, Mark V; Wishart, David S

    2017-11-01

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

  17. Relative Configuration of Natural Products Using NMR Chemical Shifts

    USDA-ARS?s Scientific Manuscript database

    By comparing calculated with experimental NMR chemical shifts, we were able to determine the relative configurations of three monoterpene diastereomers produced by the walkingstick Anisomorpha buprestoides. The combined RMSDs of both 1H and 13C quantum chemically calculated shifts were able to predi...

  18. Nickel Complexes of a Binucleating Ligand Derived from an SCS Pincer

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Peterson, Sonja M.; Helm, Monte L.; Appel, Aaron M.

    2015-01-01

    A binucleating ligand has been prepared that contains an SCS pincer and three oxygen donor ligands in a partial crown ether loop. To enable metalation with Ni0, a bromoarene precursor was used and resulted in the formation of a nickel-bromide complex in the SCS pincer. Reaction of the nickel complex with a lithium salt yielded a heterobimetallic complex with bromide bridging the two metal centers. The solid-state structures were determined for this heterobimetallic complex and the nickel-bromide precursor, and the two complexes were characterized electrochemically to determine the influence of coordinating the second metal. This research was supported by themore » US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. MLH was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.« less

  19. Molecular dynamics averaging of Xe chemical shifts in liquids.

    PubMed

    Jameson, Cynthia J; Sears, Devin N; Murad, Sohail

    2004-11-15

    The Xe nuclear magnetic resonance chemical shift differences that afford the discrimination between various biological environments are of current interest for biosensor applications and medical diagnostic purposes. In many such environments the Xe signal appears close to that in water. We calculate average Xe chemical shifts (relative to the free Xe atom) in solution in eleven liquids: water, isobutane, perfluoro-isobutane, n-butane, n-pentane, neopentane, perfluoroneopentane, n-hexane, n-octane, n-perfluorooctane, and perfluorooctyl bromide. The latter is a liquid used for intravenous Xe delivery. We calculate quantum mechanically the Xe shielding response in Xe-molecule van der Waals complexes, from which calculations we develop Xe (atomic site) interpolating functions that reproduce the ab initio Xe shielding response in the complex. By assuming additivity, these Xe-site shielding functions can be used to calculate the shielding for any configuration of such molecules around Xe. The averaging over configurations is done via molecular dynamics (MD). The simulations were carried out using a MD technique that one of us had developed previously for the simulation of Henry's constants of gases dissolved in liquids. It is based on separating a gaseous compartment in the MD system from the solvent using a semipermeable membrane that is permeable only to the gas molecules. We reproduce the experimental trends in the Xe chemical shifts in n-alkanes with increasing number of carbons and the large chemical shift difference between Xe in water and in perfluorooctyl bromide. We also reproduce the trend for a given solvent of decreasing Xe chemical shift with increasing temperature. We predict chemical shift differences between Xe in alkanes vs their perfluoro counterparts.

  20. Spin-Center Shift-Enabled Direct Enantioselective α-Benzylation of Aldehydes with Alcohols.

    PubMed

    Nacsa, Eric D; MacMillan, David W C

    2018-03-07

    Nature routinely engages alcohols as leaving groups, as DNA biosynthesis relies on the removal of water from ribonucleoside diphosphates by a radical-mediated "spin-center shift" (SCS) mechanism. Alcohols, however, remain underused as alkylating agents in synthetic chemistry due to their low reactivity in two-electron pathways. We report herein an enantioselective α-benzylation of aldehydes using alcohols as alkylating agents based on the mechanistic principle of spin-center shift. This strategy harnesses the dual activation modes of photoredox and organocatalysis, engaging the alcohol by SCS and capturing the resulting benzylic radical with a catalytically generated enamine. Mechanistic studies provide evidence for SCS as a key elementary step, identify the origins of competing reactions, and enable improvements in chemoselectivity by rational photocatalyst design.

  1. Spinal Cord Stimulation (SCS) with Anatomically Guided (3D) Neural Targeting Shows Superior Chronic Axial Low Back Pain Relief Compared to Traditional SCS-LUMINA Study.

    PubMed

    Veizi, Elias; Hayek, Salim M; North, James; Brent Chafin, T; Yearwood, Thomas L; Raso, Louis; Frey, Robert; Cairns, Kevin; Berg, Anthony; Brendel, John; Haider, Nameer; McCarty, Matthew; Vucetic, Henry; Sherman, Alden; Chen, Lilly; Mekel-Bobrov, Nitzan

    2017-08-01

    The aim of this study was to determine whether spinal cord stimulation (SCS) using 3D neural targeting provided sustained overall and low back pain relief in a broad routine clinical practice population. This was a multicenter, open-label observational study with an observational arm and retrospective analysis of a matched cohort. After IPG implantation, programming was done using a patient-specific, model-based algorithm to adjust for lead position (3D neural targeting) or previous generation software (traditional). Demographics, medical histories, SCS parameters, pain locations, pain intensities, disabilities, and safety data were collected for all patients. A total of 213 patients using 3D neural targeting were included, with a trial-to-implant ratio of 86%. Patients used seven different lead configurations, with 62% receiving 24 to 32 contacts, and a broad range of stimulation parameters utilizing a mean of 14.3 (±6.1) contacts. At 24 months postimplant, pain intensity decreased significantly from baseline (ΔNRS = 4.2, N = 169, P  < 0.0001) and even more in in the severe pain subgroup (ΔNRS = 5.3, N = 91, P  < 0.0001). Axial low back pain also decreased significantly from baseline to 24 months (ΔNRS = 4.1, N = 70, P  < 0.0001, on the overall cohort and ΔNRS = 5.6, N = 38, on the severe subgroup). Matched cohort comparison with 213 patients treated with traditional SCS at the same centers showed overall pain responder rates of 51% (traditional SCS) and 74% (neural targeting SCS) and axial low back pain responder rates of 41% and 71% in the traditional SCS and neural targeting SCS cohorts, respectively. Lastly, complications occurred in a total of 33 of the 213 patients, with a 1.6% lead replacement rate and a 1.6% explant rate. Our results suggest that 3D neural targeting SCS and its associated hardware flexibility provide effective treatment for both chronic leg and chronic axial low back pain that is

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

    PubMed

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

    2015-01-01

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

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

    PubMed

    Koes, David R; Vries, John K

    2017-01-01

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

  4. Beyond the SCS curve number: A new stochastic spatial runoff approach

    NASA Astrophysics Data System (ADS)

    Bartlett, M. S., Jr.; Parolari, A.; McDonnell, J.; Porporato, A. M.

    2015-12-01

    The Soil Conservation Service curve number (SCS-CN) method is the standard approach in practice for predicting a storm event runoff response. It is popular because its low parametric complexity and ease of use. However, the SCS-CN method does not describe the spatial variability of runoff and is restricted to certain geographic regions and land use types. Here we present a general theory for extending the SCS-CN method. Our new theory accommodates different event based models derived from alternative rainfall-runoff mechanisms or distributions of watershed variables, which are the basis of different semi-distributed models such as VIC, PDM, and TOPMODEL. We introduce a parsimonious but flexible description where runoff is initiated by a pure threshold, i.e., saturation excess, that is complemented by fill and spill runoff behavior from areas of partial saturation. To facilitate event based runoff prediction, we derive simple equations for the fraction of the runoff source areas, the probability density function (PDF) describing runoff variability, and the corresponding average runoff value (a runoff curve analogous to the SCS-CN). The benefit of the theory is that it unites the SCS-CN method, VIC, PDM, and TOPMODEL as the same model type but with different assumptions for the spatial distribution of variables and the runoff mechanism. The new multiple runoff mechanism description for the SCS-CN enables runoff prediction in geographic regions and site runoff types previously misrepresented by the traditional SCS-CN method. In addition, we show that the VIC, PDM, and TOPMODEL runoff curves may be more suitable than the SCS-CN for different conditions. Lastly, we explore predictions of sediment and nutrient transport by applying the PDF describing runoff variability within our new framework.

  5. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 5: Study analysis report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex (PTC) at the Marshall Space Flight Center (MSFC). The PTC will train the space station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be on-board the Freedom Space Station. The further analysis performed on the SCS study as part of task 2-Perform Studies and Parametric Analysis-of the SCS study contract is summarized. These analyses were performed to resolve open issues remaining after the completion of task 1, and the publishing of the SCS study issues report. The results of these studies provide inputs into SCS task 3-Develop and present SCS requirements, and SCS task 4-develop SCS conceptual designs. The purpose of these studies is to resolve the issues into usable requirements given the best available information at the time of the study. A list of all the SCS study issues is given.

  6. Automated and assisted RNA resonance assignment using NMR chemical shift statistics

    PubMed Central

    Aeschbacher, Thomas; Schmidt, Elena; Blatter, Markus; Maris, Christophe; Duss, Olivier; Allain, Frédéric H.-T.; Güntert, Peter; Schubert, Mario

    2013-01-01

    The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and 1H and 13C chemical shifts. Statistics of resonances from regularly Watson–Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H1′/C1′ chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stem-loop RNAs and a 42 nt siRNA, assigning 92–100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding 13C resonances, which provides an important step toward automated structure determination of RNAs. PMID:23921634

  7. Project SCS (Special Communication Services).

    ERIC Educational Resources Information Center

    Curtis, John A.

    This extensive report describes and provides documentation on Special Communications Services for the Sensory Impaired (SCS), a Virginia-based telecommunications delivery system developed by the Center for Excellence, Inc. (CenTex), to provide information and entertainment broadcasting services to the visually handicapped, the hearing impaired,…

  8. Calculation of NMR chemical shifts in organic solids: accounting for motional effects.

    PubMed

    Dumez, Jean-Nicolas; Pickard, Chris J

    2009-03-14

    NMR chemical shifts were calculated from first principles for well defined crystalline organic solids. These density functional theory calculations were carried out within the plane-wave pseudopotential framework, in which truly extended systems are implicitly considered. The influence of motional effects was assessed by averaging over vibrational modes or over snapshots taken from ab initio molecular dynamics simulations. It is observed that the zero-point correction to chemical shifts can be significant, and that thermal effects are particularly noticeable for shielding anisotropies and for a temperature-dependent chemical shift. This study provides insight into the development of highly accurate first principles calculations of chemical shifts in solids, highlighting the role of motional effects on well defined systems.

  9. Time averaging of NMR chemical shifts in the MLF peptide in the solid state.

    PubMed

    De Gortari, Itzam; Portella, Guillem; Salvatella, Xavier; Bajaj, Vikram S; van der Wel, Patrick C A; Yates, Jonathan R; Segall, Matthew D; Pickard, Chris J; Payne, Mike C; Vendruscolo, Michele

    2010-05-05

    Since experimental measurements of NMR chemical shifts provide time and ensemble averaged values, we investigated how these effects should be included when chemical shifts are computed using density functional theory (DFT). We measured the chemical shifts of the N-formyl-L-methionyl-L-leucyl-L-phenylalanine-OMe (MLF) peptide in the solid state, and then used the X-ray structure to calculate the (13)C chemical shifts using the gauge including projector augmented wave (GIPAW) method, which accounts for the periodic nature of the crystal structure, obtaining an overall accuracy of 4.2 ppm. In order to understand the origin of the difference between experimental and calculated chemical shifts, we carried out first-principles molecular dynamics simulations to characterize the molecular motion of the MLF peptide on the picosecond time scale. We found that (13)C chemical shifts experience very rapid fluctuations of more than 20 ppm that are averaged out over less than 200 fs. Taking account of these fluctuations in the calculation of the chemical shifts resulted in an accuracy of 3.3 ppm. To investigate the effects of averaging over longer time scales we sampled the rotameric states populated by the MLF peptides in the solid state by performing a total of 5 micros classical molecular dynamics simulations. By averaging the chemical shifts over these rotameric states, we increased the accuracy of the chemical shift calculations to 3.0 ppm, with less than 1 ppm error in 10 out of 22 cases. These results suggests that better DFT-based predictions of chemical shifts of peptides and proteins will be achieved by developing improved computational strategies capable of taking into account the averaging process up to the millisecond time scale on which the chemical shift measurements report.

  10. SCS-CN based time-distributed sediment yield model

    NASA Astrophysics Data System (ADS)

    Tyagi, J. V.; Mishra, S. K.; Singh, Ranvir; Singh, V. P.

    2008-05-01

    SummaryA sediment yield model is developed to estimate the temporal rates of sediment yield from rainfall events on natural watersheds. The model utilizes the SCS-CN based infiltration model for computation of rainfall-excess rate, and the SCS-CN-inspired proportionality concept for computation of sediment-excess. For computation of sedimentographs, the sediment-excess is routed to the watershed outlet using a single linear reservoir technique. Analytical development of the model shows the ratio of the potential maximum erosion (A) to the potential maximum retention (S) of the SCS-CN method is constant for a watershed. The model is calibrated and validated on a number of events using the data of seven watersheds from India and the USA. Representative values of the A/S ratio computed for the watersheds from calibration are used for the validation of the model. The encouraging results of the proposed simple four parameter model exhibit its potential in field application.

  11. Metathesis Activity Encoded in the Metallacyclobutane Carbon-13 NMR Chemical Shift Tensors

    PubMed Central

    2017-01-01

    Metallacyclobutanes are an important class of organometallic intermediates, due to their role in olefin metathesis. They can have either planar or puckered rings associated with characteristic chemical and physical properties. Metathesis active metallacyclobutanes have short M–Cα/α′ and M···Cβ distances, long Cα/α′–Cβ bond length, and isotropic 13C chemical shifts for both early d0 and late d4 transition metal compounds for the α- and β-carbons appearing at ca. 100 and 0 ppm, respectively. Metallacyclobutanes that do not show metathesis activity have 13C chemical shifts of the α- and β-carbons at typically 40 and 30 ppm, respectively, for d0 systems, with upfield shifts to ca. −30 ppm for the α-carbon of metallacycles with higher dn electron counts (n = 2 and 6). Measurements of the chemical shift tensor by solid-state NMR combined with an orbital (natural chemical shift, NCS) analysis of its principal components (δ11 ≥ δ22 ≥ δ33) with two-component calculations show that the specific chemical shift of metathesis active metallacyclobutanes originates from a low-lying empty orbital lying in the plane of the metallacyclobutane with local π*(M–Cα/α′) character. Thus, in the metathesis active metallacyclobutanes, the α-carbons retain some residual alkylidene character, while their β-carbon is shielded, especially in the direction perpendicular to the ring. Overall, the chemical shift tensors directly provide information on the predictive value about the ability of metallacyclobutanes to be olefin metathesis intermediates. PMID:28776018

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

    PubMed Central

    Wang, Xianlong; Wang, Chengfei; Zhao, Hui

    2012-01-01

    Computational chemistry is an important tool for signal assignment of 27Al nuclear magnetic resonance spectra in order to elucidate the species of aluminum(III) in aqueous solutions. The accuracy of the popular theoretical models for computing the 27Al chemical shifts was evaluated by comparing the calculated and experimental chemical shifts in more than one hundred aluminum(III) complexes. In order to differentiate the error due to the chemical shielding tensor calculation from that due to the inadequacy of the molecular geometry prediction, single-crystal X-ray diffraction determined structures were used to build the isolated molecule models for calculating the chemical shifts. The results were compared with those obtained using the calculated geometries at the B3LYP/6-31G(d) level. The isotropic chemical shielding constants computed at different levels have strong linear correlations even though the absolute values differ in tens of ppm. The root-mean-square difference between the experimental chemical shifts and the calculated values is approximately 5 ppm for the calculations based on the X-ray structures, but more than 10 ppm for the calculations based on the computed geometries. The result indicates that the popular theoretical models are adequate in calculating the chemical shifts while an accurate molecular geometry is more critical. PMID:23203134

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

    PubMed

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

    2008-03-01

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

  14. The relativistic theory of the chemical shift

    NASA Astrophysics Data System (ADS)

    Pyper, N. C.

    1983-04-01

    A relativistic theory of the NMR chemical shift for a closed-shell system is presented. The final expression for the shielding, derived by, applying two Gordon decompositions to the Dirac current operator, closely parallels the Ramsey non-relativistic result.

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

    PubMed

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

    2008-06-01

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

  16. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 3: Refined conceptual design report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The results of the refined conceptual design phase (task 5) of the Simulation Computer System (SCS) study are reported. The SCS is the computational portion of the Payload Training Complex (PTC) providing simulation based training on payload operations of the Space Station Freedom (SSF). In task 4 of the SCS study, the range of architectures suitable for the SCS was explored. Identified system architectures, along with their relative advantages and disadvantages for SCS, were presented in the Conceptual Design Report. Six integrated designs-combining the most promising features from the architectural formulations-were additionally identified in the report. The six integrated designs were evaluated further to distinguish the more viable designs to be refined as conceptual designs. The three designs that were selected represent distinct approaches to achieving a capable and cost effective SCS configuration for the PTC. Here, the results of task 4 (input to this task) are briefly reviewed. Then, prior to describing individual conceptual designs, the PTC facility configuration and the SSF systems architecture that must be supported by the SCS are reviewed. Next, basic features of SCS implementation that have been incorporated into all selected SCS designs are considered. The details of the individual SCS designs are then presented before making a final comparison of the three designs.

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

    NASA Astrophysics Data System (ADS)

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

    2015-10-01

    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), 1H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong 1H-1H homonuclear dipolar couplings and narrow 1H 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) 1H 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 1H-1H 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-level structural and dynamical information for

  18. Estimating the SCS runoff curve number in forest catchments of Korea

    NASA Astrophysics Data System (ADS)

    Choi, Hyung Tae; Kim, Jaehoon; Lim, Hong-geun

    2016-04-01

    To estimate flood runoff discharge is a very important work in design for many hydraulic structures in streams, rivers and lakes such as dams, bridges, culverts, and so on. So, many researchers have tried to develop better methods for estimating flood runoff discharge. The SCS runoff curve number is an empirical parameter determined by empirical analysis of runoff from small catchments and hillslope plots monitored by the USDA. This method is an efficient method for determining the approximate amount of runoff from a rainfall even in a particular area, and is very widely used all around the world. However, there is a quite difference between the conditions of Korea and USA in topography, geology and land use. Therefore, examinations in adaptability of the SCS runoff curve number need to raise the accuracy of runoff prediction using SCS runoff curve number method. The purpose of this study is to find the SCS runoff curve number based on the analysis of observed data from several experimental forest catchments monitored by the National Institute of Forest Science (NIFOS), as a pilot study to modify SCS runoff curve number for forest lands in Korea. Rainfall and runoff records observed in Gwangneung coniferous and broad leaves forests, Sinwol, Hwasoon, Gongju and Gyeongsan catchments were selected to analyze the variability of flood runoff coefficients during the last 5 years. This study shows that runoff curve numbers of the experimental forest catchments range from 55 to 65. SCS Runoff Curve number method is a widely used method for estimating design discharge for small ungauged watersheds. Therefore, this study can be helpful technically to estimate the discharge for forest watersheds in Korea with more accuracy.

  19. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 6: Study issues report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex (PTC) at the Marshall Space Flight Center (MSFC). The PTC will train the space station payload specialists and mission specialists to operate the wide variety of experiments that will be on-board the Freedom Space Station. This simulation Computer System (SCS) study issues report summarizes the analysis and study done as task 1-identify and analyze the CSC study issues- of the SCS study contract.This work was performed over the first three months of the SCS study which began in August of 1988. First issues were identified from all sources. These included the NASA SOW, the TRW proposal, and working groups which focused the experience of NASA and the contractor team performing the study-TRW, Essex, and Grumman. The final list is organized into training related issues, and SCS associated development issues. To begin the analysis of the issues, a list of all the functions for which the SCS could be used was created, i.e., when the computer is turned on, what will it be doing. Analysis was continued by creating an operational functions matrix of SCS users vs. SCS functions to insure all the functions considered were valid, and to aid in identification of users as the analysis progressed. The functions will form the basis for the requirements, which are currently being developed under task 3 of the SCS study.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu

    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 rendermore » 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

  1. Relativistically corrected nuclear magnetic resonance chemical shifts calculated with the normalized elimination of the small component using an effective potential-NMR chemical shifts of molybdenum and tungsten

    NASA Astrophysics Data System (ADS)

    Filatov, Michael; Cremer, Dieter

    2003-07-01

    A new method for relativistically corrected nuclear magnetic resonance (NMR) chemical shifts is developed by combining the individual gauge for the localized orbital approach for density functional theory with the normalized elimination of a small component using an effective potential. The new method is used for the calculation of the NMR chemical shifts of 95Mo and 183W in various molybdenum and tungsten compounds. It is shown that quasirelativistic corrections lead to an average improvement of calculated NMR chemical shift values by 300 and 120 ppm in the case of 95Mo and 183W, respectively, which is mainly due to improvements in the paramagnetic contributions. The relationship between electronic structure of a molecule and the relativistic paramagnetic corrections is discussed. Relativistic effects for the diamagnetic part of the magnetic shielding caused by a relativistic contraction of the s,p orbitals in the core region concern only the shielding values, however, have little consequence for the shift values because of the large independence from electronic structure and a cancellation of these effects in the shift values. It is shown that the relativistic corrections can be improved by level shift operators and a B3LYP hybrid functional, for which Hartree-Fock exchange is reduced to 15%.

  2. Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

    NASA Astrophysics Data System (ADS)

    Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

    2015-04-01

    In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

  3. SLUDGE PARTICLE SEPAPATION EFFICIENCIES DURING SETTLER TANK RETRIEVAL INTO SCS-CON-230

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    DEARING JI; EPSTEIN M; PLYS MG

    2009-07-16

    The purpose of this document is to release, into the Hanford Document Control System, FA1/0991, Sludge Particle Separation Efficiencies for the Rectangular SCS-CON-230 Container, by M. Epstein and M. G. Plys, Fauske & Associates, LLC, June 2009. The Sludge Treatment Project (STP) will retrieve sludge from the 105-K West Integrated Water Treatment System (IWTS) Settler Tanks and transfer it to container SCS-CON-230 using the Settler Tank Retrieval System (STRS). The sludge will enter the container through two distributors. The container will have a filtration system that is designed to minimize the overflow of sludge fines from the container to themore » basin. FAI/09-91 was performed to quantify the effect of the STRS on sludge distribution inside of and overflow out of SCS-CON-230. Selected results of the analysis and a system description are discussed. The principal result of the analysis is that the STRS filtration system reduces the overflow of sludge from SCS-CON-230 to the basin by roughly a factor of 10. Some turbidity can be expected in the center bay where the container is located. The exact amount of overflow and subsequent turbidity is dependent on the density of the sludge (which will vary with location in the Settler Tanks) and the thermal gradient between the SCS-CON-230 and the basin. Attachment A presents the full analytical results. These results are applicable specifically to SCS-CON-230 and the STRS filtration system's expected operating duty cycles.« less

  4. Use of 13Cα Chemical-Shifts in Protein Structure Determination

    PubMed Central

    Vila, Jorge A.; Ripoll, Daniel R.; Scheraga, Harold A.

    2008-01-01

    A physics-based method, aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts, is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid all-α-helical protein, namely the B. Subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank. PMID:17516673

  5. Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Burns, Lori A.; Marshall, Michael S.; Sherrill, C. David, E-mail: sherrill@gatech.edu

    2014-12-21

    A systematic examination of noncovalent interactions as modeled by wavefunction theory is presented in comparison to gold-standard quality benchmarks available for 345 interaction energies of 49 bimolecular complexes. Quantum chemical techniques examined include spin-component-scaling (SCS) variations on second-order perturbation theory (MP2) [SCS, SCS(N), SCS(MI)] and coupled cluster singles and doubles (CCSD) [SCS, SCS(MI)]; also, method combinations designed to improve dispersion contacts [DW-MP2, MP2C, MP2.5, DW-CCSD(T)-F12]; where available, explicitly correlated (F12) counterparts are also considered. Dunning basis sets augmented by diffuse functions are employed for all accessible ζ-levels; truncations of the diffuse space are also considered. After examination of both accuracymore » and performance for 394 model chemistries, SCS(MI)-MP2/cc-pVQZ can be recommended for general use, having good accuracy at low cost and no ill-effects such as imbalance between hydrogen-bonding and dispersion-dominated systems or non-parallelity across dissociation curves. Moreover, when benchmarking accuracy is desirable but gold-standard computations are unaffordable, this work recommends silver-standard [DW-CCSD(T**)-F12/aug-cc-pVDZ] and bronze-standard [MP2C-F12/aug-cc-pVDZ] model chemistries, which support accuracies of 0.05 and 0.16 kcal/mol and efficiencies of 97.3 and 5.5 h for adenine·thymine, respectively. Choice comparisons of wavefunction results with the best symmetry-adapted perturbation theory [T. M. Parker, L. A. Burns, R. M. Parrish, A. G. Ryno, and C. D. Sherrill, J. Chem. Phys. 140, 094106 (2014)] and density functional theory [L. A. Burns, Á. Vázquez-Mayagoitia, B. G. Sumpter, and C. D. Sherrill, J. Chem. Phys. 134, 084107 (2011)] methods previously studied for these databases are provided for readers' guidance.« less

  6. Hydrography synthesis using LANDSAT remote sensing and the SCS models

    NASA Technical Reports Server (NTRS)

    Ragan, R. M.; Jackson, T. J.

    1976-01-01

    The land cover requirements of the Soil Conservation Service (SCS) Model used for hydrograph synthesis in urban areas were modified to be LANDSAT compatible. The Curve Numbers obtained with these alternate land cover categories compare well with those obtained in published example problems using the conventional categories. Emergency spillway hydrographs and synthetic flood frequency flows computed for a 21.1 sq. mi. test area showed excellent agreement between the conventional aerial photo-based and the Landsat-based SCS approaches.

  7. Intramolecular interactions of L-phenylalanine revealed by inner shell chemical shift

    NASA Astrophysics Data System (ADS)

    Ganesan, Aravindhan; Wang, Feng

    2009-07-01

    Intramolecular interactions of the functional groups, carboxylic acid, amino, and phenyl in L-phenylalanine have been revealed through inner shell chemical shift. The chemical shift and electronic structures are studied using its derivatives, 2-phenethylamine (PEA) and 3-phenylpropionic acid (PPA), through substitutions of the functional groups on the chiral carbon Cα, i.e., carboxylic acid (-COOH) and amino (-NH2) groups. Inner shell ionization spectra of L-phenylalanine are simulated using density functional theory based B3LYP/TZVP and LB94/et-pVQZ models, which achieve excellent agreement with the most recently available synchrotron sourced x-ray photoemission spectroscopy of L-phenylalanine (Elettra, Italy). The present study reveals insight into behavior of the peptide bond (CO-NH) through chemical shift of the C1-Cα-Cβ(-Cγ) chain and intramolecular interactions with phenyl. It is found that the chemical shift of the carbonyl C1(=O) site exhibits an apparently redshift (smaller energy) when interacting with the phenyl aromatic group. Removal of the amino group (-NH2) from L-phenylalanine (which forms PPA) brings this energy on C1 close to that in L-alanine (δ <0.01 eV). Chemical environment of Cα and Cβ exhibits more significant differences in L-alanine than in the aromatic species, indicating that the phenyl group indeed affects the peptide bond in the amino acid fragment. No direct evidences are found that the carbonyl acid and amino group interact with the phenyl ring through conventional hydrogen bonds.

  8. Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

    PubMed

    Boomsma, Wouter; Tian, Pengfei; Frellsen, Jes; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Lindorff-Larsen, Kresten; Vendruscolo, Michele

    2014-09-23

    Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.

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

    PubMed

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

    2013-12-01

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

  10. Ligand Binding Analysis and Screening by Chemical Denaturation Shift

    PubMed Central

    Sch n, Arne; Brown, Richard K.; Hutchins, Burleigh M.; Freire, Ernesto

    2013-01-01

    The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Towards this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Since ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities and the ligand rank order obtained at denaturation temperatures (60°C or higher) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations in which binding changes the cooperativity of the unfolding transition. In this paper we develop the basic analytical equations and provide several experimental examples. PMID:23994566

  11. Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene.

    PubMed

    Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

    2018-07-01

    Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. Graphical Abstract ᅟ.

  12. Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene

    NASA Astrophysics Data System (ADS)

    Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

    2018-04-01

    Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. [Figure not available: see fulltext.

  13. Modeling 15N NMR chemical shift changes in protein backbone with pressure

    NASA Astrophysics Data System (ADS)

    La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

    2016-08-01

    Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

  14. Improved Electrostatic Embedding for Fragment-Based Chemical Shift Calculations in Molecular Crystals.

    PubMed

    Hartman, Joshua D; Balaji, Ashwin; Beran, Gregory J O

    2017-12-12

    Fragment-based methods predict nuclear magnetic resonance (NMR) chemical shielding tensors in molecular crystals with high accuracy and computational efficiency. Such methods typically employ electrostatic embedding to mimic the crystalline environment, and the quality of the results can be sensitive to the embedding treatment. To improve the quality of this embedding environment for fragment-based molecular crystal property calculations, we borrow ideas from the embedded ion method to incorporate self-consistently polarized Madelung field effects. The self-consistent reproduction of the Madelung potential (SCRMP) model developed here constructs an array of point charges that incorporates self-consistent lattice polarization and which reproduces the Madelung potential at all atomic sites involved in the quantum mechanical region of the system. The performance of fragment- and cluster-based 1 H, 13 C, 14 N, and 17 O chemical shift predictions using SCRMP and density functionals like PBE and PBE0 are assessed. The improved embedding model results in substantial improvements in the predicted 17 O chemical shifts and modest improvements in the 15 N ones. Finally, the performance of the model is demonstrated by examining the assignment of the two oxygen chemical shifts in the challenging γ-polymorph of glycine. Overall, the SCRMP-embedded NMR chemical shift predictions are on par with or more accurate than those obtained with the widely used gauge-including projector augmented wave (GIPAW) model.

  15. Effects of protein-pheromone complexation on correlated chemical shift modulations.

    PubMed

    Perazzolo, Chiara; Wist, Julien; Loth, Karine; Poggi, Luisa; Homans, Steve; Bodenhausen, Geoffrey

    2005-12-01

    Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{C'N} and DQC{C'N}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand).

  16. Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

    PubMed Central

    Christensen, Anders S.; Linnet, Troels E.; 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 (h3 JNC') 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. PMID:24391900

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

    PubMed

    Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert

    2017-02-01

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

  18. Efficient degradation of sulfamethazine in simulated and real wastewater at slightly basic pH values using Co-SAM-SCS /H2O2 Fenton-like system.

    PubMed

    Cheng, Min; Zeng, Guangming; Huang, Danlian; Lai, Cui; Liu, Yang; Zhang, Chen; Wan, Jia; Hu, Liang; Zhou, Chengyun; Xiong, Weiping

    2018-07-01

    The presence of antibiotics in aquatic environments has attracted global concern. Fenton process is an attractive yet challenging method for antibiotics degradation, especially when such a reaction can be conducted at neutral pH values. In this study, a novel composite Fe/Co catalyst was synthesized via the modification of steel converter slag (SCS) by salicylic acid-methanol (SAM) and cobalt nitrate (Co(NO 3 ) 2 ). The catalysts were characterized by N 2 -Brunauer-Emmett-Teller (BET), X-ray diffraction (XRD), Fourier transform infrared (FT-IR), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The results indicated that the Co-SAM-SCS/H 2 O 2 Fenton-like system was very effective for sulfamethazine (SMZ) degradation at a wide pH range. At initial pH of 7.0, the degradation rate of SMZ in Co-SAM-SCS/H 2 O 2 system was 2.48, 3.20, 6.18, and 16.21 times of that in Fe-SAM-SCS/H 2 O 2 , SAM-SCS/H 2 O 2 , Co(NO 3 ) 2 /H 2 O 2 and SCS/H 2 O 2 system, respectively. The preliminary analysis suggested that high surface area of Co-SAM-SCS sample and synergistic effect between introduced Co and SAM-SCS are responsible for the efficient catalytic activity. During the degradation, three main intermediates were identified by high performance liquid chromatography-mass spectrometry (HPLC-MS) analysis. Based on this, a possible degradation pathway was proposed. The SEM images, XRD patterns and XPS spectra before and after the reactions demonstrate that the crystal and chemical structure of Co-SAM-SCS after five cycles are almost unchanged. Besides, the Co-SAM-SCS presented low iron and cobalt leaching (0.17 mg/L and 2.36 mg/L, respectively). The studied Fenton-like process also showed high degradation of SMZ in river water and municipal wastewater. The progress will bring valuable insights to develop high-performance heterogeneous Fenton-like catalysts for environmental remediation. Copyright © 2018

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

    PubMed Central

    Hong, Mei

    2016-01-01

    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 command

  20. Identification of helix capping and β-turn motifs from NMR chemical shifts

    PubMed Central

    Shen, Yang; Bax, Ad

    2012-01-01

    We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13Cβ chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ 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 β-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 that 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. PMID:22314702

  1. Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions.

    PubMed

    Hartman, Joshua D; Day, Graeme M; Beran, Gregory J O

    2016-11-02

    Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13 C and 15 N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.

  2. Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions

    PubMed Central

    2016-01-01

    Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study. PMID:27829821

  3. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 2: Concept document

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) concept document describes and establishes requirements for the functional performance of the SCS system, including interface, logistic, and qualification requirements. The SCS is the computational communications and display segment of the Marshall Space Flight Center (MSFC) Payload Training Complex (PTC). The PTC is the MSFC facility that will train onboard and ground operations personnel to operate the payloads and experiments on board the international Space Station Freedom. The requirements to be satisfied by the system implementation are identified here. The SCS concept document defines the requirements to be satisfied through the implementation of the system capability. The information provides the operational basis for defining the requirements to be allocated to the system components and enables the system organization to assess whether or not the completed system complies with the requirements of the system.

  4. Evolution of the SCS curve number method and its applications to continuous runoff simulation

    USDA-ARS?s Scientific Manuscript database

    The Natural Resources Conservation Service (NRCS) [previously Soil Conservation Service (SCS)] developed the SCS runoff curve-number (CN) method for estimating direct runoff from storm rainfall. The NRCS uses the CN method for designing structures and for evaluating their effectiveness. Structural...

  5. First-principles calculations of Ti and O NMR chemical shift tensors in ferroelectric perovskites

    NASA Astrophysics Data System (ADS)

    Pechkis, Daniel; Walter, Eric; Krakauer, Henry

    2011-03-01

    Complementary chemical shift calculations were carried out with embedded clusters, using quantum chemistry methods, and with periodic boundary conditions, using the GIPAW approach within the Quantum Espresso package. Compared to oxygen chemical shifts, δ̂ (O), cluster calculations for δ̂ (Ti) were found to be more sensitive to size effects, termination, and choice of gaussian-type atomic basis set, while GIPAW results were found to be more sensitive to the pseudopotential construction. The two approaches complemented each other in optimizing these factors. We show that the two approaches yield comparable chemical shifts for suitably converged simulations, and results are compared with available experimental measurements. Supported by ONR.

  6. Chemical (knight) shift distortions of quadrupole-split deuteron powder spectra in solids

    NASA Astrophysics Data System (ADS)

    Torgeson, D. R.; Schoenberger, R. J.; Barnes, R. G.

    In strong magnetic fields (e.g., 8 Tesla) anisotropy of the shift tensor (chemical or Knight shift) can alter the spacings of the features of quadrupole-split deuteron spectra of polycrystalline samples. Analysis of powder spectra yields both correct quadrupole coupling and symmetry parameters and all the components of the shift tensor. Synthetic and experimental examples are given to illustrate such behavior.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jeong, Keunhong; Slack, Clancy C.; Vassiliou, Christophoros C.

    2015-09-17

    Recent work has shown that xenon chemical shifts in cryptophane-cage sensors are affected when tethered chelators bind to metals. Here in this paper, we explore the xenon shifts in response to a wide range of metal ions binding to diastereomeric forms of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) linked to cryptophane-A. The shifts induced by the binding of Ca 2+, Cu 2+, Ce 3+, Zn 2+, Cd 2+, Ni 2+, Co 2+, Cr 2+, Fe 3+, and Hg 2+ are distinct. In addition, the different responses of the diastereomers for the same metal ion indicate that shifts are affected by partial folding withmore » a correlation between the expected coordination number of the metal in the DOTA complex and the chemical shift of 129Xe. Lastly, these sensors may be used to detect and quantify many important metal ions, and a better understanding of the basis for the induced shifts could enhance future designs.« less

  8. Modeling {sup 15}N NMR chemical shift changes in protein backbone with pressure

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    La Penna, Giovanni, E-mail: glapenna@iccom.cnr.it; Mori, Yoshiharu, E-mail: ymori@ims.ac.jp; Kitahara, Ryo, E-mail: ryo@ph.ritsumei.ac.jp

    2016-08-28

    Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change inmore » the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.« less

  9. Measurement of residual chemical shift anisotropies in compressed polymethylmethacrylate gels. Automatic compensation of gel isotropic shift contribution.

    PubMed

    Hallwass, Fernando; Teles, Rubens R; Hellemann, Erich; Griesinger, Christian; Gil, Roberto R; Navarro-Vázquez, Armando

    2018-05-01

    Mechanical compression of polymer gels provides a simple way for the measurement of residual chemical shift anisotropies, which then can be employed, on its own, or in combination with residual dipolar couplings, for structural elucidation purposes. Residual chemical shift anisotropies measured using compression devices needed a posteriori correction to account for the increase of the polymer to solvent ratio inside the swollen gel. This correction has been cast before in terms of a single-free parameter which, as shown here, can be simultaneously optimized along with the components of the alignment tensor while still retaining discriminating power of the different relative configurations as illustrated in the stereochemical analysis of α-santonin and 10-epi-8-deoxycumambrin B. Copyright © 2018 John Wiley & Sons, Ltd.

  10. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Phased development plan

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station payload scientists, station scientists and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is made up of computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

  11. A physiologically motivated sparse, compact, and smooth (SCS) approach to EEG source localization.

    PubMed

    Cao, Cheng; Akalin Acar, Zeynep; Kreutz-Delgado, Kenneth; Makeig, Scott

    2012-01-01

    Here, we introduce a novel approach to the EEG inverse problem based on the assumption that principal cortical sources of multi-channel EEG recordings may be assumed to be spatially sparse, compact, and smooth (SCS). To enforce these characteristics of solutions to the EEG inverse problem, we propose a correlation-variance model which factors a cortical source space covariance matrix into the multiplication of a pre-given correlation coefficient matrix and the square root of the diagonal variance matrix learned from the data under a Bayesian learning framework. We tested the SCS method using simulated EEG data with various SNR and applied it to a real ECOG data set. We compare the results of SCS to those of an established SBL algorithm.

  12. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Operations concept report

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is made up of computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

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

    PubMed

    Tamiola, Kamil; Mulder, Frans A A

    2012-10-01

    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 available and idiosyncratic sensitivity of backbone chemical shifts to structural information is treated in a sensible manner. In the present paper, we describe methods to detect structural protein changes from chemical shifts, and present an online tool [ncSPC (neighbour-corrected Structural Propensity Calculator)], which unites aspects of several current approaches. Examples of structural propensity calculations are given for two well-characterized systems, namely the binding of α-synuclein to micelles and light activation of photoactive yellow protein. These examples spotlight the great power of NMR chemical shift analysis for the quantitative assessment of protein disorder at the atomic level, and further our understanding of biologically important problems.

  14. Usefulness of chemical-shift MRI in discriminating increased liver echogenicity in glycogenosis.

    PubMed

    Pozzato, C; Dall'asta, C; Radaelli, G; Torcoletti, M; Formenti, A; Riva, E; Cornalba, G; Pontiroli, A E

    2007-11-01

    Glycogen storage diseases are inherited defects which cause accumulation of glycogen in the tissues. Hepatic steatosis is defined as accumulation of fat within hepatocytes. On sonography, liver shows increased echogenicity both in glycogen storage diseases and steatosis. Liver hyperechogenicity in glycogen storage diseases may depend on accumulation of glycogen and/or fat. Chemical-shift magnetic resonance imaging can discriminate tissues only containing water from those containing both fat and water. The primary aim of the present study was to evaluate the usefulness of liver chemical-shift magnetic resonance imaging for detecting liver steatosis in patients with metabolic impairment due to glycogen storage diseases. Twelve patients with type I (n=8) or type III (n=4) glycogen storage diseases were studied and compared to 12 obese-overweight subjects with known liver steatosis. As control group 12 lean normal voluntary subjects were recruited. Liver was evaluated by sonography and chemical-shift magnetic resonance imaging to calculate hepatic fat fraction. A significant difference in echogenicity between patients with glycogen storage diseases and normal subjects was observed (p<0.05), while this difference was not present between overweight-obese and glycogen storage diseases patients. On the contrary, fat fraction was similar between glycogen storage diseases patients and normal subjects and different between glycogen storage diseases patients and overweight-obese (p<0.05). The present data suggest that chemical-shift magnetic resonance imaging may exclude fat deposition as a cause of liver hyperechogenicity in subjects with glycogen storage diseases.

  15. Theoretical study of the NMR chemical shift of Xe in supercritical condition.

    PubMed

    Lacerda, Evanildo G; Sauer, Stephan P A; Mikkelsen, Kurt V; Coutinho, Kaline; Canuto, Sylvio

    2018-02-20

    In this work we investigate the level of theory necessary for reproducing the non-linear variation of the 129 Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the 129 Xe chemical shift depends under supercritical conditions on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xe n clusters (n = 2 - 8 depending on the density). The analysis of the relativistic effects is made at the level of 4-component Hartree-Fock calculations (4c-HF) and electron correlation effects are considered using second order Møller-Plesset perturbation theory (MP2). To simplify the calculations of the relativistic and electron correlation effects we adopted an additive scheme, where the calculations on the Xe n clusters are carried out at the non-relativistic Hartree-Fock (HF) level, while electron correlation and relativistic corrections are added for all the pairs of Xe atoms in the clusters. Using this approach we obtain very good agreement with the experimental data, showing that the chemical shift of 129 Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects.

  16. 1H NMR spectra part 31: 1H chemical shifts of amides in DMSO solvent.

    PubMed

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

    2014-07-01

    The (1)H chemical shifts of 48 amides in DMSO solvent are assigned and presented. The solvent shifts Δδ (DMSO-CDCl3 ) are large (1-2 ppm) for the NH protons but smaller and negative (-0.1 to -0.2 ppm) for close range protons. A selection of the observed solvent shifts is compared with calculated shifts from the present model and from GIAO calculations. Those for the NH protons agree with both calculations, but other solvent shifts such as Δδ(CHO) are not well reproduced by the GIAO calculations. The (1)H chemical shifts of the amides in DMSO were analysed using a functional approach for near ( ≤ 3 bonds removed) protons and the electric field, magnetic anisotropy and steric effect of the amide group for more distant protons. The chemical shifts of the NH protons of acetanilide and benzamide vary linearly with the π density on the αN and βC atoms, respectively. The C=O anisotropy and steric effect are in general little changed from the values in CDCl3. The effects of substituents F, Cl, Me on the NH proton shifts are reproduced. The electric field coefficient for the protons in DMSO is 90% of that in CDCl3. There is no steric effect of the C=O oxygen on the NH proton in an NH…O=C hydrogen bond. The observed deshielding is due to the electric field effect. The calculated chemical shifts agree well with the observed shifts (RMS error of 0.106 ppm for the data set of 257 entries). Copyright © 2014 John Wiley & Sons, Ltd.

  17. Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

    PubMed

    Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

    2012-03-07

    Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

  18. RFID - based Staff Control System (SCS) in Kazakhstan

    NASA Astrophysics Data System (ADS)

    Saparkhojayev, N.

    2015-06-01

    RFID - based Staff Control System (SCS) will allow complete hands-free access control, monitoring the whereabouts of employee and record the attendance of the employee as well. Moreover, with a help of this system, it is possible to have a nice report at the end of the month and based on the total number of worked hours, the salary will be allocated to each personnel. The access tag can be read up to 10 centimeters from the RFID reader. The proposed system is based on UHF RFID readers, supported with antennas at gate and transaction sections, and employee identification cards containing RFID-transponders which are able to electronically store information that can be read / written even without the physical contact with the help of radio medium. This system is an innovative system, which describes the benefits of applying RFID- technology in the Education System process of Republic of Kazakhstan. This paper presents the experiments conducted to set up RFID based SCS.

  19. AmeriFlux US-SCs Southern California Climate Gradient - Coastal Sage

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Goulden, Mike

    This is the AmeriFlux version of the carbon flux data for the site US-SCs Southern California Climate Gradient - Coastal Sage. Site Description - Half hourly data are available at https://www.ess.uci.edu/~california/. This site is one of six Southern California Climate Gradient flux towers operated along an elevation gradient (sites are US-SCg, US-SCs, US-SCf, US-SCw, US-SCc, US-SCd). This site is a coastal sage shrubland. Coastal sage is a small stature, closed canopy vegetation dominated by drought deciduous shrubs. The site has historically burned every 10-20 years, with the wild fire in October 2007. The tower data sets includes this recovery process.

  20. The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins.

    PubMed

    Frach, Roland; Kibies, Patrick; Böttcher, Saraphina; Pongratz, Tim; Strohfeldt, Steven; Kurrmann, Simon; Koehler, Joerg; Hofmann, Martin; Kremer, Werner; Kalbitzer, Hans Robert; Reiser, Oliver; Horinek, Dominik; Kast, Stefan M

    2016-07-18

    High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the (15) N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Evaluation of Motor Neuron-Like Cell Differentiation of hEnSCs on Biodegradable PLGA Nanofiber Scaffolds.

    PubMed

    Ebrahimi-Barough, Somayeh; Norouzi Javidan, Abbas; Saberi, Hoshangh; Joghataei, Mohammad Tghi; Rahbarghazi, Reza; Mirzaei, Esmaeil; Faghihi, Faezeh; Shirian, Sadegh; Ai, Armin; Ai, Jafar

    2015-12-01

    Human endometrium is a high-dynamic tissue that contains human endometrial stem cells (hEnSCs) which can be differentiated into a number of cell lineages. The differentiation of hEnSCs into many cell lineages such as osteoblast, adipocyte, and neural cells has been investigated previously. However, the differentiation of these stem cells into motor neuron-like cells has not been investigated yet. Different biochemical and topographical cues can affect the differentiation of stem cells into a specific cell. The aim of this study was to investigate the capability of hEnSCs to be differentiated into motor neuron-like cells under biochemical and topographical cues. The biocompatible and biodegradable poly(lactic-co-glycolic acid) (PLGA) electrospun nanofibrous scaffold was used as a topographical cue. Human EnSCs were cultured on the PLGA scaffold and tissue culture polystyrene (TCP), then differentiation of hEnSCs into motor neuron-like cells under induction media including retinoic acid (RA) and sonic hedgehog (Shh) were evaluated for 15 days. The proliferation rate of cells was assayed by using MTT assay. The morphology of cells was studied by scanning electron microscopy imaging, and the expression of motor neuron-specific markers by real-time PCR and immunocytochemistry. Results showed that survival and differentiation of hEnSCs into motor neuron-like cells on the PLGA scaffold were better than those on the TCP group. Taken together, the results suggest that differentiated hEnSCs on PLGA can provide a suitable, three-dimensional situation for neuronal survival and outgrowth for regeneration of the central nervous system, and these cells may be a potential candidate in cellular therapy for motor neuron diseases.

  2. Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

    NASA Astrophysics Data System (ADS)

    Borowski, Piotr

    2012-01-01

    Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

  3. NMRDSP: an accurate prediction of protein shape strings from NMR chemical shifts and sequence data.

    PubMed

    Mao, Wusong; Cong, Peisheng; Wang, Zhiheng; Lu, Longjian; Zhu, Zhongliang; Li, Tonghua

    2013-01-01

    Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp.

  4. Handling the influence of chemical shift in amplitude-modulated heteronuclear dipolar recoupling solid-state NMR

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Basse, Kristoffer; Shankar, Ravi; Bjerring, Morten

    We present a theoretical analysis of the influence of chemical shifts on amplitude-modulated heteronuclear dipolar recoupling experiments in solid-state NMR spectroscopy. The method is demonstrated using the Rotor Echo Short Pulse IRrAdiaTION mediated Cross-Polarization ({sup RESPIRATION}CP) experiment as an example. By going into the pulse sequence rf interaction frame and employing a quintuple-mode operator-based Floquet approach, we describe how chemical shift offset and anisotropic chemical shift affect the efficiency of heteronuclear polarization transfer. In this description, it becomes transparent that the main attribute leading to non-ideal performance is a fictitious field along the rf field axis, which is generated frommore » second-order cross terms arising mainly between chemical shift tensors and themselves. This insight is useful for the development of improved recoupling experiments. We discuss the validity of this approach and present quaternion calculations to determine the effective resonance conditions in a combined rf field and chemical shift offset interaction frame transformation. Based on this, we derive a broad-banded version of the {sup RESPIRATION}CP experiment. The new sequence is experimentally verified using SNNFGAILSS amyloid fibrils where simultaneous {sup 15}N → {sup 13}CO and {sup 15}N → {sup 13}C{sub α} coherence transfer is demonstrated on high-field NMR instrumentation, requiring great offset stability.« less

  5. Evaluation of SCS-CN method using a fully distributed physically based coupled surface-subsurface flow model

    NASA Astrophysics Data System (ADS)

    Shokri, Ali

    2017-04-01

    The hydrological cycle contains a wide range of linked surface and subsurface flow processes. In spite of natural connections between surface water and groundwater, historically, these processes have been studied separately. The current trend in hydrological distributed physically based model development is to combine distributed surface water models with distributed subsurface flow models. This combination results in a better estimation of the temporal and spatial variability of the interaction between surface and subsurface flow. On the other hand, simple lumped models such as the Soil Conservation Service Curve Number (SCS-CN) are still quite common because of their simplicity. In spite of the popularity of the SCS-CN method, there have always been concerns about the ambiguity of the SCS-CN method in explaining physical mechanism of rainfall-runoff processes. The aim of this study is to minimize these ambiguity by establishing a method to find an equivalence of the SCS-CN solution to the DrainFlow model, which is a fully distributed physically based coupled surface-subsurface flow model. In this paper, two hypothetical v-catchment tests are designed and the direct runoff from a storm event are calculated by both SCS-CN and DrainFlow models. To find a comparable solution to runoff prediction through the SCS-CN and DrainFlow, the variance between runoff predictions by the two models are minimized by changing Curve Number (CN) and initial abstraction (Ia) values. Results of this study have led to a set of lumped model parameters (CN and Ia) for each catchment that is comparable to a set of physically based parameters including hydraulic conductivity, Manning roughness coefficient, ground surface slope, and specific storage. Considering the lack of physical interpretation in CN and Ia is often argued as a weakness of SCS-CN method, the novel method in this paper gives a physical explanation to CN and Ia.

  6. Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

    PubMed

    Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

    2018-01-01

    Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

  7. Factors affecting the use of 13Cα chemical shifts to determine, refine, and validate protein structures

    PubMed Central

    Vila, Jorge A.; Scheraga, Harold A.

    2008-01-01

    Interest centers here on the analysis of two different, but related, phenomena that affect side-chain conformations and consequently 13Cα chemical shifts and their applications to determine, refine, and validate protein structures. The first is whether 13Cα chemical shifts, computed at the DFT level of approximation with charged residues is a better approximation of observed 13Cα chemical shifts than those computed with neutral residues for proteins in solution. Accurate computation of 13Cα chemical shifts requires a proper representation of the charges, which might not take on integral values. For this analysis, the charges for 139 conformations of the protein ubiquitin were determined by explicit consideration of protein binding equilibria, at a given pH, that is, by exploring the 2ξ possible ionization states of the whole molecule, with ξ being the number of ionizable groups. The results of this analysis, as revealed by the shielding/deshield-ing of the 13Cα nucleus, indicated that: (i) there is a significant difference in the computed 13Cα chemical shifts, between basic and acidic groups, as a function of the degree of charge of the side chain; (ii) this difference is attributed to the distance between the ionizable groups and the 13Cα nucleus, which is shorter for the acidic Asp and Glu groups as compared with that for the basic Lys and Arg groups; and (iii) the use of neutral, rather than charged, basic and acidic groups is a better approximation of the observed 13Cα chemical shifts of a protein in solution. The second is how side-chain flexibility influences computed 13Cα chemical shifts in an additional set of ubiquitin conformations, in which the side chains are generated from an NMR-derived structure with the backbone conformation assumed to be fixed. The 13Cα chemical shift of a given amino acid residue in a protein is determined, mainly, by its own backbone and side-chain torsional angles, independent of the neighboring residues; the

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

    PubMed

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

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

  9. Beyond the SCS-CN method: A theoretical framework for spatially lumped rainfall-runoff response

    NASA Astrophysics Data System (ADS)

    Bartlett, M. S.; Parolari, A. J.; McDonnell, J. J.; Porporato, A.

    2016-06-01

    Since its introduction in 1954, the Soil Conservation Service curve number (SCS-CN) method has become the standard tool, in practice, for estimating an event-based rainfall-runoff response. However, because of its empirical origins, the SCS-CN method is restricted to certain geographic regions and land use types. Moreover, it does not describe the spatial variability of runoff. To move beyond these limitations, we present a new theoretical framework for spatially lumped, event-based rainfall-runoff modeling. In this framework, we describe the spatially lumped runoff model as a point description of runoff that is upscaled to a watershed area based on probability distributions that are representative of watershed heterogeneities. The framework accommodates different runoff concepts and distributions of heterogeneities, and in doing so, it provides an implicit spatial description of runoff variability. Heterogeneity in storage capacity and soil moisture are the basis for upscaling a point runoff response and linking ecohydrological processes to runoff modeling. For the framework, we consider two different runoff responses for fractions of the watershed area: "prethreshold" and "threshold-excess" runoff. These occur before and after infiltration exceeds a storage capacity threshold. Our application of the framework results in a new model (called SCS-CNx) that extends the SCS-CN method with the prethreshold and threshold-excess runoff mechanisms and an implicit spatial description of runoff. We show proof of concept in four forested watersheds and further that the resulting model may better represent geographic regions and site types that previously have been beyond the scope of the traditional SCS-CN method.

  10. Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics.

    PubMed

    Klukowski, Piotr; Schubert, Mario

    2018-06-15

    A better understanding of oligosaccharides and their wide-ranging functions in almost every aspect of biology and medicine promises to uncover hidden layers of biology and will support the development of better therapies. Elucidating the chemical structure of an unknown oligosaccharide is still a challenge. Efficient tools are required for non-targeted glycomics. Chemical shifts are a rich source of information about the topology and configuration of biomolecules, whose potential is however not fully explored for oligosaccharides. We hypothesize that the chemical shifts of each monosaccharide are unique for each saccharide type with a certain linkage pattern, so that correlated data measured by NMR spectroscopy can be used to identify the chemical nature of a carbohydrate. We present here an efficient search algorithm, GlycoNMRSearch, that matches either a subset or the entire set of chemical shifts of an unidentified monosaccharide spin system to all spin systems in an NMR database. The search output is much more precise than earlier search functions and highly similar matches suggest the chemical structure of the spin system within the oligosaccharide. Thus searching for connected chemical shift correlations within all electronically available NMR data of oligosaccharides is a very efficient way of identifying the chemical structure of unknown oligosaccharides. With an improved database in the future, GlycoNMRSearch will be even more efficient deducing chemical structures of oligosaccharides and there is a high chance that it becomes an indispensable technique for glycomics. The search algorithm presented here, together with a graphical user interface, is available at http://glyconmrsearch.santos.pwr.edu.pl. Supplementary data are available at Bioinformatics online.

  11. NMR Mapping of Protein Conformational Landscapes using Coordinated Behavior of Chemical Shifts upon Ligand Binding

    PubMed Central

    Cembran, Alessandro; Kim, Jonggul; Gao, Jiali; Veglia, Gianluigi

    2014-01-01

    Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often carried out through low-populated conformational states that occupy high energy basins. Ligand binding shifts the populations of these states, changing the distribution of these conformers. Understanding how the equilibrium among the states is altered upon ligand binding, interaction with other binding partners, and/or mutations and post-translational modifications is of critical importance for explaining allosteric signaling in proteins. Here, we propose a statistical analysis of the chemical shifts (CONCISE, COordiNated ChemIcal Shifts bEhavior) for the interpretation of protein conformational equilibria following linear trajectories of NMR chemical shifts. CONCISE enables one to quantitatively measure the population shifts associated with ligand titrations and estimate the degree of collectiveness of the protein residues’ response to ligand binding, giving a concise view of the structural transitions. The combination of CONCISE with thermocalorimetric and kinetic data allows one to depict a protein’s approximate conformational energy landscape. We tested this method with the catalytic subunit of cAMP-dependent protein kinase A, a ubiquitous enzyme that undergoes conformational transitions upon both nucleotide and pseudo-substrate binding. When complemented with chemical shift covariance analysis (CHESCA), this new method offers both collective response and residue-specific correlations for ligand binding to proteins. PMID:24604024

  12. Validity and extension of the SCS-CN method for computing infiltration and rainfall-excess rates

    NASA Astrophysics Data System (ADS)

    Mishra, Surendra Kumar; Singh, Vijay P.

    2004-12-01

    A criterion is developed for determining the validity of the Soil Conservation Service curve number (SCS-CN) method. According to this criterion, the existing SCS-CN method is found to be applicable when the potential maximum retention, S, is less than or equal to twice the total rainfall amount. The criterion is tested using published data of two watersheds. Separating the steady infiltration from capillary infiltration, the method is extended for predicting infiltration and rainfall-excess rates. The extended SCS-CN method is tested using 55 sets of laboratory infiltration data on soils varying from Plainfield sand to Yolo light clay, and the computed and observed infiltration and rainfall-excess rates are found to be in good agreement.

  13. Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

    PubMed Central

    Shen, Yang; Bax, Ad

    2015-01-01

    Summary Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors and the artificial neural network based TALOS-N program has been trained to extract backbone and sidechain torsion angles from 1H, 15N and 13C shifts. The program is quite robust, and typically yields backbone torsion angles for more than 90% of the residues, and sidechain χ1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and 13Cβ nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations. PMID:25502373

  14. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Concept document

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station Payload of experiments that will be onboard the Space Station Freedom. The simulation will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nagamura, Naoka, E-mail: NAGAMURA.Naoka@nims.go.jp; Kitada, Yuta; Honma, Itaru

    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 correspondingmore » to band bending by the field effect, resulting in p-type doping.« less

  16. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Volume 2: Baseline architecture report

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

  17. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Volume 1: Baseline architecture report

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is made up of the computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

  18. An extrapolation scheme for solid-state NMR chemical shift calculations

    NASA Astrophysics Data System (ADS)

    Nakajima, Takahito

    2017-06-01

    Conventional quantum chemical and solid-state physical approaches include several problems to accurately calculate solid-state nuclear magnetic resonance (NMR) properties. We propose a reliable computational scheme for solid-state NMR chemical shifts using an extrapolation scheme that retains the advantages of these approaches but reduces their disadvantages. Our scheme can satisfactorily yield solid-state NMR magnetic shielding constants. The estimated values have only a small dependence on the low-level density functional theory calculation with the extrapolation scheme. Thus, our approach is efficient because the rough calculation can be performed in the extrapolation scheme.

  19. Utilization of multiple spinal cord stimulation (SCS) waveforms in chronic pain patients.

    PubMed

    Berg, Anthony P; Mekel-Bobrov, Nitzan; Goldberg, Edward; Huynh, Dat; Jain, Roshini

    2017-08-01

    Advances in spinal cord stimulation (SCS) have improved patient outcomes, leading to its increased utilization for chronic pain. Chronic pain is dynamic showing exacerbations, variable severity, and evolving pain patterns. Given this complexity, SCS systems that provide a broad range of stimulation waveforms may be valuable. The aim of this research was to characterize the usage pattern of stimulation waveforms and field shapes in chronic pain patients implanted with the Spectra System. A review of daily device usage in a cohort of 250 patients implanted for a minimum duration of one month was conducted. With follow-ups ranging between 1 month and 1 year post-implant, 72.8% of patients used Standard Rate, 34.8% Anode Intensification, 23.2% Higher Rate, and 8.4% Burst stimulation waveforms. Collectively, 60% used 1 or more advanced waveforms, either exclusively or along with Standard Rate. A trend showed patients continuing to use up to 3 programs one year post-implant. When given a choice, SCS patients often utilize a variety of waveforms, suggesting that patients may benefit from a single system that provides multiple waveforms and field shapes to customize therapy and improve efficacy.

  20. Chemical characterization of synthetic cannabinoids by electrospray ionization FT-ICR mass spectrometry.

    PubMed

    Kill, Jade B; Oliveira, Izabela F; Tose, Lilian V; Costa, Helber B; Kuster, Ricardo M; Machado, Leandro F; Correia, Radigya M; Rodrigues, Rayza R T; Vasconcellos, Géssica A; Vaz, Boniek G; Romão, Wanderson

    2016-09-01

    The synthetic cannabinoids (SCs) represent the most recent advent of the new psychotropic substances (NPS) and has become popularly known to mitigate the effects of the Δ(9)-THC. The SCs are dissolved in organic solvents and sprayed in a dry herbal blend. However, little information is reported on active ingredients of SCs as well as the excipients or diluents added to the herbal blend. In this work, the direct infusion electrospray ionization Fourier transform ion cyclotron mass spectrometry technique (ESI-FT-ICR MS) was applied to explore the chemical composition of nine samples of herbal extract blends, where a total of 11 SCs (UR-144, JWH-073, XLR-11, JWH-250, JWH-122, AM-2201, AKB48, JWH-210, JWH-081, MAM-2201 and 5F-AKB48) were identified in the positive ionization mode, ESI(+), and other 44 chemical species (saturated and unsaturated fatty acids, sugars, flavonoids, etc.) were detected in the negative ionization mode, ESI(-). Additionally, CID experiments were performed, and fragmentation pathways were proposed to identify the connectivity of SCs. Thus, the direct infusion ESI-FT-ICR MS technique is a powerful tool in forensic chemistry that enables the rapid and unequivocal way for the determination of molecular formula, the degree of unsaturation (DBE-double bond equivalent) and exact mass (<1ppm) of a total of 55 chemical species without the prior separation step. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. Topography Estimation of the Core Mantle Boundary with ScS Reverberations and Diffraction Waves

    NASA Astrophysics Data System (ADS)

    Hein, B. E.; Nakata, N.

    2017-12-01

    In this study, we use the propagation of global seismic waves to study the Core Mantle Boundary (CMB). We focus on the use of S-wave reflections at the CMB (ScS reverberations) and outer-core diffracted waves. It is difficult imaging the CMB with the ScS wave because the complexity of the structure in the near surface ( 50 km); the complex structure degrades the signal-to-noise ratio of of the ScS. To avoid estimating the structure in the crust, we rely on the concept of seismic interferometry to extract wave propagation through mantle, but not through the crust. Our approach is compute the deconvolution between the ScS (and its reverberation) and direct S waves generated by intermediate to deep earthquakes (>50 km depth). Through this deconvolution, we have the ability to filter out the direct S wave and retrieve the wave field propagating from only the hypocenter to the outer core, but not between the hypocenter to the receiver. After the deconvolution, we can isolate the CMB reflected waves from the complicated wave phenomena because of the near-surface structure. Utilizing intermediate and deep earthquakes is key since we can suppress the near-surface effect from the surface to the hypocenter of the earthquakes. The variation of such waves (e.g., travel-time perturbation and/or wavefield decorrelation) at different receivers and earthquakes provides the information of the topography of the CMB. In order to get a more detailed image of the topography of the CMB we use diffracted seismic waves such as Pdiff , Sdiff, and P'P'. By using two intermediate to deep earthquakes on a great circle path with a station we can extract the wave propagation between the two earthquakes to simplify the waveform, similar to how it is preformed using the ScS wave. We generate more illumination of the CMB by using diffracted waves rather than only using ScS reverberations. The accurate topography of CMB obtained by these deconvolution analyses may provide new insight of the

  2. 125Te NMR chemical-shift trends in PbTe–GeTe and PbTe–SnTe alloys

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Njegic, Bosiljka; Levin, Evgenii M.; Schmidt-Rohr, Klaus

    2013-10-08

    Complex tellurides, such as doped PbTe, GeTe, and their alloys, are among the best thermoelectric materials. Knowledge of the change in 125Te NMR chemical shift due to bonding to dopant or “solute” atoms is useful for determination of phase composition, peak assignment, and analysis of local bonding. We have measured the 125Te NMR chemical shifts in PbTe-based alloys, Pb 1-xGe xTe and Pb 1-xSn xTe, which have a rocksalt-like structure, and analyzed their trends. For low x, several peaks are resolved in the 22-kHz MAS 125Te NMR spectra. A simple linear trend in chemical shifts with the number of Pbmore » neighbors is observed. No evidence of a proposed ferroelectric displacement of Ge atoms in a cubic PbTe matrix is detected at low Ge concentrations. The observed chemical shift trends are compared with the results of DFT calculations, which confirm the linear dependence on the composition of the first-neighbor shell. The data enable determination of the composition of various phases in multiphase telluride materials. They also provide estimates of the 125Te chemical shifts of GeTe and SnTe (+970 and +400±150 ppm, respectively, from PbTe), which are otherwise difficult to access due to Knight shifts of many hundreds of ppm in neat GeTe and SnTe.« less

  3. Experimental and DFT evaluation of the 1H and 13C NMR chemical shifts for calix[4]arenes

    NASA Astrophysics Data System (ADS)

    Guzzo, Rodrigo N.; Rezende, Michelle Jakeline Cunha; Kartnaller, Vinicius; Carneiro, José Walkimar de M.; Stoyanov, Stanislav R.; Costa, Leonardo Moreira da

    2018-04-01

    The density functional theory is employed to determine the efficiency of 11 exchange-correlation (XC) functionals to compute the 1H and 13C NMR chemical shifts of p-tert-butylcalix[4]arene (ptcx4, R1 = C(CH3)3) and congeners using the 6-31G(d,p) basis set. The statistical analysis shows that B3LYP, B3PW91 and PBE1PBE are the best XC functionals for the calculation of 1H chemical shifts. Moreover, the best results for the 13C chemical shifts are obtained using the LC-WPBE, M06-2X and wB97X-D functionals. The performance of these XC functionals is tested for three other calix[4]arenes: p-sulfonic acid calix[4]arene (sfxcx4 - R1 = SO3H), p-nitro-calix[4]arene (ncx4, R1 = NO2) and calix[4]arene (cx4 - R1 = H). For 1H chemical shifts B3LYP, B3PW91 and PBE1PBE yield similar results, although B3PW91 shows more consistency in the calculated error for the different structures. For 13C NMR chemical shifts, the XC functional that stood out as best is LC-WPBE. Indeed, the three functionals selected for each of 1H and 13C show good accuracy and can be used in future studies involving the prediction of 1H and 13C chemical shifts for this type of compounds.

  4. 13C and (15)N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine.

    PubMed

    Stueber, Dirk; Grant, David M

    2002-09-04

    The (13)C and (15)N chemical shift tensor principal values for adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine are measured on natural abundance samples. Additionally, the (13)C and (15)N chemical shielding tensor principal values in these four nucleosides are calculated utilizing various theoretical approaches. Embedded ion method (EIM) calculations improve significantly the precision with which the experimental principal values are reproduced over calculations on the corresponding isolated molecules with proton-optimized geometries. The (13)C and (15)N chemical shift tensor orientations are reliably assigned in the molecular frames of the nucleosides based upon chemical shielding tensor calculations employing the EIM. The differences between principal values obtained in EIM calculations and in calculations on isolated molecules with proton positions optimized inside a point charge array are used to estimate the contributions to chemical shielding arising from intermolecular interactions. Moreover, the (13)C and (15)N chemical shift tensor orientations and principal values correlate with the molecular structure and the crystallographic environment for the nucleosides and agree with data obtained previously for related compounds. The effects of variations in certain EIM parameters on the accuracy of the shielding tensor calculations are investigated.

  5. The converse approach to NMR chemical shifts from first-principles: application to finite and infinite aromatic compounds

    NASA Astrophysics Data System (ADS)

    Thonhauser, T.; Ceresoli, D.; Marzari, N.

    2009-03-01

    We present first-principles, density-functional theory calculations of the NMR chemical shifts for polycyclic aromatic hydrocarbons, starting with benzene and increasing sizes up to the one- and two-dimensional infinite limits of graphene ribbons and sheets. Our calculations are performed using a combination of the recently developed theory of orbital magnetization in solids, and a novel approach to NMR calculations where chemical shifts are obtained from the derivative of the orbital magnetization with respect to a microscopic, localized magnetic dipole. Using these methods we study on equal footing the ^1H and ^13C shifts in benzene, pyrene, coronene, in naphthalene, anthracene, naphthacene, and pentacene, and finally in graphene, graphite, and an infinite graphene ribbon. Our results show very good agreement with experiments and allow us to characterize the trends for the chemical shifts as a function of system size.

  6. Spin-echo based diagonal peak suppression in solid-state MAS NMR homonuclear chemical shift correlation spectra

    NASA Astrophysics Data System (ADS)

    Wang, Kaiyu; Zhang, Zhiyong; Ding, Xiaoyan; Tian, Fang; Huang, Yuqing; Chen, Zhong; Fu, Riqiang

    2018-02-01

    The feasibility of using the spin-echo based diagonal peak suppression method in solid-state MAS NMR homonuclear chemical shift correlation experiments is demonstrated. A complete phase cycling is designed in such a way that in the indirect dimension only the spin diffused signals are evolved, while all signals not involved in polarization transfer are refocused for cancellation. A data processing procedure is further introduced to reconstruct this acquired spectrum into a conventional two-dimensional homonuclear chemical shift correlation spectrum. A uniformly 13C, 15N labeled Fmoc-valine sample and the transmembrane domain of a human protein, LR11 (sorLA), in native Escherichia coli membranes have been used to illustrate the capability of the proposed method in comparison with standard 13C-13C chemical shift correlation experiments.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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.

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

    PubMed

    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.

  9. An Improved Experiment to Illustrate the Effect of Electronegativity on Chemical Shift.

    ERIC Educational Resources Information Center

    Boggess, Robert K.

    1988-01-01

    Describes a method for using nuclear magnetic resonance to observe the effect of electronegativity on the chemical shift of protons in similar compounds. Suggests the use of 1,3-dihalopropanes as samples. Includes sample questions. (MVL)

  10. General calibration methodology for a combined Horton-SCS infiltration scheme in flash flood modeling

    NASA Astrophysics Data System (ADS)

    Gabellani, S.; Silvestro, F.; Rudari, R.; Boni, G.

    2008-12-01

    Flood forecasting undergoes a constant evolution, becoming more and more demanding about the models used for hydrologic simulations. The advantages of developing distributed or semi-distributed models have currently been made clear. Now the importance of using continuous distributed modeling emerges. A proper schematization of the infiltration process is vital to these types of models. Many popular infiltration schemes, reliable and easy to implement, are too simplistic for the development of continuous hydrologic models. On the other hand, the unavailability of detailed and descriptive information on soil properties often limits the implementation of complete infiltration schemes. In this work, a combination between the Soil Conservation Service Curve Number method (SCS-CN) and a method derived from Horton equation is proposed in order to overcome the inherent limits of the two schemes. The SCS-CN method is easily applicable on large areas, but has structural limitations. The Horton-like methods present parameters that, though measurable to a point, are difficult to achieve a reliable estimate at catchment scale. The objective of this work is to overcome these limits by proposing a calibration procedure which maintains the large applicability of the SCS-CN method as well as the continuous description of the infiltration process given by the Horton's equation suitably modified. The estimation of the parameters of the modified Horton method is carried out using a formal analogy with the SCS-CN method under specific conditions. Some applications, at catchment scale within a distributed model, are presented.

  11. Characterization of human brown adipose tissue by chemical-shift water-fat MRI.

    PubMed

    Hu, Houchun H; Perkins, Thomas G; Chia, Jonathan M; Gilsanz, Vicente

    2013-01-01

    The purpose of this study was to characterize human brown adipose tissue (BAT) with chemical-shift water-fat MRI and to determine whether trends and differences in fat-signal fractions and T2(*) relaxation times between BAT and white adipose tissue (WAT) are consistently observed postmortem and in vivo in infants, adolescents, and adults. A postmortem body and eight patients were studied. A six-echo spoiled gradient-echo chemical-shift water-fat MRI sequence was performed at 3 T to jointly quantify fat-signal fraction and T2(*) in interscapular-supraclavicular BAT and subcutaneous WAT. To confirm BAT identity, biopsy and histology served as the reference in the postmortem study and PET/CT was used in five of the eight patients who required examination for medical care. Fat-signal fractions and T2(*) times were lower in BAT than in WAT in the postmortem example and in seven of eight patients. With the exception of one case, nominal comparisons between brown and white adipose tissues were statistically significant (p < 0.05). Between subjects, a large range of fat-signal fraction values was observed in BAT but not in WAT. We have shown that fat-signal fractions and T2(*) values jointly derived from chemical-shift water-fat MRI are lower in BAT than in WAT likely because of differences in cellular structures, triglyceride content, and vascularization. The two metrics can serve as complementary biomarkers in the detection of BAT.

  12. 129 Xe chemical shift in human blood and pulmonary blood oxygenation measurement in humans using hyperpolarized 129 Xe NMR.

    PubMed

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

    2017-04-01

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

  13. Robustness of Fat Quantification using Chemical Shift Imaging

    PubMed Central

    Hansen, Katie H; Schroeder, Michael E; Hamilton, Gavin; Sirlin, Claude B; Bydder, Mark

    2011-01-01

    This purpose of this study was to investigate the effect of parameter changes that can potentially lead to unreliable measurements in fat quantification. Chemical shift imaging was performed using spoiled gradient echo sequences with systematic variations in the following: 2D/3D sequence, number of echoes, delta echo time, fractional echo factor, slice thickness, repetition time, flip angle, bandwidth, matrix size, flow compensation and field strength. Results indicated no significant (or significant but small) changes in fat fraction with parameter. The significant changes can be attributed to known effects of T1 bias and the two forms of noise bias. PMID:22055856

  14. A Selective-Echo Method for Chemical-Shift Imaging of Two-Component Systems

    NASA Astrophysics Data System (ADS)

    Gerald, Rex E., II; Krasavin, Anatoly O.; Botto, Robert E.

    A simple and effective method for selectively imaging either one of two chemical species in a two-component system is presented and demonstrated experimentally. The pulse sequence employed, selective- echo chemical- shift imaging (SECSI), is a hybrid (frequency-selective/ T1-contrast) technique that is executed in a short period of time, utilizes the full Boltzmann magnetization of each chemical species to form the corresponding image, and requires only hard pulses of quadrature phase. This approach provides a direct and unambiguous representation of the spatial distribution of the two chemical species. In addition, the performance characteristics and the advantages of the SECSI sequence are compared on a common basis to those of other pulse sequences.

  15. A Chemical View on X-ray Photoelectron Spectroscopy: the ESCA Molecule and Surface-to-Bulk XPS Shifts.

    PubMed

    Delesma, Francisco A; Van den Bossche, Maxime; Grönbeck, Henrik; Calaminici, Patrizia; Köster, Andreas M; Pettersson, Lars G M

    2018-01-19

    In this paper we remind the reader of a simple, intuitive picture of chemical shifts in X-ray photoelectron spectroscopy (XPS) as the difference in chemical bonding between the probed atom and its neighbor to the right in the periodic table, the so called Z+1 approximation. We use the classical ESCA molecule, ethyl trifluoroacetate, and 4d-transition metals to explicitly demonstrate agreement between core-level shifts computed as differences between final core-hole states and the approach where each core-ionized atom is replaced by a Z+1 atom. In this final state, or total energy picture, the XPS shift arises due to the more or less unfavorable chemical bonding of the effective nitrogen in the carbon geometry for the ESCA molecule. Surface core level shifts in metals are determined by whether the Z+1 atom as an alloy segregates to the surface or is more soluble in the bulk. As further illustration of this more chemical picture, we compare the geometry of C 1s and O 1s core-ionized CO with that of, respectively, NO + and CF + . The scope is not to propose a new method to compute XPS shifts but rather to stress the validity of this simple interpretation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. 17O NMR studies on 4- and 4'-substituted chalcones and p-substituted β-nitrostyrenes

    NASA Astrophysics Data System (ADS)

    Boykin, D. W.; Baumstark, A. L.; Balakrishnan, P.; Perjéssy, A.; Hrnc˜iar, P.

    The 17O NMR chemical shift data for 17O-enriched 4- and 4'-chalcones in toluene at 90°C and for p-substituted β-nitrostyrenes (natural abundance) in acetonitrile at 70°C are reported. The SCS (substituent chemical shift) range for the 4-chalcones p-CH 3O to p-NO 2 is 16.3 ppm; the range for the 4'-chalcones p-CH 3O to p-NO 2 is 32.4 ppm. The SCS range for the p-substituted-β-nitrostyrenes p-CH 3O to p-NO 2 is 13.2 ppm. The data for the three series gave good correlations with σ + constants, while the Dual Substitutent Parameter treatment only slightly improved the correlations using σ R+ constants. Plots of the 17O chemical shifts for both 4- and 4'-chalcones with 17O data for acetophenones and correlation of 17O chemical shift data for the β-nitrostyrenes with that of nitrobenzenes gave good correlations. Plots of the 17O data for all the three series with their respective functional group stretching frequencies gave fair correlations.

  17. Nonlinear detection of secondary isotopic chemical shifts in NMR through spin noise

    PubMed Central

    Pöschko, Maria Theresia; Rodin, Victor V.; Schlagnitweit, Judith; Müller, Norbert; Desvaux, Hervé

    2017-01-01

    The detection of minor species in the presence of large amounts of similar main components remains a key challenge in analytical chemistry, for instance, to obtain isotopic fingerprints. As an alternative to the classical NMR scheme based on coherent excitation and detection, here we introduce an approach based on spin-noise detection. Chemical shifts and transverse relaxation rates are determined using only the detection circuit. Thanks to a nonlinear effect in mixtures with small chemical shift dispersion, small signals on top of a larger one can be observed with increased sensitivity as bumps on a dip; the latter being the signature of the main magnetization. Experimental observations are underpinned by an analytical theory: the coupling between the magnetization and the coil provides an amplified detection capability of both small static magnetic field inhomogeneities and small NMR signals. This is illustrated by two-bond 12C/13C isotopic measurements. PMID:28067218

  18. Catchment area-based evaluation of the AMC-dependent SCS-CN-based rainfall-runoff models

    NASA Astrophysics Data System (ADS)

    Mishra, S. K.; Jain, M. K.; Pandey, R. P.; Singh, V. P.

    2005-09-01

    Using a large set of rainfall-runoff data from 234 watersheds in the USA, a catchment area-based evaluation of the modified version of the Mishra and Singh (2002a) model was performed. The model is based on the Soil Conservation Service Curve Number (SCS-CN) methodology and incorporates the antecedent moisture in computation of direct surface runoff. Comparison with the existing SCS-CN method showed that the modified version performed better than did the existing one on the data of all seven area-based groups of watersheds ranging from 0.01 to 310.3 km2.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hartman, Joshua D.; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu; Monaco, Stephen

    2015-09-14

    We assess the quality of fragment-based ab initio isotropic {sup 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 {sup 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 readilymore » 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.« less

  20. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

    PubMed

    Zhu, Tong; Zhang, John Z H; He, Xiao

    2014-09-14

    In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

  1. Study of chemical shift in Kα, Kβ1,3 and Kβ// X-ray emission lines of 37Rb compounds with WDXRF

    NASA Astrophysics Data System (ADS)

    Kainth, Harpreet Singh; Singh, Ranjit; Singh, Tejbir; Mehta, D.; Shahi, J. S.; Kumar, Sanjeev

    2018-05-01

    The positive and negative chemical shifts in Kα, Kβ1,3 and Kβ// X-ray emission lines of rubidium compounds were measured with high resolution WDXRF spectrometer. The measured energy shifts in Kα emission lines ranges from -2.95 eV to -3.64 eV, Kβ1,3 emission lines ranges from 1.16 eV to 1.32 eV and Kβ// emission lines ranges from 1.31 eV to 4.36 eV respectively. In the present work, it has been found that chemical shift in Kβ// X-ray emission lines were found to be larger than Kα and Kβ1,3 X-ray emission lines. To find the cause of chemical shift, various factors like effective charge, line intensity ratio, bond length and electro-negativity were calculated and correlated with the chemical shift.

  2. Validation of the Spanish versions of the long (26 items) and short (12 items) forms of the Self-Compassion Scale (SCS).

    PubMed

    Garcia-Campayo, Javier; Navarro-Gil, Mayte; Andrés, Eva; Montero-Marin, Jesús; López-Artal, Lorena; Demarzo, Marcelo Marcos Piva

    2014-01-10

    Self-compassion is a key psychological construct for assessing clinical outcomes in mindfulness-based interventions. The aim of this study was to validate the Spanish versions of the long (26 item) and short (12 item) forms of the Self-Compassion Scale (SCS). The translated Spanish versions of both subscales were administered to two independent samples: Sample 1 was comprised of university students (n = 268) who were recruited to validate the long form, and Sample 2 was comprised of Aragon Health Service workers (n = 271) who were recruited to validate the short form. In addition to SCS, the Mindful Attention Awareness Scale (MAAS), the State-Trait Anxiety Inventory-Trait (STAI-T), the Beck Depression Inventory (BDI) and the Perceived Stress Questionnaire (PSQ) were administered. Construct validity, internal consistency, test-retest reliability and convergent validity were tested. The Confirmatory Factor Analysis (CFA) of the long and short forms of the SCS confirmed the original six-factor model in both scales, showing goodness of fit. Cronbach's α for the 26 item SCS was 0.87 (95% CI = 0.85-0.90) and ranged between 0.72 and 0.79 for the 6 subscales. Cronbach's α for the 12-item SCS was 0.85 (95% CI = 0.81-0.88) and ranged between 0.71 and 0.77 for the 6 subscales. The long (26-item) form of the SCS showed a test-retest coefficient of 0.92 (95% CI = 0.89-0.94). The Intraclass Correlation (ICC) for the 6 subscales ranged from 0.84 to 0.93. The short (12-item) form of the SCS showed a test-retest coefficient of 0.89 (95% CI: 0.87-0.93). The ICC for the 6 subscales ranged from 0.79 to 0.91. The long and short forms of the SCS exhibited a significant negative correlation with the BDI, the STAI and the PSQ, and a significant positive correlation with the MAAS. The correlation between the total score of the long and short SCS form was r = 0.92. The Spanish versions of the long (26-item) and short (12-item) forms of the SCS are valid and

  3. Validation of the Spanish versions of the long (26 items) and short (12 items) forms of the Self-Compassion Scale (SCS)

    PubMed Central

    2014-01-01

    Background Self-compassion is a key psychological construct for assessing clinical outcomes in mindfulness-based interventions. The aim of this study was to validate the Spanish versions of the long (26 item) and short (12 item) forms of the Self-Compassion Scale (SCS). Methods The translated Spanish versions of both subscales were administered to two independent samples: Sample 1 was comprised of university students (n = 268) who were recruited to validate the long form, and Sample 2 was comprised of Aragon Health Service workers (n = 271) who were recruited to validate the short form. In addition to SCS, the Mindful Attention Awareness Scale (MAAS), the State-Trait Anxiety Inventory–Trait (STAI-T), the Beck Depression Inventory (BDI) and the Perceived Stress Questionnaire (PSQ) were administered. Construct validity, internal consistency, test-retest reliability and convergent validity were tested. Results The Confirmatory Factor Analysis (CFA) of the long and short forms of the SCS confirmed the original six-factor model in both scales, showing goodness of fit. Cronbach’s α for the 26 item SCS was 0.87 (95% CI = 0.85-0.90) and ranged between 0.72 and 0.79 for the 6 subscales. Cronbach’s α for the 12-item SCS was 0.85 (95% CI = 0.81-0.88) and ranged between 0.71 and 0.77 for the 6 subscales. The long (26-item) form of the SCS showed a test-retest coefficient of 0.92 (95% CI = 0.89–0.94). The Intraclass Correlation (ICC) for the 6 subscales ranged from 0.84 to 0.93. The short (12-item) form of the SCS showed a test-retest coefficient of 0.89 (95% CI: 0.87-0.93). The ICC for the 6 subscales ranged from 0.79 to 0.91. The long and short forms of the SCS exhibited a significant negative correlation with the BDI, the STAI and the PSQ, and a significant positive correlation with the MAAS. The correlation between the total score of the long and short SCS form was r = 0.92. Conclusion The Spanish versions of the long (26-item) and short

  4. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 4: Conceptual design report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex (PTC) at Marshall Space Flight Center (MSFC). The PTC will train the space station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. In the first step of this task, a methodology was developed to ensure that all relevant design dimensions were addressed, and that all feasible designs could be considered. The development effort yielded the following method for generating and comparing designs in task 4: (1) Extract SCS system requirements (functions) from the system specification; (2) Develop design evaluation criteria; (3) Identify system architectural dimensions relevant to SCS system designs; (4) Develop conceptual designs based on the system requirements and architectural dimensions identified in step 1 and step 3 above; (5) Evaluate the designs with respect to the design evaluation criteria developed in step 2 above. The results of the method detailed in the above 5 steps are discussed. The results of the task 4 work provide the set of designs which two or three candidate designs are to be selected by MSFC as input to task 5-refine SCS conceptual designs. The designs selected for refinement will be developed to a lower level of detail, and further analyses will be done to begin to determine the size and speed of the components required to implement these designs.

  5. Using a topographic index to distribute variable source area runoff predicted with the SCS curve-number equation

    NASA Astrophysics Data System (ADS)

    Lyon, Steve W.; Walter, M. Todd; Gérard-Marchant, Pierre; Steenhuis, Tammo S.

    2004-10-01

    Because the traditional Soil Conservation Service curve-number (SCS-CN) approach continues to be used ubiquitously in water quality models, new application methods are needed that are consistent with variable source area (VSA) hydrological processes in the landscape. We developed and tested a distributed approach for applying the traditional SCS-CN equation to watersheds where VSA hydrology is a dominant process. Predicting the location of source areas is important for watershed planning because restricting potentially polluting activities from runoff source areas is fundamental to controlling non-point-source pollution. The method presented here used the traditional SCS-CN approach to predict runoff volume and spatial extent of saturated areas and a topographic index, like that used in TOPMODEL, to distribute runoff source areas through watersheds. The resulting distributed CN-VSA method was applied to two subwatersheds of the Delaware basin in the Catskill Mountains region of New York State and one watershed in south-eastern Australia to produce runoff-probability maps. Observed saturated area locations in the watersheds agreed with the distributed CN-VSA method. Results showed good agreement with those obtained from the previously validated soil moisture routing (SMR) model. When compared with the traditional SCS-CN method, the distributed CN-VSA method predicted a similar total volume of runoff, but vastly different locations of runoff generation. Thus, the distributed CN-VSA approach provides a physically based method that is simple enough to be incorporated into water quality models, and other tools that currently use the traditional SCS-CN method, while still adhering to the principles of VSA hydrology.

  6. Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

    PubMed

    Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

    2018-03-22

    Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

  7. Electrochemical Characterization of a Novel Exoelectrogenic Bacterium Strain SCS5, Isolated from a Mediator-Less Microbial Fuel Cell and Phylogenetically Related to Aeromonas jandaei.

    PubMed

    Sharma, Subed Chandra Dev; Feng, Cuijie; Li, Jiangwei; Hu, Anyi; Wang, Han; Qin, Dan; Yu, Chang-Ping

    2016-09-29

    A facultative anaerobic bacterium, designated as strain SCS5, was isolated from the anodic biofilm of a mediator-less microbial fuel cell using acetate as the electron donor and α-FeOOH as the electron acceptor. The isolate was Gram-negative, motile, and shaped as short rods (0.9-1.3 μm in length and 0.4-0.5 μm in width). A phylogenetic analysis of the 16S rRNA, gyrB, and rpoD genes suggested that strain SCS5 belonged to the Aeromonas genus in the Aeromonadaceae family and exhibited the highest 16S rRNA gene sequence similarity (99.45%) with Aeromonas jandaei ATCC 49568. However, phenotypic, cellular fatty acid profile, and DNA G+C content analyses revealed that there were some distinctions between strain SCS5 and the type strain A. jandaei ATCC 49568. The optimum growth temperature, pH, and NaCl (%) for strain SCS5 were 35°C, 7.0, and 0.5% respectively. The DNA G+C content of strain SCS5 was 59.18%. The isolate SCS5 was capable of reducing insoluble iron oxide (α-FeOOH) and transferring electrons to extracellular material (the carbon electrode). The electrochemical activity of strain SCS5 was corroborated by cyclic voltammetry and a Raman spectroscopic analysis. The cyclic voltammogram of strain SCS5 revealed two pairs of oxidation-reduction peaks under anaerobic and aerobic conditions. In contrast, no redox pair was observed for A. jandaei ATCC 49568. Thus, isolated strain SCS5 is a novel exoelectrogenic bacterium phylogenetically related to A. jandaei, but shows distinct electrochemical activity from its close relative A. jandaei ATCC 49568.

  8. Theoretical Modeling of 99 Tc NMR Chemical Shifts

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hall, Gabriel B.; Andersen, Amity; Washton, Nancy M.

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

  9. Solution and solid-state effects on NMR chemical shifts in sesquiterpene lactones: NMR, X-ray, and theoretical methods.

    PubMed

    Dračínský, Martin; Buděšínský, Miloš; Warżajtis, Beata; Rychlewska, Urszula

    2012-01-12

    Selected guaianolide type sesquiterpene lactones were studied combining solution and solid-state NMR spectroscopy with theoretical calculations of the chemical shifts in both environments and with the X-ray data. The experimental (1)H and (13)C chemical shifts in solution were successfully reproduced by theoretical calculations (with the GIAO method and DFT B3LYP 6-31++G**) after geometry optimization (DFT B3LYP 6-31 G**) in vacuum. The GIPAW method was used for calculations of solid-state (13)C chemical shifts. The studied cases involved two polymorphs of helenalin, two pseudopolymorphs of 6α-hydroxydihydro-aromaticin and two cases of multiple asymmetric units in crystals: one in which the symmetry-independent molecules were connected by a series of hydrogen bonds (geigerinin) and the other in which the symmetry-independent molecules, deprived of any specific intermolecular interactions, differed in the conformation of the side chain (badkhysin). Geometrically different molecules present in the crystal lattices could be easily distinguished in the solid-state NMR spectra. Moreover, the experimental differences in the (13)C chemical shifts corresponding to nuclei in different polymorphs or in geometrically different molecules were nicely reproduced with the GIPAW calculations.

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

    PubMed

    Sahakyan, Aleksandr B; Vendruscolo, Michele

    2013-02-21

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

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

    PubMed

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

    2012-10-01

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

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

    PubMed Central

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

    2012-01-01

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

  13. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 1: Overview and summary

    NASA Technical Reports Server (NTRS)

    1989-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned Marshall Space Flight Center (MSFC) Payload Training Complex (PTC) required to meet this need will train the space station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs. This study was performed August 1988 to October 1989. Thus, the results are based on the SSFP August 1989 baseline, i.e., pre-Langley configuration/budget review (C/BR) baseline. Some terms, e.g., combined trainer, are being redefined. An overview of the study activities and a summary of study results are given here.

  14. GIS Based Distributed Runoff Predictions in Variable Source Area Watersheds Employing the SCS-Curve Number

    NASA Astrophysics Data System (ADS)

    Steenhuis, T. S.; Mendoza, G.; Lyon, S. W.; Gerard Marchant, P.; Walter, M. T.; Schneiderman, E.

    2003-04-01

    Because the traditional Soil Conservation Service Curve Number (SCS-CN) approach continues to be ubiquitously used in GIS-BASED water quality models, new application methods are needed that are consistent with variable source area (VSA) hydrological processes in the landscape. We developed within an integrated GIS modeling environment a distributed approach for applying the traditional SCS-CN equation to watersheds where VSA hydrology is a dominant process. Spatial representation of hydrologic processes is important for watershed planning because restricting potentially polluting activities from runoff source areas is fundamental to controlling non-point source pollution. The methodology presented here uses the traditional SCS-CN method to predict runoff volume and spatial extent of saturated areas and uses a topographic index to distribute runoff source areas through watersheds. The resulting distributed CN-VSA method was incorporated in an existing GWLF water quality model and applied to sub-watersheds of the Delaware basin in the Catskill Mountains region of New York State. We found that the distributed CN-VSA approach provided a physically-based method that gives realistic results for watersheds with VSA hydrology.

  15. Second ISCB Latin American Student Council Symposium (LA-SCS) 2016

    PubMed Central

    Monzon, Alexander Miguel; Hasenahuer, Marcia A.; Mancini, Estefanía; Coimbra, Nilson; Cravero, Fiorella; Cáceres-Molina, Javier; Ramírez-Sarmiento, César A.; Palopoli, Nicolas; Meysman, Pieter; Parra, R. Gonzalo

    2017-01-01

    This report summarizes the scientific content and activities of the second edition of the Latin American Symposium (LA-SCS), organized by the Student Council (SC) of the International Society for Computational Biology (ISCB), held in conjunction with the Fourth Latin American conference from the International Society for Computational Biology (ISCB-LA 2016) in Buenos Aires, Argentina, on November 19, 2016. PMID:28928937

  16. All-ceramic or metal-ceramic tooth-supported fixed dental prostheses (FDPs)? A systematic review of the survival and complication rates. Part I: Single crowns (SCs).

    PubMed

    Sailer, Irena; Makarov, Nikolay Alexandrovich; Thoma, Daniel Stefan; Zwahlen, Marcel; Pjetursson, Bjarni Elvar

    2015-06-01

    To assess the 5-year survival of metal-ceramic and all-ceramic tooth-supported single crowns (SCs) and to describe the incidence of biological, technical and esthetic complications. Medline (PubMed), Embase, Cochrane Central Register of Controlled Trials (CENTRAL) searches (2006-2013) were performed for clinical studies focusing on tooth-supported fixed dental prostheses (FDPs) with a mean follow-up of at least 3 years. This was complimented by an additional hand search and the inclusion of 34 studies from a previous systematic review [1,2]. Survival and complication rates were analyzed using robust Poisson's regression models to obtain summary estimates of 5-year proportions. Sixty-seven studies reporting on 4663 metal-ceramic and 9434 all-ceramic SCs fulfilled the inclusion criteria. Seventeen studies reported on metal-ceramic crowns, and 54 studies reported on all-ceramic crowns. Meta-analysis of the included studies indicated an estimated survival rate of metal-ceramic SCs of 94.7% (95% CI: 94.1-96.9%) after 5 years. This was similar to the estimated 5-year survival rate of leucit or lithium-disilicate reinforced glass ceramic SCs (96.6%; 95% CI: 94.9-96.7%), of glass infiltrated alumina SCs (94.6%; 95% CI: 92.7-96%) and densely sintered alumina and zirconia SCs (96%; 95% CI: 93.8-97.5%; 92.1%; 95% CI: 82.8-95.6%). In contrast, the 5-year survival rates of feldspathic/silica-based ceramic crowns were lower (p<0.001). When the outcomes in anterior and posterior regions were compared feldspathic/silica-based ceramic and zirconia crowns exhibited significantly lower survival rates in the posterior region (p<0.0001), the other crown types performed similarly. Densely sintered zirconia SCs were more frequently lost due to veneering ceramic fractures than metal-ceramic SCs (p<0.001), and had significantly more loss of retention (p<0.001). In total higher 5 year rates of framework fracture were reported for the all-ceramic SCs than for metal-ceramic SCs. Survival

  17. Sum-over-states density functional perturbation theory: Prediction of reliable 13C, 15N, and 17O nuclear magnetic resonance chemical shifts

    NASA Astrophysics Data System (ADS)

    Olsson, Lars; Cremer, Dieter

    1996-11-01

    Sum-over-states density functional perturbation theory (SOS-DFPT) has been used to calculate 13C, 15N, and 17O NMR chemical shifts of 20 molecules, for which accurate experimental gas-phase values are available. Compared to Hartree-Fock (HF), SOS-DFPT leads to improved chemical shift values and approaches the degree of accuracy obtained with second order Møller-Plesset perturbation theory (MP2). This is particularly true in the case of 15N chemical shifts where SOS-DFPT performs even better than MP2. Additional improvements of SOS-DFPT chemical shifts can be obtained by empirically correcting diamagnetic and paramagnetic contributions to compensate for deficiencies which are typical of DFT.

  18. Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

    PubMed

    Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

    2014-01-14

    The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

  19. Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine.

    PubMed

    Tredwell, Gregory D; Bundy, Jacob G; De Iorio, Maria; Ebbels, Timothy M D

    2016-01-01

    Despite the use of buffering agents the 1 H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. To investigate the acid, base and metal ion dependent 1 H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl 2 , MgCl 2 , NaCl or KCl, and their 1 H NMR spectra were acquired. Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na + , K + , Ca 2+ and Mg 2+ , were also measured. These data will be a valuable resource for 1 H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1 H NMR spectra.

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

    PubMed

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

    2017-04-01

    While magnetic susceptibility is a major contributor to NMR resonance frequency variations in the human brain, a substantial contribution may come from the chemical exchange of protons between water and other molecules. Exchange-induced frequency shifts f e have been measured in tissue and protein solutions, but relatively lipid-rich white matter (WM) has a larger f e than gray matter, suggesting that lipids could contribute. Galactocerebrosides (GC) are a prime candidate as they are abundant in WM and susceptible to exchange. To investigate this, f e was measured in a model of WM lipid membranes in the form of multilamellar vesicles (MLVs), consisting of a 1:2 molar ratio of GC and phospholipids (POPC), and in MLVs with POPC only. Chemical shift imaging with 15% volume fraction of dioxane, an internal reference whose protons are assumed not to undergo chemical exchange, was used to remove susceptibility-induced frequency shifts in an attempt to measure f e in MLVs at several lipid concentrations. Initial analysis of these measurements indicated a necessity to correct for small unexpected variations in dioxane concentration due to its effect on the water frequency shift. To achieve this, the actual dioxane concentration was inferred from spectral analysis and its additional contribution to f e was removed through separate experiments which showed that the water-dioxane frequency shift depended linearly on the dioxane concentration at low concentrations with a proportionality constant of -0.021 ± 0.002 ppb/mM in agreement with published experiments. Contrary to expectations and uncorrected results, for GC + POPC vesicles, the dependence of the corrected f e on GC concentration was insignificant (0.023 ± 0.037 ppb/mM; r 2  = 0.085, p > 0.57), whereas for the POPC-only vesicles a small but significant linear increase with POPC concentration was found: 0.044 ± 0.008 ppb/mM (r 2  = 0.877, p < 0.01). These findings suggest that

  1. A Magic-Angle Spinning NMR Method for the Site-Specific Measurement of Proton Chemical-Shift Anisotropy in Biological and Organic Solids.

    PubMed

    Hou, Guangjin; Gupta, Rupal; Polenova, Tatyana; Vega, Alexander J

    2014-02-01

    Proton chemical shifts are a rich probe of structure and hydrogen bonding environments in organic and biological molecules. Until recently, measurements of 1 H chemical shift tensors have been restricted to either solid systems with sparse proton sites or were based on the indirect determination of anisotropic tensor components from cross-relaxation and liquid-crystal experiments. We have introduced an MAS approach that permits site-resolved determination of CSA tensors of protons forming chemical bonds with labeled spin-1/2 nuclei in fully protonated solids with multiple sites, including organic molecules and proteins. This approach, originally introduced for the measurements of chemical shift tensors of amide protons, is based on three RN -symmetry based experiments, from which the principal components of the 1 H CS tensor can be reliably extracted by simultaneous triple fit of the data. In this article, we expand our approach to a much more challenging system involving aliphatic and aromatic protons. We start with a review of the prior work on experimental-NMR and computational-quantum-chemical approaches for the measurements of 1 H chemical shift tensors and for relating these to the electronic structures. We then present our experimental results on U- 13 C, 15 N-labeled histdine demonstrating that 1 H chemical shift tensors can be reliably determined for the 1 H 15 N and 1 H 13 C spin pairs in cationic and neutral forms of histidine. Finally, we demonstrate that the experimental 1 H(C) and 1 H(N) chemical shift tensors are in agreement with Density Functional Theory calculations, therefore establishing the usefulness of our method for characterization of structure and hydrogen bonding environment in organic and biological solids.

  2. Quantum-Chemical Approach to NMR Chemical Shifts in Paramagnetic Solids Applied to LiFePO4 and LiCoPO4.

    PubMed

    Mondal, Arobendo; Kaupp, Martin

    2018-04-05

    A novel protocol to compute and analyze NMR chemical shifts for extended paramagnetic solids, accounting comprehensively for Fermi-contact (FC), pseudocontact (PC), and orbital shifts, is reported and applied to the important lithium ion battery cathode materials LiFePO 4 and LiCoPO 4 . Using an EPR-parameter-based ansatz, the approach combines periodic (hybrid) DFT computation of hyperfine and orbital-shielding tensors with an incremental cluster model for g- and zero-field-splitting (ZFS) D-tensors. The cluster model allows the use of advanced multireference wave function methods (such as CASSCF or NEVPT2). Application of this protocol shows that the 7 Li shifts in the high-voltage cathode material LiCoPO 4 are dominated by spin-orbit-induced PC contributions, in contrast with previous assumptions, fundamentally changing interpretations of the shifts in terms of covalency. PC contributions are smaller for the 7 Li shifts of the related LiFePO 4 , where FC and orbital shifts dominate. The 31 P shifts of both materials finally are almost pure FC shifts. Nevertheless, large ZFS contributions can give rise to non-Curie temperature dependences for both 7 Li and 31 P shifts.

  3. 13C chemical-shift anisotropy of alkyl-substituted aromatic carbon in anthracene derivatives.

    PubMed

    Hoop, Cody L; Iuliucci, Robbie J

    2013-06-01

    The (13)C chemical-shift anisotropy in anthracene derivatives (9,10-dimethylanthracene, 9,10-dihydroanthracene, dianthracene, and triptycene) has been measured by the 2D FIREMAT timed pulse sequence and the corresponding set of principal values has been determined by the TIGER processing method. These molecules expand the data base of (13)C CSA measurements of fused aromatic rings some bridged by sp(3) carbon resulting in an unusual bonding configuration, which leads to distinctive aromatic (13)C CSA values. Crystal lattice distortions to the CSA were observed to change the isotropic shift by 2.5 to 3.3 ppm and changes as large as 8.3 ppm in principal components. Modeling of the CSA data by GIPAW DFT (GGA-PBE/ultrafine) shielding calculations resulted in an rms chemical-shift distance of 2.8 ppm after lattice including geometry optimization of the diffraction structures by the GIPAW method at GGA-PBE/ultrafine level. Attention is given to the substituted aromatic carbon in the phenyl groups (here forth referred to as the α-carbon) with respect to CSA modeling with electronic methods. The (13)C CSA of this position is accurately determined due to its spectral isolation of the isotropic shift that limits overlap in the FIREMAT spectrum. In cases where the bridging ring is sp(3) carbon, the current density is reduced from extending beyond the peripheral phenyl groups; this plays a significant role in the magnetic shielding of the α-position. Nuclear independent chemical-shift calculations based on GIAO DFT (B3LYP/6-31G(d)) shielding calculations were used to model the intramolecular π-interactions in dianthracene and triptycene. These NICS results estimate the isotropic shift of the α-position in dianthracene to be insignificantly affected by the presence of the neighboring aromatic rings. However, a notable change in isotropic shielding, Δσ(iso)=-2.1 ppm, is predicted for the α- position of triptycene. Experimentally, the δ22 principal component at the

  4. Relativistic Spin-Orbit Heavy Atom on the Light Atom NMR Chemical Shifts: General Trends Across the Periodic Table Explained.

    PubMed

    Vícha, Jan; Komorovsky, Stanislav; Repisky, Michal; Marek, Radek; Straka, Michal

    2018-06-12

    The importance of relativistic effects on the NMR parameters in heavy-atom (HA) compounds, particularly the SO-HALA (Spin-Orbit Heavy Atom on the Light Atom) effect on NMR chemical shifts, has been known for about 40 years. Yet, a general correlation between the electronic structure and SO-HALA effect has been missing. By analyzing 1 H NMR chemical shifts of the sixth-period hydrides (Cs-At), we discovered general electronic-structure principles and mechanisms that dictate the size and sign of the SO-HALA NMR chemical shifts. In brief, partially occupied HA valence shells induce relativistic shielding at the light atom (LA) nuclei, while empty HA valence shells induce relativistic deshielding. In particular, the LA nucleus is relativistically shielded in 5d 2 -5d 8 and 6p 4 HA hydrides and deshielded in 4f 0 , 5d 0 , 6s 0 , and 6p 0 HA hydrides. This general and intuitive concept explains periodic trends in the 1 H NMR chemical shifts along the sixth-period hydrides (Cs-At) studied in this work. We present substantial evidence that the introduced principles have a general validity across the periodic table and can be extended to nonhydride LAs. The decades-old question of why compounds with occupied frontier π molecular orbitals (MOs) cause SO-HALA shielding at the LA nuclei, while the frontier σ MOs cause deshielding is answered. We further derive connection between the SO-HALA NMR chemical shifts and Spin-Orbit-induced Electron Deformation Density (SO-EDD), a property that can be obtained easily from differential electron densities and can be represented graphically. SO-EDD provides an intuitive understanding of the SO-HALA effect in terms of the depletion/concentration of the electron density at LA nuclei caused by spin-orbit coupling due to HA in the presence of a magnetic field. Using an analogy between the SO-EDD concept and arguments from classic NMR theory, the complex question of the SO-HALA NMR chemical shifts becomes easily understandable for a wide

  5. U.S.-Vietnamese Security Cooperation for Access to the SCS

    DTIC Science & Technology

    2015-06-16

    of the claimants to islands in the SCS, China has more Coast Guard/MLE vessels than Japan, Indonesia, Malaysia , and the Philippines combined.7...45 In 2011, the U.S. looked at Vietnam, along with other Southeast Asian countries, for its Naval Medical ...human rights; culture, tourism , and sports; as well as continued annual defense dialogue meetings.47 Both Vietnam and the U.S. are concerned about

  6. Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

    PubMed

    Hartman, Joshua D; Beran, Gregory J O

    2014-11-11

    First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations.

  7. Density functional study of the 13C NMR chemical shifts in small-to-medium-diameter infinite single-walled carbon nanotubes.

    PubMed

    Zurek, Eva; Pickard, Chris J; Walczak, Brian; Autschbach, Jochen

    2006-11-02

    NMR chemical shifts were calculated for semiconducting (n,0) single-walled carbon nanotubes (SWNTs) with n ranging from 7 to 17. Infinite isolated SWNTs were calculated using a gauge-including projector-augmented plane-wave (GIPAW) approach with periodic boundary conditions and density functional theory (DFT). In order to minimize intertube interactions in the GIPAW computations, an intertube distance of 8 A was chosen. For the infinite tubes, we found a chemical shift range of over 20 ppm for the systems considered here. The SWNT family with lambda = mod(n, 3) = 0 has much smaller chemical shifts compared to the other two families with lambda = 1 and lambda = 2. For all three families, the chemical shifts decrease roughly inversely proportional to the tube's diameter. The results were compared to calculations of finite capped SWNT fragments using a gauge-including atomic orbital (GIAO) basis. Direct comparison of the two types of calculations could be made if benzene was used as the internal (computational) reference. The NMR chemical shifts of finite SWNTs were found to converge very slowly, if at all, to the infinite limit, indicating that capping has a strong effect (at least for the (9,0) tubes) on the calculated properties. Our results suggest that (13)C NMR has the potential for becoming a useful tool in characterizing SWNT samples.

  8. Accurate determination of chemical shift tensor orientations of single-crystals by solid-state magic angle spinning NMR

    NASA Astrophysics Data System (ADS)

    Avadhut, Yamini S.; Weber, Johannes; Schmedt auf der Günne, Jörn

    2017-09-01

    An improved implementation of single-crystal magic-angle-spinning (MAS) NMR is presented which gives access to chemical shift tensors both in orientation (relative to the crystal axis system) and principal axis values. For mounting arbitrary crystals inside ordinary MAS rotors, a mounting tool is described which allows to relate the crystal orientation determined by diffraction techniques to the rotor coordinate system. The crystal is finally mounted into a MAS rotor equipped with a special insert which allows a defined reorientation of the single-crystal by 90°. The approach is based on the idea that the dispersive spectra, which are obtained when applying read-pulses at specific rotor-phases, not only yield the size of the eigenvalues but also encode the orientation of the different chemical shift (rank-2) tensors. For this purpose two 2D-data sets with orthogonal crystal orientation are fitted simultaneously. The presented analysis for chemical shift tensors is supported by an analytical formula which allows fast calculation of phase and amplitude of individual spinning side-bands and by a protocol which solves the problem of finding the correct reference phase of the spectrum. Different rotor-synchronized pulse-sequences are introduced for the same reason. Experiments are performed on L-alanine and O-phosphorylethanolamine and the observed errors are analyzed in detail. The experimental data are opposed to DFT-computed chemical shift tensors which have been obtained by the extended embedded ion method.

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Improving runoff risk estimates: Formulating runoff as a bivariate process using the SCS curve number method

    NASA Astrophysics Data System (ADS)

    Shaw, Stephen B.; Walter, M. Todd

    2009-03-01

    The Soil Conservation Service curve number (SCS-CN) method is widely used to predict storm runoff for hydraulic design purposes, such as sizing culverts and detention basins. As traditionally used, the probability of calculated runoff is equated to the probability of the causative rainfall event, an assumption that fails to account for the influence of variations in soil moisture on runoff generation. We propose a modification to the SCS-CN method that explicitly incorporates rainfall return periods and the frequency of different soil moisture states to quantify storm runoff risks. Soil moisture status is assumed to be correlated to stream base flow. Fundamentally, this approach treats runoff as the outcome of a bivariate process instead of dictating a 1:1 relationship between causative rainfall and resulting runoff volumes. Using data from the Fall Creek watershed in western New York and the headwaters of the French Broad River in the mountains of North Carolina, we show that our modified SCS-CN method improves frequency discharge predictions in medium-sized watersheds in the eastern United States in comparison to the traditional application of the method.

  11. Solvation effects on chemical shifts by embedded cluster integral equation theory.

    PubMed

    Frach, Roland; Kast, Stefan M

    2014-12-11

    The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

  12. Protein dielectric constants determined from NMR chemical shift perturbations.

    PubMed

    Kukic, Predrag; Farrell, Damien; McIntosh, Lawrence P; García-Moreno E, Bertrand; Jensen, Kristine Steen; Toleikis, Zigmantas; Teilum, Kaare; Nielsen, Jens Erik

    2013-11-13

    Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatic calculations are essential for this purpose, but their use has been limited by a long-standing discussion on which value to use for the dielectric constants (ε(eff) and ε(p)) required in Coulombic and Poisson-Boltzmann models. The currently used values for ε(eff) and ε(p) are essentially empirical parameters calibrated against thermodynamic properties that are indirect measurements of protein electric fields. We determine optimal values for ε(eff) and ε(p) by measuring protein electric fields in solution using direct detection of NMR chemical shift perturbations (CSPs). We measured CSPs in 14 proteins to get a broad and general characterization of electric fields. Coulomb's law reproduces the measured CSPs optimally with a protein dielectric constant (ε(eff)) from 3 to 13, with an optimal value across all proteins of 6.5. However, when the water-protein interface is treated with finite difference Poisson-Boltzmann calculations, the optimal protein dielectric constant (ε(p)) ranged from 2 to 5 with an optimum of 3. It is striking how similar this value is to the dielectric constant of 2-4 measured for protein powders and how different it is from the ε(p) of 6-20 used in models based on the Poisson-Boltzmann equation when calculating thermodynamic parameters. Because the value of ε(p) = 3 is obtained by analysis of NMR chemical shift perturbations instead of thermodynamic parameters such as pK(a) values, it is likely to describe only the electric field and thus represent a more general, intrinsic, and transferable ε(p) common to most folded proteins.

  13. Benchmark fragment-based 1H, 13C, 15N and 17O chemical shift predictions in molecular crystals†

    PubMed Central

    Hartman, Joshua D.; Kudla, Ryan A.; Day, Graeme M.; Mueller, Leonard J.; Beran, Gregory J. O.

    2016-01-01

    The performance of fragment-based ab initio 1H, 13C, 15N and 17O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. 1H, 13C, 15N, and 17O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same 1H, 13C, 15N, and 17O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tertbutyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2. PMID:27431490

  14. Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

    PubMed

    Hartman, Joshua D; Kudla, Ryan A; Day, Graeme M; Mueller, Leonard J; Beran, Gregory J O

    2016-08-21

    The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.

  15. Chemical shifts of diamagnetic azafullerenes: (C 59N) 2 and C 59HN

    NASA Astrophysics Data System (ADS)

    Bühl, Michael; Curioni, Alessandro; Andreoni, Wanda

    1997-08-01

    13C and 15N chemical shifts have been calculated for the azafullerenes (C 59N) 2 and C 59HN using the GIAO (gauge including atomic orbitals)-SCF method based on the geometry obtained with the density functional theory BLYP scheme Our results are in good agreement with experimental data, in particular, for the "anomalous" shift of the saturated carbon. Combined with previous calculations of the structural stability and electronic as well as vibrational properties, the present findings confirm the calculated structures for both molecules and establish the [6,6]-closed configuration for the dimer.

  16. Fatigue-life behavior and matrix fatigue crack spacing in unnotched SCS-6/Timetal 21S metal matrix composites

    NASA Technical Reports Server (NTRS)

    Ward, G. T.; Herrmann, D. J.; Hillberry, B. M.

    1993-01-01

    Fatigue tests of the SCS-6/Timetal 21S composite system were performed to characterize the fatigue behavior for unnotched conditions. The stress-life behavior of the unnotched (9/90)2s laminates was investigated for stress ratios of R = 0.1 and R = 0.3. The occurrence of matrix cracking was also examined in these specimens. This revealed multiple matrix crack initiation sites throughout the composite, as well as evenly spaced surface cracks along the length of the specimens. No difference in fatigue lives were observed for stress ratios of R = 0.1 and R = 0.3 when compared on a stress range basis. The unnotched SCS-6/Timetal 21S composites had shorter fatigue lives than the SCS-6/Ti-15-3 composites, however the neat Timetal 21S matrix material had a longer fatigue life than the neat Ti-15-3.

  17. Application and comparison of the SCS-CN-based rainfall-runoff model in meso-scale watershed and field scale

    NASA Astrophysics Data System (ADS)

    Luo, L.; Wang, Z.

    2010-12-01

    Soil Conservation Service Curve Number (SCS-CN) based hydrologic model, has widely been used for agricultural watersheds in recent years. However, there will be relative error when applying it due to differentiation of geographical and climatological conditions. This paper introduces a more adaptable and propagable model based on the modified SCS-CN method, which specializes into two different scale cases of research regions. Combining the typical conditions of the Zhanghe irrigation district in southern part of China, such as hydrometeorologic conditions and surface conditions, SCS-CN based models were established. The Xinbu-Qiao River basin (area =1207 km2) and the Tuanlin runoff test area (area =2.87 km2)were taken as the study areas of basin scale and field scale in Zhanghe irrigation district. Applications were extended from ordinary meso-scale watershed to field scale in Zhanghe paddy field-dominated irrigated . Based on actual measurement data of land use, soil classification, hydrology and meteorology, quantitative evaluation and modifications for two coefficients, i.e. preceding loss and runoff curve, were proposed with corresponding models, table of CN values for different landuse and AMC(antecedent moisture condition) grading standard fitting for research cases were proposed. The simulation precision was increased by putting forward a 12h unit hydrograph of the field area, and 12h unit hydrograph were simplified. Comparison between different scales show that it’s more effectively to use SCS-CN model on field scale after parameters calibrated in basin scale These results can help discovering the rainfall-runoff rule in the district. Differences of established SCS-CN model's parameters between the two study regions are also considered. Varied forms of landuse and impacts of human activities were the important factors which can impact the rainfall-runoff relations in Zhanghe irrigation district.

  18. Orientation-dependent surface core-level shifts and chemical shifts on clean and H 2S-covered GaAs

    NASA Astrophysics Data System (ADS)

    Ranke, W.; Finster, J.; Kuhr, H. J.

    1987-08-01

    Photoelectron spectra of the As 3d and Ga 3d core levels were studied in situ on a cylindrically shaped GaAs single crystal for the six inequivalent orientations (001), (113), (111), (110), (11¯1) and (11¯3). On the clean surface, prepared by molecular beam epitaxy (MBE), surface core levels are shifted by 0.25 to 0.55 eV towards smaller binding energy (BE) for As 3d and -0.25 to -0.35 eV towards higher BE for Ga, depending on orientation. Additional As causes As 3d contributions shifted between -0.45 and -0.7 eV towards higher BE. The position and intensity of them is influenced by H 2S adsorption. At 150 K, H 2S adsorbs preferentially on As sites. As chemical shifts appear at -0.6 to -0.9 eV towards higher BE. Simultaneously, As accumulation occurs on all orientations with the exception of (110). High temperature adsorption (550 K, 720 K) influences mainly the Ga 3d peaks. Two peaks shifted by about -0.45 and -0.8 eV towards higher Be were found which are attributed to Ga atoms with one or two sulfur ligands, respectively. At 720 K, also As depletion is observed. The compatibility of surface core-level positions and intensities with recent structural models for the (111) and (11¯1) surfaces is discussed.

  19. Criteria to average out the chemical shift anisotropy in solid-state NMR when irradiated with BABA I, BABA II, and C7 radiofrequency pulse sequences.

    PubMed

    Stephane Mananga, Eugene

    2013-01-01

    Floquet-Magnus expansion is used to study the effect of chemical shift anisotropy in solid-state NMR of rotating solids. The chemical shift interaction is irradiated with two types of radiofrequency pulse sequences: BABA and C7. The criteria for the chemical shift anisotropy to be averaged out in each rotor period are obtained. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. 13C and 15N—Chemical Shift Anisotropy of Ampicillin and Penicillin-V Studied by 2D-PASS and CP/MAS NMR

    NASA Astrophysics Data System (ADS)

    Antzutkin, Oleg N.; Lee, Young K.; Levitt, Malcolm H.

    1998-11-01

    The principal values of the chemical shift tensors of all13C and15N sites in two antibiotics, ampicillin and penicillin-V, were determined by 2-dimensionalphaseadjustedspinningsideband (2D-PASS) and conventional CP/MAS experiments. The13C and15N chemical shift anisotropies (CSA), and their confidence limits, were evaluated using a Mathematica program. The CSA values suggest a revised assignment of the 2-methyl13C sites in the case of ampicillin. We speculate on a relationship between the chemical shift principal values of many of the13C and15N sites and the β-lactam ring conformation.

  1. Quantitative Chemical Shift-Encoded MRI Is an Accurate Method to Quantify Hepatic Steatosis

    PubMed Central

    Kühn, Jens-Peter; Hernando, Diego; Mensel, Birger; Krüger, Paul C.; Ittermann, Till; Mayerle, Julia; Hosten, Norbert; Reeder, Scott B.

    2014-01-01

    Purpose To compare the accuracy of liver fat quantification using a three-echo chemical shift-encoded magnetic resonance imaging (MRI) technique without and with correction for confounders with spectroscopy (MRS) as the reference standard. Materials and Methods Fifty patients (23 women, mean age 56.6 ± 13.2 years) with fatty liver disease were enrolled. Patients underwent T2-corrected single-voxel MRS and a three-echo chemical shift-encoded gradient echo (GRE) sequence at 3.0T. MRI fat fraction (FF) was calculated without and with T2* and T1 correction and multispectral modeling of fat and compared with MRS-FF using linear regression. Results The spectroscopic range of liver fat was 0.11%–38.7%. Excellent correlation between MRS-FF and MRI-FF was observed when using T2* correction (R2=0.96). With use of T2* correction alone, the slope was significantly different from 1 (1.16 ± 0.03, P < 0.001) and the intercept was different from 0 (1.14% ± 0.50%, P < 0.023). This slope was significantly different than 1.0 when no T1 correction was used (P=0.001). When T2*, T1, and spectral complexity of fat were addressed, the results showed equivalence between fat quantification using MRI and MRS (slope: 1.02 ± 0.03, P=0.528; intercept: 0.26% ± 0.46%, P=0.572). Conclusion Complex three-echo chemical shift-encoded MRI is equivalent to MRS for quantifying liver fat, but only with correction for T2* decay and T1 recovery and use of spectral modeling of fat. This is necessary because T2* decay, T1 recovery, and multispectral complexity of fat are processes which may otherwise bias the measurements. PMID:24123655

  2. Quantitative chemical shift-encoded MRI is an accurate method to quantify hepatic steatosis.

    PubMed

    Kühn, Jens-Peter; Hernando, Diego; Mensel, Birger; Krüger, Paul C; Ittermann, Till; Mayerle, Julia; Hosten, Norbert; Reeder, Scott B

    2014-06-01

    To compare the accuracy of liver fat quantification using a three-echo chemical shift-encoded magnetic resonance imaging (MRI) technique without and with correction for confounders with spectroscopy (MRS) as the reference standard. Fifty patients (23 women, mean age 56.6 ± 13.2 years) with fatty liver disease were enrolled. Patients underwent T2-corrected single-voxel MRS and a three-echo chemical shift-encoded gradient echo (GRE) sequence at 3.0T. MRI fat fraction (FF) was calculated without and with T2* and T1 correction and multispectral modeling of fat and compared with MRS-FF using linear regression. The spectroscopic range of liver fat was 0.11%-38.7%. Excellent correlation between MRS-FF and MRI-FF was observed when using T2* correction (R(2)  = 0.96). With use of T2* correction alone, the slope was significantly different from 1 (1.16 ± 0.03, P < 0.001) and the intercept was different from 0 (1.14% ± 0.50%, P < 0.023). This slope was significantly different than 1.0 when no T1 correction was used (P = 0.001). When T2*, T1, and spectral complexity of fat were addressed, the results showed equivalence between fat quantification using MRI and MRS (slope: 1.02 ± 0.03, P = 0.528; intercept: 0.26% ± 0.46%, P = 0.572). Complex three-echo chemical shift-encoded MRI is equivalent to MRS for quantifying liver fat, but only with correction for T2* decay and T1 recovery and use of spectral modeling of fat. This is necessary because T2* decay, T1 recovery, and multispectral complexity of fat are processes which may otherwise bias the measurements. Copyright © 2013 Wiley Periodicals, Inc.

  3. Application of the PJ and NPS evaporation duct models over the South China Sea (SCS) in winter

    PubMed Central

    Yang, Shaobo; Li, Xingfei; Wu, Chao; He, Xin; Zhong, Ying

    2017-01-01

    The detection of duct height has a significant effect on marine radar or wireless apparatus applications. The paper presents two models to verify the adaptation of evaporation duct models in the SCS in winter. A meteorological gradient instrument used to measure evaporation ducts was fabricated using hydrological and meteorological sensors at different heights. An experiment on the adaptive characteristics of evaporation duct models was carried out over the SCS. The heights of the evaporation ducts were measured by means of log-linear fit, Paulus-Jeske (PJ) and Naval Postgraduate School (NPS) models. The results showed that NPS model offered significant advantages in stability compared with the PJ model. According the collected data computed by the NPS model, the mean deviation (MD) was -1.7 m, and the Standard Deviation (STD) of the MD was 0.8 m compared with the true value. The NPS model may be more suitable for estimating the evaporation duct height in the SCS in winter due to its simpler system characteristics compared with meteorological gradient instruments. PMID:28273113

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

    PubMed

    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. © 2011 American Institute of Physics

  5. Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    PubMed

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

    2017-10-01

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

  6. Theoretical studies of the low-lying states of ScO, ScS, VO, and VS

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1986-01-01

    Bonding in the low-lying states of ScO, ScS, VO, and VS is theoretically studied. Excellent agreement is obtained with experimental spectroscopic constants for the low-lying states of ScO and VO. The results for VS and ScS show that the bonding in the oxides and sulfides is similar, but that the smaller electronegativity in S leads to a smaller ionic component in the bonding. The computed D0 of the sulfides are about 86 percent of the corresponding oxides, and the low-lying excited states are lower in the sulfides than in the corresponding oxides. The CPF method is shown to be an accurate and cost-effective method for obtaining reliable spectroscopic constants for these systems.

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

    ERIC Educational Resources Information Center

    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…

  8. Computation of Chemical Shifts for Paramagnetic Molecules: A Laboratory Experiment for the Undergraduate Curriculum

    ERIC Educational Resources Information Center

    Pritchard, Benjamin P.; Simpson, Scott; Zurek, Eva; Autschbach, Jochen

    2014-01-01

    A computational experiment investigating the [superscript 1]H and [superscript 13]C nuclear magnetic resonance (NMR) chemical shifts of molecules with unpaired electrons has been developed and implemented. This experiment is appropriate for an upper-level undergraduate laboratory course in computational, physical, or inorganic chemistry. The…

  9. Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

    PubMed

    Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

    2014-04-23

    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(2-2H)ethane 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.

  10. Reply to comment by Fred L. Ogden et al. on "Beyond the SCS-CN method: A theoretical framework for spatially lumped rainfall-runoff response"

    NASA Astrophysics Data System (ADS)

    Bartlett, M. S.; Parolari, A. J.; McDonnell, J. J.; Porporato, A.

    2017-07-01

    Though Ogden et al. list several shortcomings of the original SCS-CN method, fit for purpose is a key consideration in hydrological modelling, as shown by the adoption of SCS-CN method in many design standards. The theoretical framework of Bartlett et al. [2016a] reveals a family of semidistributed models, of which the SCS-CN method is just one member. Other members include event-based versions of the Variable Infiltration Capacity (VIC) model and TOPMODEL. This general model allows us to move beyond the limitations of the original SCS-CN method under different rainfall-runoff mechanisms and distributions for soil and rainfall variability. Future research should link this general model approach to different hydrogeographic settings, in line with the call for action proposed by Ogden et al.

  11. The influence of sulfur configuration in 1 H NMR chemical shifts of diasteromeric five-membered cyclic sulfites.

    PubMed

    Obregón-Mendoza, Marco A; Sánchez-Castellanos, Mariano; Cuevas, Gabriel; Gnecco, Dino; Cassani, Julia; Poveda-Jaramillo, Juan C; Reynolds, William F; Enríquez, Raúl G

    2017-03-01

    The effect of the stereochemistry of the sulfur atom on 1 H chemical shifts of the diasteromeric pair of cyclic sulfites of 4-[methoxy(4-nitrophenyl)methyl]-5-phenyl-1,3,2-dioxathiolan-2-oxide was investigated. The complete 1 H and 13 C NMR spectral assignment was achieved by the use of one-dimensional and two-dimensional NMR techniques in combination with X-ray data. A correlation of experimental data with theoretical calculations of chemical shift tensors using density functional theory and topological theory of atoms in molecules was made. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Intermolecular shielding contributions studied by modeling the 13C chemical-shift tensors of organic single crystals with plane waves

    PubMed Central

    Johnston, Jessica C.; Iuliucci, Robbie J.; Facelli, Julio C.; Fitzgerald, George; Mueller, Karl T.

    2009-01-01

    In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all 13C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm. PMID:19831448

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

    PubMed Central

    Shen, Yang; Bax, Ad

    2013-01-01

    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 12°. 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. PMID:23728592

  14. Measurement of 13C chemical shift tensor principal values with a magic-angle turning experiment.

    PubMed

    Hu, J Z; Orendt, A M; Alderman, D W; Pugmire, R J; Ye, C; Grant, D M

    1994-08-01

    The magic-angle turning (MAT) experiment introduced by Gan is developed into a powerful and routine method for measuring the principal values of 13C chemical shift tensors in powdered solids. A large-volume MAT probe with stable rotation frequencies down to 22 Hz is described. A triple-echo MAT pulse sequence is introduced to improve the quality of the two-dimensional baseplane. It is shown that measurements of the principal values of chemical shift tensors in complex compounds can be enhanced by using either short contact times or dipolar dephasing pulse sequences to isolate the powder patterns from protonated or non-protonated carbons, respectively. A model compound, 1,2,3-trimethoxybenzene, is used to demonstrate these techniques, and the 13C principal values in 2,3-dimethylnaphthalene and Pocahontas coal are reported as typical examples.

  15. 31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Mi; Yoo, Chang Geun; Pu, Yunqiao

    The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

  16. 31P NMR Chemical Shifts of Solvents and Products Impurities in Biomass Pretreatments

    DOE PAGES

    Li, Mi; Yoo, Chang Geun; Pu, Yunqiao; ...

    2017-12-05

    The identification of chemical impurities is crucial in elucidating the structures of biorefinery products using nuclear magnetic resonance (NMR) spectroscopic analysis. In the current biorefinery platform, contaminants derived from pretreatment solvents and decomposition byproducts may lead to misassignment of the NMR spectra of biorefinery products (e.g, lignin and bio-oils). Therefore, we investigated in this paper 54 commonly reported compounds including alcohols, carbohydrates, organic acids, aromatics, aldehydes, and ionic liquids associated with biomass pretreatment using 31P NMR. The chemical shifts of these chemicals after derivatizing with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) were provided. Finally, the 31P NMR signals of these derivatives could serve asmore » valuable and informative spectral data in characterizing lignocellulose-based compounds.« less

  17. Self-Compassion Scale (SCS): Psychometric Properties of The French Translation and Its Relations with Psychological Well-Being, Affect and Depression.

    PubMed

    Kotsou, Ilios; Leys, Christophe

    2016-01-01

    Over the past few years, the topic of self-compassion has attracted increasing attention from both scientific and clinical fields. The Self-Compassion Scale (SCS) was created to specifically capture this way of being kind and understanding towards oneself in moments of turmoil. In this article, we present a French adaptation of the SCS. We first explore the psychometric properties of this adaptation and then investigate its relation to psychological well-being. As in the original version of the SCS, the French adaptation has a strong 6-factor structure but a weaker hierarchical second order structure. However the bi-factor model yields a good omega index suggesting the relevance of a single score accounting for self-compassion. Moreover, there was a relation between the SCS and classical outcomes such as a positive relation with psychological well-being and negative relation with depressive symptoms. We then hypothesized that self-compassion would have a moderating role on the relation between affect and depression. This hypothesis was confirmed: expressing negative affect is correlated with depressive symptoms; however, being kind with oneself lowers depressive symptoms even when expressing negative affect. In conclusion, this research presents a valid self-compassion measure for French-speaking researchers and clinicians and outlines the need for further research on the concept of self-compassion.

  18. Striking Similarity in the Gene Expression Levels of Individual Myc Module Members among ESCs, EpiSCs, and Partial iPSCs

    PubMed Central

    Hirasaki, Masataka; Hiraki-Kamon, Keiko; Kamon, Masayoshi; Suzuki, Ayumu; Katano, Miyuki; Nishimoto, Masazumi; Okuda, Akihiko

    2013-01-01

    Predominant transcriptional subnetworks called Core, Myc, and PRC modules have been shown to participate in preservation of the pluripotency and self-renewality of embryonic stem cells (ESCs). Epiblast stem cells (EpiSCs) are another cell type that possesses pluripotency and self-renewality. However, the roles of these modules in EpiSCs have not been systematically examined to date. Here, we compared the average expression levels of Core, Myc, and PRC module genes between ESCs and EpiSCs. EpiSCs showed substantially higher and lower expression levels of PRC and Core module genes, respectively, compared with those in ESCs, while Myc module members showed almost equivalent levels of average gene expression. Subsequent analyses revealed that the similarity in gene expression levels of the Myc module between these two cell types was not just overall, but striking similarities were evident even when comparing the expression of individual genes. We also observed equivalent levels of similarity in the expression of individual Myc module genes between induced pluripotent stem cells (iPSCs) and partial iPSCs that are an unwanted byproduct generated during iPSC induction. Moreover, our data demonstrate that partial iPSCs depend on a high level of c-Myc expression for their self-renewal properties. PMID:24386274

  19. Autoregressive moving average modeling for spectral parameter estimation from a multigradient echo chemical shift acquisition

    PubMed Central

    Taylor, Brian A.; Hwang, Ken-Pin; Hazle, John D.; Stafford, R. Jason

    2009-01-01

    The authors investigated the performance of the iterative Steiglitz–McBride (SM) algorithm on an autoregressive moving average (ARMA) model of signals from a fast, sparsely sampled, multiecho, chemical shift imaging (CSI) acquisition using simulation, phantom, ex vivo, and in vivo experiments with a focus on its potential usage in magnetic resonance (MR)-guided interventions. The ARMA signal model facilitated a rapid calculation of the chemical shift, apparent spin-spin relaxation time (T2*), and complex amplitudes of a multipeak system from a limited number of echoes (≤16). Numerical simulations of one- and two-peak systems were used to assess the accuracy and uncertainty in the calculated spectral parameters as a function of acquisition and tissue parameters. The measured uncertainties from simulation were compared to the theoretical Cramer–Rao lower bound (CRLB) for the acquisition. Measurements made in phantoms were used to validate the T2* estimates and to validate uncertainty estimates made from the CRLB. We demonstrated application to real-time MR-guided interventions ex vivo by using the technique to monitor a percutaneous ethanol injection into a bovine liver and in vivo to monitor a laser-induced thermal therapy treatment in a canine brain. Simulation results showed that the chemical shift and amplitude uncertainties reached their respective CRLB at a signal-to-noise ratio (SNR)≥5 for echo train lengths (ETLs)≥4 using a fixed echo spacing of 3.3 ms. T2* estimates from the signal model possessed higher uncertainties but reached the CRLB at larger SNRs and∕or ETLs. Highly accurate estimates for the chemical shift (<0.01 ppm) and amplitude (<1.0%) were obtained with ≥4 echoes and for T2* (<1.0%) with ≥7 echoes. We conclude that, over a reasonable range of SNR, the SM algorithm is a robust estimator of spectral parameters from fast CSI acquisitions that acquire ≤16 echoes for one- and two-peak systems. Preliminary ex vivo and in vivo

  20. Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

    PubMed

    Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

    2016-04-01

    A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  1. pH-Dependent spin state population and 19F NMR chemical shift via remote ligand protonation in an iron(ii) complex.

    PubMed

    Gaudette, Alexandra I; Thorarinsdottir, Agnes E; Harris, T David

    2017-11-30

    An Fe II complex that features a pH-dependent spin state population, by virtue of a variable ligand protonation state, is described. This behavior leads to a highly pH-dependent 19 F NMR chemical shift with a sensitivity of 13.9(5) ppm per pH unit at 37 °C, thereby demonstrating the potential utility of the complex as a 19 F chemical shift-based pH sensor.

  2. Computation of deuterium isotope perturbation of 13C NMR chemical shifts of alkanes: a local mode zero-point level approach.

    PubMed

    Yang, Kin S; Hudson, Bruce

    2010-11-25

    Replacement of H by D perturbs the (13)C NMR chemical shifts of an alkane molecule. This effect is largest for the carbon to which the D is attached, diminishing rapidly with intervening bonds. The effect is sensitive to stereochemistry and is large enough to be measured reliably. A simple model based on the ground (zero point) vibrational level and treating only the C-H(D) degrees of freedom (local mode approach) is presented. The change in CH bond length with H/D substitution as well as the reduction in the range of the zero-point level probability distribution for the stretch and both bend degrees of freedom are computed. The (13)C NMR chemical shifts are computed with variation in these three degrees of freedom, and the results are averaged with respect to the H and D distribution functions. The resulting differences in the zero-point averaged chemical shifts are compared with experimental values of the H/D shifts for a series of cycloalkanes, norbornane, adamantane, and protoadamantane. Agreement is generally very good. The remaining differences are discussed. The proton spectrum of cyclohexane- is revisited and updated with improved agreement with experiment.

  3. Whole-heart chemical shift encoded water-fat MRI.

    PubMed

    Taviani, Valentina; Hernando, Diego; Francois, Christopher J; Shimakawa, Ann; Vigen, Karl K; Nagle, Scott K; Schiebler, Mark L; Grist, Thomas M; Reeder, Scott B

    2014-09-01

    To develop and evaluate a free-breathing chemical-shift-encoded (CSE) spoiled gradient-recalled echo (SPGR) technique for whole-heart water-fat imaging at 3 Tesla (T). We developed a three-dimensional (3D) multi-echo SPGR pulse sequence with electrocardiographic gating and navigator echoes and evaluated its performance at 3T in healthy volunteers (N = 6) and patients (N = 20). CSE-SPGR, 3D SPGR, and 3D balanced-SSFP with chemical fat saturation were compared in six healthy subjects with images evaluated for overall image quality, level of residual artifacts, and quality of fat suppression. A similar scoring system was used for the patient datasets. Images of diagnostic quality were acquired in all but one subject. CSE-SPGR performed similarly to SPGR with fat saturation, although it provided a more uniform fat suppression over the whole field of view. Balanced-SSFP performed worse than SPGR-based methods. In patients, CSE-SPGR produced excellent fat suppression near metal. Overall image quality was either good (7/20) or excellent (12/20) in all but one patient. There were significant artifacts in 5/20 clinical cases. CSE-SPGR is a promising technique for whole-heart water-fat imaging during free-breathing. The robust fat suppression in the water-only image could improve assessment of complex morphology at 3T and in the presence of off-resonance, with additional information contained in the fat-only image. Copyright © 2013 Wiley Periodicals, Inc.

  4. A Converse Approach to NMR Chemical Shifts for Norm-Conserving Pseudopotentials

    NASA Astrophysics Data System (ADS)

    Lopez, Graham; Ceresoli, Davide; Marzari, Nicola; Thonhauser, Timo

    2010-03-01

    Building on the recently developed converse approach for the ab-initio calculation of NMR chemical shifts [1], we present a corresponding framework that is suitable in connection with norm-conserving pseudopotentials. Our approach uses the GIPAW transformation [2] to set up a formalism where the derivative of the orbital magnetization [3] is taken with respect to a microscopic, localized magnetic dipole in the presence of pseudopotentials. The advantages of our method are that it is conceptually simple, the need for a linear-response framework is avoided, and it is applicable to large systems. We present results for calculations of several well-studied systems, including the carbon, hydrogen, fluorine, and phosphorus shifts in various molecules and solids. Our results are in very good agreement with both linear-response calculations and experimental results.[4pt] [1] T. Thonhauser et al., J. Chem. Phys. 131, 101101 (2009).[2] C. J. Pickard and F. Mauri, Phys. Rev. B 63, 245101 (2001).[3] T. Thonhauser et al., Phys. Rev. Lett. 95, 137205 (2005).

  5. Computer programming for nucleic acid studies. II. Total chemical shifts calculation of all protons of double-stranded helices.

    PubMed

    Giessner-Prettre, C; Ribas Prado, F; Pullman, B; Kan, L; Kast, J R; Ts'o, P O

    1981-01-01

    A FORTRAN computer program called SHIFTS is described. Through SHIFTS, one can calculate the NMR chemical shifts of the proton resonances of single and double-stranded nucleic acids of known sequences and of predetermined conformations. The program can handle RNA and DNA for an arbitrary sequence of a set of 4 out of the 6 base types A,U,G,C,I and T. Data files for the geometrical parameters are available for A-, A'-, B-, D- and S-conformations. The positions of all the atoms are calculated using a modified version of the SEQ program [1]. Then, based on this defined geometry three chemical shift effects exerted by the atoms of the neighboring nucleotides on the protons of each monomeric unit are calculated separately: the ring current shielding effect: the local atomic magnetic susceptibility effect (including both diamagnetic and paramagnetic terms); and the polarization or electric field effect. Results of the program are compared with experimental results for a gamma (ApApGpCpUpU) 2 helical duplex and with calculated results on this same helix based on model building of A'-form and B-form and on graphical procedure for evaluating the ring current effects.

  6. Natural Abundance 15 N and 13 C Solid-State NMR Chemical Shifts: High Sensitivity Probes of the Halogen Bond Geometry.

    PubMed

    Cerreia Vioglio, Paolo; Catalano, Luca; Vasylyeva, Vera; Nervi, Carlo; Chierotti, Michele R; Resnati, Giuseppe; Gobetto, Roberto; Metrangolo, Pierangelo

    2016-11-14

    Solid-state nuclear magnetic resonance (SSNMR) spectroscopy is a versatile characterization technique that can provide a plethora of information complementary to single crystal X-ray diffraction (SCXRD) analysis. Herein, we present an experimental and computational investigation of the relationship between the geometry of a halogen bond (XB) and the SSNMR chemical shifts of the non-quadrupolar nuclei either directly involved in the interaction ( 15 N) or covalently bonded to the halogen atom ( 13 C). We have prepared two series of X-bonded co-crystals based upon two different dipyridyl modules, and several halobenzenes and diiodoalkanes, as XB-donors. SCXRD structures of three novel co-crystals between 1,2-bis(4-pyridyl)ethane, and 1,4-diiodobenzene, 1,6-diiodododecafluorohexane, and 1,8-diiodohexadecafluorooctane were obtained. For the first time, the change in the 15 N SSNMR chemical shifts upon XB formation is shown to experimentally correlate with the normalized distance parameter of the XB. The same overall trend is confirmed by density functional theory (DFT) calculations of the chemical shifts. 13 C NQS experiments show a positive, linear correlation between the chemical shifts and the C-I elongation, which is an indirect probe of the strength of the XB. These correlations can be of general utility to estimate the strength of the XB occurring in diverse adducts by using affordable SSNMR analysis. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. A sediment graph model based on SCS-CN method

    NASA Astrophysics Data System (ADS)

    Singh, P. K.; Bhunya, P. K.; Mishra, S. K.; Chaube, U. C.

    2008-01-01

    SummaryThis paper proposes new conceptual sediment graph models based on coupling of popular and extensively used methods, viz., Nash model based instantaneous unit sediment graph (IUSG), soil conservation service curve number (SCS-CN) method, and Power law. These models vary in their complexity and this paper tests their performance using data of the Nagwan watershed (area = 92.46 km 2) (India). The sensitivity of total sediment yield and peak sediment flow rate computations to model parameterisation is analysed. The exponent of the Power law, β, is more sensitive than other model parameters. The models are found to have substantial potential for computing sediment graphs (temporal sediment flow rate distribution) as well as total sediment yield.

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

    PubMed

    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.

  9. NMR crystallography of campho[2,3-c]pyrazole (Z' = 6): combining high-resolution 1H-13C solid-state MAS NMR spectroscopy and GIPAW chemical-shift calculations.

    PubMed

    Webber, Amy L; Emsley, Lyndon; Claramunt, Rosa M; Brown, Steven P

    2010-09-30

    (1)H-(13)C two-dimensional magic-angle spinning (MAS) solid-state NMR correlation spectra, recorded with the MAS-J-HMQC experiment, are presented for campho[2,3-c]pyrazole. For each (13)C moiety, there are six resonances associated with the six distinct molecules in the asymmetric unit cell (Z' = 6). The one-bond C-H correlations observed in the 2D (1)H-(13)C MAS-J-HMQC spectra allow the experimental determination of the (1)H and (13)C chemical shifts associated with the separate CH, CH(2), and CH(3) groups. (1)H and (13)C chemical shifts calculated by using the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach are presented. Calculations for the whole unit cell (12 × 29 = 348 atoms, with geometry optimization of all atoms) allow the assignment of the experimental (1)H and (13)C chemical shifts to the six distinct molecules. The calculated chemical shifts for the full crystal structure are compared with those for isolated molecules as extracted from the geometry-optimized crystal structure. In this way, the effect of intermolecular interactions on the observed chemical shifts is quantified. In particular, the calculations are sufficiently precise to differentiate the small (<1 ppm) differences between the (1)H chemical shifts of the six resonances associated with each distinct CH or CH(2) moiety.

  10. [Spinal cord stimulation (SCS) as a treatment for the spread phenomenon related to complex regional pain syndrome type- I (CRPS-I )].

    PubMed

    Goto, Shinichi; Taira, Takaomi; Hori, Tomokatsu

    2009-09-01

    The authors describe an experience of spinal cord stimulation (SCS) in a 30-year-old woman who developed complex regional pain syndrome type-I (CRPS-I) with spread phenomenon. She had received lumbar SCS under a diagnosis of CRPS-I in her left leg for 8 years. She had refractory pain in her right arm for the recent two years. There was no new lesion explaining her refractory pain on physical or radiological examination. Thus, the pain in her right upper arm was considered as spread phenomenon of CRPS-I. Test stimulation with cervical epidural spinal electrode showed good results and the pulse generator was implanted. It is suggested that the symptom of CRPS-I involving spread phenomenon was possibly due to a cortical reorganization. But a certain effect of SCS may be contributing to the favorable results of test stimulation for the treatment of CRPS-I with spread phenomenon in this case.

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

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed

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

    2016-08-01

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

  13. Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

    PubMed

    Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

    2018-05-10

    Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

  14. Quantitation Error in 1H MRS Caused by B1 Inhomogeneity and Chemical Shift Displacement.

    PubMed

    Watanabe, Hidehiro; Takaya, Nobuhiro

    2017-11-08

    The quantitation accuracy in proton magnetic resonance spectroscopy ( 1 H MRS) improves at higher B 0 field. However, a larger chemical shift displacement (CSD) and stronger B 1 inhomogeneity exist. In this work, we evaluate the quantitation accuracy for the spectra of metabolite mixtures in phantom experiments at 4.7T. We demonstrate a position-dependent error in quantitation and propose a correction method by measuring water signals. All experiments were conducted on a whole-body 4.7T magnetic resonance (MR) system with a quadrature volume coil for transmission and reception. We arranged three bottles filled with metabolite solutions of N-acetyl aspartate (NAA) and creatine (Cr) in a vertical row inside a cylindrical phantom filled with water. Peak areas of three singlets of NAA and Cr were measured on three 1 H spectra at three volume of interests (VOIs) inside three bottles. We also measured a series of water spectra with a shifted carrier frequency and measured a reception sensitivity map. The ratios of NAA and Cr at 3.92 ppm to Cr at 3.01 ppm differed amongst the three VOIs in peak area, which leads to a position-dependent error. The nature of slope depicting the relationship between peak areas and the shifted values of frequency was like that between the reception sensitivities and displacement at every VOI. CSD and inhomogeneity of reception sensitivity cause amplitude modulation along the direction of chemical shift on the spectra, resulting in a quantitation error. This error may be more significant at higher B 0 field where CSD and B 1 inhomogeneity are more severe. This error may also occur in reception using a surface coil having inhomogeneous B 1 . Since this type of error is around a few percent, the data should be analyzed with greater attention while discussing small differences in the studies of 1 H MRS.

  15. Is the Lamb shift chemically significant?

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Bauschlicher, Charles W., Jr.; Schwenke, David W.; Pyykko, Pekka; Arnold, James (Technical Monitor)

    2001-01-01

    The contribution of the Lamb shift to the atomization energies of some prototype molecules, BF3, AlF3, and GaF3, is estimated by a perturbation procedure. It is found to be in the range of 3-5% of the one-electron scalar relativistic contribution to the atomization energy. The maximum absolute value is 0.2 kcal/mol for GaF3. These sample calculations indicate that the Lamb shift is probably small enough to be neglected for energetics of molecules containing light atoms if the target accuracy is 1 kcal/mol, but for higher accuracy calculations and for molecules containing heavy elements it must be considered.

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

    NASA Astrophysics Data System (ADS)

    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.

  17. A Critical Assessment of the Performance of Protein-ligand Scoring Functions Based on NMR Chemical Shift Perturbations

    PubMed Central

    Wang, Bing; Westerhoff, Lance M.; Merz, Kenneth M.

    2008-01-01

    We have generated docking poses for the FKBP-GPI complex using eight docking programs, and compared their scoring functions with scoring based on NMR chemical shift perturbations (NMRScore). Because the chemical shift perturbation (CSP) is exquisitely sensitive on the orientation of ligand inside the binding pocket, NMRScore offers an accurate and straightforward approach to score different poses. All scoring functions were inspected by their abilities to highly rank the native-like structures and separate them from decoy poses generated for a protein-ligand complex. The overall performance of NMRScore is much better than that of energy-based scoring functions associated with docking programs in both aspects. In summary, we find that the combination of docking programs with NMRScore results in an approach that can robustly determine the binding site structure for a protein-ligand complex, thereby, providing a new tool facilitating the structure-based drug discovery process. PMID:17867664

  18. 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.

    PubMed

    Kanematsu, Yusuke; Tachikawa, Masanori

    2014-04-28

    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.

  19. A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package.

    PubMed

    Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M

    2013-01-01

    Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs.

  20. Speeding up spin-component-scaled third-order pertubation theory with the chain of spheres approximation: the COSX-SCS-MP3 method

    NASA Astrophysics Data System (ADS)

    Izsák, Róbert; Neese, Frank

    2013-07-01

    The 'chain of spheres' approximation, developed earlier for the efficient evaluation of the self-consistent field exchange term, is introduced here into the evaluation of the external exchange term of higher order correlation methods. Its performance is studied in the specific case of the spin-component-scaled third-order Møller--Plesset perturbation (SCS-MP3) theory. The results indicate that the approximation performs excellently in terms of both computer time and achievable accuracy. Significant speedups over a conventional method are obtained for larger systems and basis sets. Owing to this development, SCS-MP3 calculations on molecules of the size of penicillin (42 atoms) with a polarised triple-zeta basis set can be performed in ∼3 hours using 16 cores of an Intel Xeon E7-8837 processor with a 2.67 GHz clock speed, which represents a speedup by a factor of 8-9 compared to the previously most efficient algorithm. Thus, the increased accuracy offered by SCS-MP3 can now be explored for at least medium-sized molecules.

  1. Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

    NASA Astrophysics Data System (ADS)

    Maeda, M.; Yamamoto, K.; Mizokawa, T.; Saini, N. L.; Arita, M.; Namatame, H.; Taniguchi, M.; Tan, G.; Zhao, L. D.; Kanatzidis, M. G.

    2018-03-01

    We have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. The large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

  2. Velocity encoding with the slice select refocusing gradient for faster imaging and reduced chemical shift-induced phase errors.

    PubMed

    Middione, Matthew J; Thompson, Richard B; Ennis, Daniel B

    2014-06-01

    To investigate a novel phase-contrast MRI velocity-encoding technique for faster imaging and reduced chemical shift-induced phase errors. Velocity encoding with the slice select refocusing gradient achieves the target gradient moment by time shifting the refocusing gradient, which enables the use of the minimum in-phase echo time (TE) for faster imaging and reduced chemical shift-induced phase errors. Net forward flow was compared in 10 healthy subjects (N = 10) within the ascending aorta (aAo), main pulmonary artery (PA), and right/left pulmonary arteries (RPA/LPA) using conventional flow compensated and flow encoded (401 Hz/px and TE = 3.08 ms) and slice select refocused gradient velocity encoding (814 Hz/px and TE = 2.46 ms) at 3 T. Improved net forward flow agreement was measured across all vessels for slice select refocused gradient compared to flow compensated and flow encoded: aAo vs. PA (1.7% ± 1.9% vs. 5.8% ± 2.8%, P = 0.002), aAo vs. RPA + LPA (2.1% ± 1.7% vs. 6.0% ± 4.3%, P = 0.03), and PA vs. RPA + LPA (2.9% ± 2.1% vs. 6.1% ± 6.3%, P = 0.04), while increasing temporal resolution (35%) and signal-to-noise ratio (33%). Slice select refocused gradient phase-contrast MRI with a high receiver bandwidth and minimum in-phase TE provides more accurate and less variable flow measurements through the reduction of chemical shift-induced phase errors and a reduced TE/repetition time, which can be used to increase the temporal/spatial resolution and/or reduce breath hold durations. Copyright © 2013 Wiley Periodicals, Inc.

  3. Spin-component-scaled Møller-Plesset (SCS-MP) perturbation theory: a generalization of the MP approach with improved properties.

    PubMed

    Fink, Reinhold F

    2010-11-07

    A rigorous perturbation theory is proposed, which has the same second order energy as the spin-component-scaled Møller-Plesset second order (SCS-MP2) method of Grimme [J. Chem. Phys. 118, 9095 (2003)]. This upgrades SCS-MP2 to a systematically improvable, true wave-function-based method. The perturbation theory is defined by an unperturbed Hamiltonian, Ĥ(0), that contains the ordinary Fock operator and spin operators Ŝ(2) that act either on the occupied or the virtual orbital spaces. Two choices for Ĥ(0) are discussed and the importance of a spin-pure Ĥ((0)) is underlined. Like the SCS-MP2 approach, the theory contains two parameters (c(os) and c(ss)) that scale the opposite-spin and the same-spin contributions to the second order perturbation energy. It is shown that these parameters can be determined from theoretical considerations by a Feenberg scaling approach or a fit of the wave functions from the perturbation theory to the exact one from a full configuration interaction calculation. The parameters c(os)=1.15 and c(ss)=0.75 are found to be optimal for a reasonable test set of molecules. The meaning of these parameters and the consequences following from a well defined improved MP method are discussed.

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

    PubMed

    Lee, J S; Kim, Y K; Jeong, W K; Choi, D; Lee, W J

    2015-04-01

    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. 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. 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). 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. Copyright © 2014 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

  5. Differential Dynamic Engagement within 24 SH3 Domain: Peptide Complexes Revealed by Co-Linear Chemical Shift Perturbation Analysis

    PubMed Central

    Stollar, Elliott J.; Lin, Hong; Davidson, Alan R.; Forman-Kay, Julie D.

    2012-01-01

    There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP) behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences. PMID:23251481

  6. A NMR experiment for simultaneous correlations of valine and leucine/isoleucine methyls with carbonyl chemical shifts in proteins.

    PubMed

    Tugarinov, Vitali; Venditti, Vincenzo; Marius Clore, G

    2014-01-01

    A methyl-detected 'out-and-back' NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ile(δ1), Leu(δ) and Val(γ) (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of (13)C(α), (13)Cβ and (13)CO are known from prior NMR studies and where some losses in sensitivity can be tolerated for the sake of an overall reduction in NMR acquisition time.

  7. Analysis of the temperature and pressure dependence of the 129Xe NMR chemical shift and signal intensity for the derivation of basic parameters of adsorption as applied to zeolite ZSM-5.

    PubMed

    Kawata, Yoko; Adachi, Yuko; Haga, Saori; Fukutomi, Junko; Imai, Hirohiko; Kimura, Atsuomi; Fujiwara, Hideaki

    2007-12-01

    Temperature and pressure dependences of the 129Xe NMR chemical shift and the signal intensity have been investigated using ZSM-5 as an adsorbent under routine conditions without using any high-pressure or especially high-temperature facilities. The use of a rigorously shielded system and a calibration sample for the signal intensity was found to be valuable to obtain reliable data about the chemical shift and the signal intensity. The 129Xe NMR data obtained between 0.05 and 1.5 atm and from 24 to 80 degrees C were analyzed based on the Dubinin-Radushkevich equation as well as the Langmuir type equation. In both analyses, chemical shift data succeeded only partially in providing the profile of adsorption, such as energetic aspects, surface area, saturated amount of Xe adsorption and specific parameters of 129Xe chemical shift. It was shown that the reliable total analysis was achieved when the chemical shift data were used together with the intensity data. Such an analysis of the chemical shift data, aided by the intensity data, will be useful in performing nano-material analysis on 129Xe NMR without invoking the traditional methodology of gravimetric or volumetric adsorption experiments.

  8. Dynamic metabolic imaging of hyperpolarized [2-(13) C]pyruvate using spiral chemical shift imaging with alternating spectral band excitation.

    PubMed

    Josan, Sonal; Hurd, Ralph; Park, Jae Mo; Yen, Yi-Fen; Watkins, Ron; Pfefferbaum, Adolf; Spielman, Daniel; Mayer, Dirk

    2014-06-01

    In contrast to [1-(13) C]pyruvate, hyperpolarized [2-(13) C]pyruvate permits the ability to follow the (13) C label beyond flux through pyruvate dehydrogenase complex and investigate the incorporation of acetyl-coenzyme A into different metabolic pathways. However, chemical shift imaging (CSI) with [2-(13) C]pyruvate is challenging owing to the large spectral dispersion of the resonances, which also leads to severe chemical shift displacement artifacts for slice-selective acquisitions. This study introduces a sequence for three-dimensional CSI of [2-(13) C]pyruvate using spectrally selective excitation of limited frequency bands containing a subset of metabolites. Dynamic CSI data were acquired alternately from multiple frequency bands in phantoms for sequence testing and in vivo in rat heart. Phantom experiments verified the radiofrequency pulse design and demonstrated that the signal behavior of each group of resonances was unaffected by excitation of the other frequency bands. Dynamic three-dimensional (13) C CSI data demonstrated the sequence capability to image pyruvate, lactate, acetylcarnitine, glutamate, and acetoacetate, enabling the analysis of organ-specific spectra and metabolite time courses. The presented method allows CSI of widely separated resonances without chemical shift displacement artifact, acquiring multiple frequency bands alternately to obtain dynamic time-course information. This approach enables robust imaging of downstream metabolic products of acetyl-coenzyme A with hyperpolarized [2-(13) C]pyruvate. Copyright © 2013 Wiley Periodicals, Inc.

  9. Framework for event-based semidistributed modeling that unifies the SCS-CN method, VIC, PDM, and TOPMODEL

    NASA Astrophysics Data System (ADS)

    Bartlett, M. S.; Parolari, A. J.; McDonnell, J. J.; Porporato, A.

    2016-09-01

    Hydrologists and engineers may choose from a range of semidistributed rainfall-runoff models such as VIC, PDM, and TOPMODEL, all of which predict runoff from a distribution of watershed properties. However, these models are not easily compared to event-based data and are missing ready-to-use analytical expressions that are analogous to the SCS-CN method. The SCS-CN method is an event-based model that describes the runoff response with a rainfall-runoff curve that is a function of the cumulative storm rainfall and antecedent wetness condition. Here we develop an event-based probabilistic storage framework and distill semidistributed models into analytical, event-based expressions for describing the rainfall-runoff response. The event-based versions called VICx, PDMx, and TOPMODELx also are extended with a spatial description of the runoff concept of "prethreshold" and "threshold-excess" runoff, which occur, respectively, before and after infiltration exceeds a storage capacity threshold. For total storm rainfall and antecedent wetness conditions, the resulting ready-to-use analytical expressions define the source areas (fraction of the watershed) that produce runoff by each mechanism. They also define the probability density function (PDF) representing the spatial variability of runoff depths that are cumulative values for the storm duration, and the average unit area runoff, which describes the so-called runoff curve. These new event-based semidistributed models and the traditional SCS-CN method are unified by the same general expression for the runoff curve. Since the general runoff curve may incorporate different model distributions, it may ease the way for relating such distributions to land use, climate, topography, ecology, geology, and other characteristics.

  10. Pressure response of protein backbone structure. Pressure-induced amide 15N chemical shifts in BPTI.

    PubMed Central

    Akasaka, K.; Li, H.; Yamada, H.; Li, R.; Thoresen, T.; Woodward, C. K.

    1999-01-01

    The effect of pressure on amide 15N chemical shifts was studied in uniformly 15N-labeled basic pancreatic trypsin inhibitor (BPTI) in 90%1H2O/10%2H2O, pH 4.6, by 1H-15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 +/- 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0-1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three-dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 A/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site-specific changes in phi, psi angles. For beta-sheet residues, a decrease in psi angles by 1-2 degrees/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 +/- 0.343 and 0.519 +/- 0.261 ppm/2 kbar, respectively) than for beta-sheet (0.295 +/- 0.195 ppm/2 kbar), suggesting that the pressure-induced structural changes (local compressibilities) are larger in helical and loop regions than in beta-sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in beta-sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place. PMID:10548039

  11. Effect of high temperature annealing on the microstructure of SCS-6 SiC fibers

    NASA Technical Reports Server (NTRS)

    Ning, X. J.; Pirouz, P.; Bhatt, R. T.

    1992-01-01

    The effect of annealing the SCS-6 SiC fiber for one hour at 2000 C in an argon atmosphere is reported. The SiC grains in the fiber coarsen appreciably and the intergranular carbon films segregate to the grain junctions. It would appear that grain growth in the outer part of the fiber is primarily responsible for the loss in fiber strength and improvement in fiber creep resistance.

  12. Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Maeda, M.; Yamamoto, K.; Mizokawa, T.

    In this work, we have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. Lastly, the large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

  13. Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

    DOE PAGES

    Maeda, M.; Yamamoto, K.; Mizokawa, T.; ...

    2018-03-23

    In this work, we have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. Lastly, the large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

  14. A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package

    PubMed Central

    Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M.

    2013-01-01

    Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs. PMID:24688703

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

    PubMed Central

    Chappell, P. Dreux; Whitney, LeAnn P.; Haddock, Traci L.; Menden-Deuer, Susanne; Roy, Eric G.; Wells, Mark L.; Jenkins, Bethany D.

    2013-01-01

    Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a 3-month-old Haida eddy remained largely (>80%) similar over a 2-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe) and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response. PMID:24065961

  16. Analysis of the runoff generation mechanism for the investigation of the SCS-CN method applicability to a partial area experimental watershed

    NASA Astrophysics Data System (ADS)

    Soulis, K. X.; Valiantzas, J. D.; Dercas, N.; Londra, P. A.

    2009-01-01

    The Soil Conservation Service Curve Number (SCS-CN) method is widely used for predicting direct runoff volume for a given rainfall event. The applicability of the SCS-CN method and the runoff generation mechanism were thoroughly analysed in a Mediterranean experimental watershed in Greece. The region is characterized by a Mediterranean semi-arid climate. A detailed land cover and soil survey using remote sensing and GIS techniques, showed that the watershed is dominated by coarse soils with high hydraulic conductivities, whereas a smaller part is covered with medium textured soils and impervious surfaces. The analysis indicated that the SCS-CN method fails to predict runoff for the storm events studied, and that there is a strong correlation between the CN values obtained from measured runoff and the rainfall depth. The hypothesis that this correlation could be attributed to the existence of an impermeable part in a very permeable watershed was examined in depth, by developing a numerical simulation water flow model for predicting surface runoff generated from each of the three soil types of the watershed. Numerical runs were performed using the HYDRUS-1D code. The results support the validity of this hypothesis for most of the events examined where the linear runoff formula provides better results than the SCS-CN method. The runoff coefficient of this formula can be taken equal to the percentage of the impervious area. However, the linear formula should be applied with caution in case of extreme events with very high rainfall intensities. In this case, the medium textured soils may significantly contribute to the total runoff and the linear formula may significantly underestimate the runoff produced.

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

    PubMed Central

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

    2015-01-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

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

    PubMed

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

    2015-07-01

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

  19. Increase in the Accuracy of Calculating Length of Horizontal Cable SCS in Civil Engineering

    NASA Astrophysics Data System (ADS)

    Semenov, A.

    2017-11-01

    A modification of the method for calculating the horizontal cable consumption of SCS established at civil engineering facilities is proposed. The proposed procedure preserves the prototype simplicity and provides a 5 percent accuracy increase. The values of the achieved accuracy are justified, their compliance with the practice of real projects is proved. The method is brought to the level of the engineering algorithm and formalized in the form of 12/70 rule.

  20. Providing the physical basis of SCS curve number method and its proportionality relationship from Richards' equation

    NASA Astrophysics Data System (ADS)

    Hooshyar, M.; Wang, D.

    2016-12-01

    The empirical proportionality relationship, which indicates that the ratio of cumulative surface runoff and infiltration to their corresponding potentials are equal, is the basis of the extensively used Soil Conservation Service Curve Number (SCS-CN) method. The objective of this paper is to provide the physical basis of the SCS-CN method and its proportionality hypothesis from the infiltration excess runoff generation perspective. To achieve this purpose, an analytical solution of Richards' equation is derived for ponded infiltration in shallow water table environment under the following boundary conditions: 1) the soil is saturated at the land surface; and 2) there is a no-flux boundary which moves downward. The solution is established based on the assumptions of negligible gravitational effect, constant soil water diffusivity, and hydrostatic soil moisture profile between the no-flux boundary and water table. Based on the derived analytical solution, the proportionality hypothesis is a reasonable approximation for rainfall partitioning at the early stage of ponded infiltration in areas with a shallow water table for coarse textured soils.

  1. Shift in Chemical Potential of Superconducting Bi2212 Measured by Ultrafast Photoemission Spectroscopy

    NASA Astrophysics Data System (ADS)

    Miller, Tristan; Smallwood, Chris; Zhang, Wentao; Eisaki, Hiroshi; Lee, Dung-Hai; Lanzara, Alessandra

    2015-03-01

    Time- and Angle-resolved photoemission spectroscopy (tr-ARPES) has been used to directly measure the dynamics of many different properties of high-temperature superconductors, including the quasiparticle relaxation, cooper pair recombination, and many-body interactions. There have also been several intriguing results on several materials showing how laser pulses can manipulate their chemical potential on ultrafast timescales, and it's been suggested that these effects could find applications in optoelectronic devices. Studies on GaAs have also found that laser pulses may induce a surface voltage effect. Here, we extend these studies for the first time to a Bi2212 sample in the superconducting state, and disentangle the shift in chemical potential from surface voltage effects. This work was supported by Berkeley Lab's program on Quantum Materials, funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, under Contract No. DE-AC02-05CH11231.

  2. GIAO-DFT calculation of 15 N NMR chemical shifts of Schiff bases: Accuracy factors and protonation effects.

    PubMed

    Semenov, Valentin A; Samultsev, Dmitry O; Krivdin, Leonid B

    2018-02-09

    15 N NMR chemical shifts in the representative series of Schiff bases together with their protonated forms have been calculated at the density functional theory level in comparison with available experiment. A number of functionals and basis sets have been tested in terms of a better agreement with experiment. Complimentary to gas phase results, 2 solvation models, namely, a classical Tomasi's polarizable continuum model (PCM) and that in combination with an explicit inclusion of one molecule of solvent into calculation space to form supermolecule 1:1 (SM + PCM), were examined. Best results are achieved with PCM and SM + PCM models resulting in mean absolute errors of calculated 15 N NMR chemical shifts in the whole series of neutral and protonated Schiff bases of accordingly 5.2 and 5.8 ppm as compared with 15.2 ppm in gas phase for the range of about 200 ppm. Noticeable protonation effects (exceeding 100 ppm) in protonated Schiff bases are rationalized in terms of a general natural bond orbital approach. Copyright © 2018 John Wiley & Sons, Ltd.

  3. Mutual orientation of three magnetic tensors in a polycrystalline dipeptide by dipole-modulated 15N chemical shift spectroscopy

    NASA Astrophysics Data System (ADS)

    Hartzell, C. J.; Pratum, T. K.; Drobny, G.

    1987-10-01

    This study demonstrates the mutual orientation of three tensor interactions in a single NMR experiment. The orientation of the 15N chemical shift tensor relative to the molecular frame has thus been determined in polycrystalline L-[1-13C] alanyl-L-[15N] alanine. The 13C-15N and 15N-1H dipole interactions are determined using the 1H dipole-modulated, 13C dipole-coupled 15N spectrum obtained as a transform of the data in t2. From simulations of the experimental spectra, two sets of polar angles have been determined relating the 13C-15N and 15N-1H dipoles to the 15N chemical shift tensor. The values determined are βCN =106°, αCN =5° and βNH =-19°, αNH =12°. The experiment verifies, without reference to single crystal data, that σ33 lies in the peptide plane and σ22 is nearly perpendicular to the plane.

  4. Investigation of the direct runoff generation mechanism for the analysis of the SCS-CN method applicability to a partial area experimental watershed

    NASA Astrophysics Data System (ADS)

    Soulis, K. X.; Valiantzas, J. D.; Dercas, N.; Londra, P. A.

    2009-05-01

    The Soil Conservation Service Curve Number (SCS-CN) method is widely used for predicting direct runoff volume for a given rainfall event. The applicability of the SCS-CN method and the direct runoff generation mechanism were thoroughly analysed in a Mediterranean experimental watershed in Greece. The region is characterized by a Mediterranean semi-arid climate. A detailed land cover and soil survey using remote sensing and GIS techniques, showed that the watershed is dominated by coarse soils with high hydraulic conductivities, whereas a smaller part is covered with medium textured soils and impervious surfaces. The analysis indicated that the SCS-CN method fails to predict runoff for the storm events studied, and that there is a strong correlation between the CN values obtained from measured runoff and the rainfall depth. The hypothesis that this correlation could be attributed to the existence of an impermeable part in a very permeable watershed was examined in depth, by developing a numerical simulation water flow model for predicting surface runoff generated from each of the three soil types of the watershed. Numerical runs were performed using the HYDRUS-1D code. The results support the validity of this hypothesis for most of the events examined where the linear runoff formula provides better results than the SCS-CN method. The runoff coefficient of this formula can be taken equal to the percentage of the impervious area. However, the linear formula should be applied with caution in case of extreme events with very high rainfall intensities. In this case, the medium textured soils may significantly contribute to the total runoff and the linear formula may significantly underestimate the runoff produced.

  5. Application of ChemDraw NMR Tool: Correlation of Program-Generated 13C Chemical Shifts and pKa Values of para-Substituted Benzoic Acids

    NASA Astrophysics Data System (ADS)

    Wang, Hongyi

    2005-09-01

    An application of ChemDraw NMR Tool was demonstrated by correlation of program-generated 13 C NMR chemical shifts and p K a values of para-substituted benzoic acids. Experimental 13 C NMR chemical shifts were analyzed in the same way for comparison. The project can be used as an assignment at the end of the first-year organic chemistry course to review topics or explore new techniques: Hammett equation, acid base equilibrium theory, electronic nature of functional groups, inductive and resonance effects, structure reactivity relationship, NMR spectroscopy, literature search, database search, and ChemDraw software.

  6. The genome sequence of Dyella jiangningensis FCAV SCS01 from a lignocellulose-decomposing microbial consortium metagenome reveals potential for biotechnological applications.

    PubMed

    Desiderato, Joana G; Alvarenga, Danillo O; Constancio, Milena T L; Alves, Lucia M C; Varani, Alessandro M

    2018-05-14

    Cellulose and its associated polymers are structural components of the plant cell wall, constituting one of the major sources of carbon and energy in nature. The carbon cycle is dependent on cellulose- and lignin-decomposing microbial communities and their enzymatic systems acting as consortia. These microbial consortia are under constant exploration for their potential biotechnological use. Herein, we describe the characterization of the genome of Dyella jiangningensis FCAV SCS01, recovered from the metagenome of a lignocellulose-degrading microbial consortium, which was isolated from a sugarcane crop soil under mechanical harvesting and covered by decomposing straw. The 4.7 Mbp genome encodes 4,194 proteins, including 36 glycoside hydrolases (GH), supporting the hypothesis that this bacterium may contribute to lignocellulose decomposition. Comparative analysis among fully sequenced Dyella species indicate that the genome synteny is not conserved, and that D. jiangningensis FCAV SCS01 carries 372 unique genes, including an alpha-glucosidase and maltodextrin glucosidase coding genes, and other potential biomass degradation related genes. Additional genomic features, such as prophage-like, genomic islands and putative new biosynthetic clusters were also uncovered. Overall, D. jiangningensis FCAV SCS01 represents the first South American Dyella genome sequenced and shows an exclusive feature among its genus, related to biomass degradation.

  7. Composite pulsed field gradients with refocused chemical shifts and short recovery time.

    PubMed

    Hu, H; Shaka, A J

    1999-01-01

    An improved self-compensating pulsed field gradient (PFG) technique that combines antiphase gradient pairs with broadband frequency-modulated 180 degrees pulses is proposed. The antiphase gradient pairs lead to superb system recovery. In addition, evolution under chemical shift and heteronuclear J coupling are refocused during the PFG, making it appear effectively instantaneous. This new approach makes it possible to obtain high-resolution phase-sensitive 2D spectra for the PFG version of many experiments such as COSY, DQF-COSY, and HSQC without adding extra compensating delays or pulses. While reasonable suppression of unwanted magnetization is achieved, this method also gives satisfactory retention of desired signals. As a bonus, the field-frequency lock is not perturbed during the experiments. Copyright 1999 Academic Press.

  8. Calculation of 125Te NMR Chemical Shifts at the Full Four-Component Relativistic Level with Taking into Account Solvent and Vibrational Corrections: A Gateway to Better Agreement with Experiment.

    PubMed

    Rusakova, Irina L; Rusakov, Yuriy Yu; Krivdin, Leonid B

    2017-06-29

    Four-component relativistic calculations of 125 Te NMR chemical shifts were performed in the series of 13 organotellurium compounds, potential precursors of the biologically active species, at the density functional theory level under the nonrelativistic and four-component fully relativistic conditions using locally dense basis set scheme derived from relativistic Dyall's basis sets. The relativistic effects in tellurium chemical shifts were found to be of as much as 20-25% of the total calculated values. The vibrational and solvent corrections to 125 Te NMR chemical shifts are about, accordingly, 6 and 8% of their total values. The PBE0 exchange-correlation functional turned out to give the best agreement of calculated tellurium shifts with their experimental values giving the mean absolute percentage error of 4% in the range of ∼1000 ppm, provided all corrections are taken into account.

  9. Fast CT-PRESS-based spiral chemical shift imaging at 3 Tesla.

    PubMed

    Mayer, Dirk; Kim, Dong-Hyun; Adalsteinsson, Elfar; Spielman, Daniel M

    2006-05-01

    A new sequence is presented that combines constant-time point-resolved spectroscopy (CT-PRESS) with fast spiral chemical shift imaging. It allows the acquisition of multivoxel spectra without line splitting with a minimum total measurement time of less than 5 min for a field of view of 24 cm and a nominal 1.5x1.5-cm2 in-plane resolution. Measurements were performed with 17 CS encoding steps in t1 (Deltat1=12.8 ms) and an average echo time of 151 ms, which was determined by simulating the CT-PRESS experiment for the spin systems of glutamate (Glu) and myo-inositol (mI). Signals from N-acetyl-aspartate, total creatine, choline-containing compounds (Cho), Glu, and mI were detected in a healthy volunteer with no or only minor baseline distortions within 14 min on a 3 T MR scanner. Copyright (c) 2006 Wiley-Liss, Inc.

  10. In-phase thermomechanical fatigue mechanisms in an unidirectional SCS-6/Ti 15-3 MMC

    NASA Technical Reports Server (NTRS)

    Newaz, Golam M.; Majumdar, Bhaskar S.

    1995-01-01

    The objective of this investigation was to identify the inelastic deformation and damage mechanisms under in-phase (IP) thermomechanical fatigue (TMF) in a unidirectional SCS-6/Ti 15-3 metal matrix composite (MMC). Load-controlled IP TMF tests were conducted at 300-538 C at various stress ranges in high-purity argon. A major emphasis of this work was to identify damage mechanism well before final fracture of specimens, rather than to generate life diagrams, to aid development of a realistic deformation/damage and life model.

  11. On the Confounding Effect of Temperature on Chemical Shift-Encoded Fat Quantification

    PubMed Central

    Hernando, Diego; Sharma, Samir D.; Kramer, Harald; Reeder, Scott B.

    2014-01-01

    Purpose To characterize the confounding effect of temperature on chemical shift-encoded (CSE) fat quantification. Methods The proton resonance frequency of water, unlike triglycerides, depends on temperature. This leads to a temperature dependence of the spectral models of fat (relative to water) that are commonly used by CSE-MRI methods. Simulation analysis was performed for 1.5 Tesla CSE fat–water signals at various temperatures and echo time combinations. Oil–water phantoms were constructed and scanned at temperatures between 0 and 40°C using spectroscopy and CSE imaging at three echo time combinations. An explanted human liver, rejected for transplantation due to steatosis, was scanned using spectroscopy and CSE imaging. Fat–water reconstructions were performed using four different techniques: magnitude and complex fitting, with standard or temperature-corrected signal modeling. Results In all experiments, magnitude fitting with standard signal modeling resulted in large fat quantification errors. Errors were largest for echo time combinations near TEinit ≈ 1.3 ms, ΔTE ≈ 2.2 ms. Errors in fat quantification caused by temperature-related frequency shifts were smaller with complex fitting, and were avoided using a temperature-corrected signal model. Conclusion Temperature is a confounding factor for fat quantification. If not accounted for, it can result in large errors in fat quantifications in phantom and ex vivo acquisitions. PMID:24123362

  12. Exotic open-flavor bcq¯q¯, bcs¯s¯ and qcq¯b¯, scs¯b¯ tetraquark states

    NASA Astrophysics Data System (ADS)

    Chen, Wei; Steele, T. G.; Zhu, Shi-Lin

    2014-03-01

    We study the exotic bcq¯q¯, bcs¯s¯ and qcq¯b¯, scs¯b¯ systems by constructing the corresponding tetraquark currents with JP=0+ and 1+. After investigating the two-point correlation functions and the spectral densities, we perform QCD sum rule analysis and extract the masses of these open-flavor tetraquark states. Our results indicate that the masses of both the scalar and axial vector tetraquark states are about 7.1-7.2 GeV for the bcq¯q¯ system and 7.2-7.3 GeV for the bcs¯s¯ system. For the qcq¯b¯ tetraquark states with JP=0+ and 1+, their masses are extracted to be around 7.1 GeV. The masses for the scalar and axial vector scs¯b¯ states are 7.1 and 6.9-7.1 GeV, respectively. The tetraquark states qcq¯b¯ and scs¯b¯ lie below the thresholds of D(*)B(*) and Ds(*)Bs(*) respectively, but they can decay into Bc plus a light meson. However, the tetraquark states bcq¯q¯ and bcs¯s¯ lie below the D(*)B¯(*) and Ds(*)B¯s(*) thresholds, suggesting dominantly weak decay mechanisms.

  13. Water and lipid diffusion MRI using chemical shift displacement-based separation of lipid tissue (SPLIT).

    PubMed

    Ohno, Naoki; Kan, Hirohito; Miyati, Tosiaki; Aoki, Toshitaka; Ishida, Shota; Gabata, Toshifumi

    2017-06-01

    To obtain water and lipid diffusion-weighted images (DWIs) simultaneously, we devised a novel method utilizing chemical shift displacement-based separation of lipid tissue (SPLIT) imaging. Single-shot diffusion echo-planar imaging without fat suppression was used and the imaging parameters were optimized to separate water and lipid DWIs by chemical shift displacement of the lipid signals along the phase-encoding direction. Using the optimized conditions, transverse DWIs at the maximum diameter of the right calf were scanned with multiple b-values in five healthy subjects. Then, apparent diffusion coefficients (ADCs) were calculated in the tibialis anterior muscle (TA), tibialis bone marrow (TB), and subcutaneous fat (SF), as well as restricted and perfusion-related diffusion coefficients (D and D*, respectively) and the fraction of the perfusion-related diffusion component (F) for TA. Water and lipid DWIs were separated adequately. The mean ADCs of the TA, TB, and SF were 1.56±0.03mm 2 /s, 0.01±0.01mm 2 /s, and 0.06±0.02mm 2 /s, respectively. The mean D*, D, and F of the TA were 13.7±4.3mm 2 /s, 1.48±0.05mm 2 /s, and 4.3±1.6%, respectively. SPLIT imaging makes it possible to simply and simultaneously obtain water and lipid DWIs without special pulse sequence and increases the amount of diffusion information of water and lipid tissue. Copyright © 2017. Published by Elsevier Inc.

  14. Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Feng, Yiquing; Roder, H.; Englander, S.W.

    1990-04-10

    Proton nuclear magnetic resonance assignments for reduced and oxidized equine cytochrome c show that many individual protons exhibit different chemical shifts in the two protein forms, reflecting diamagnetic shift effects due to structure change, and in addition contact and pseudocontact shifts that occur only in the paramagnetic oxidized form. To evaluate the chemical shift differences for structure change, the authors removed the pseudocontact shift contribution by a calculation based on knowledge of the electron spin g tensor. The g-tensor calculation, when repeated using only 12 available C{sub {alpha}}H proton resonances for cytochrom c from tuna, proved to be remarkably stable.more » The derived g tensor was then used together with spatial coordinates for the oxidized form to calculate the pseudocontact shift contribution to proton resonances at 400 identifiable sites throughout the protein, so that the redox-dependent chemical shift discrepancy, could be evaluated. Large residual changes in chemical shift define the Fermi contact shifts, where are found as expected to be limited to the immediate covalent structure of the heme and its ligands and to be asymmetrically distributed over the heme. The chemical shift discrepancies observed appear in the main to reflect structure-dependent diamagnetic shifts rather than hyperfine effects due to displacements in the pseudocontact shift field. Although 51 protons in 29 different residues exhibit significant chemical shift changes, the general impressions one of small structural adjustments to redox-dependent strain rather than sizeable structural displacements or rearrangements.« less

  15. Development of 19F-NMR chemical shift detection of DNA B-Z equilibrium using 19F-NMR.

    PubMed

    Nakamura, S; Yang, H; Hirata, C; Kersaudy, F; Fujimoto, K

    2017-06-28

    Various DNA conformational changes are in correlation with biological events. In particular, DNA B-Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B-Z equilibrium using 19 F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19 F-NMR chemical shift change.

  16. [Genetic polymorphism of the IL8 gene and its associations with milk traits and SCS in Chinese Holstein].

    PubMed

    Chen, Ren-Jin; Yang, Zhang-Ping; Mao, Yong-Jiang; Chen, Ying; Chang, Ling-Ling; Ji, De-Jun; Wu, Hai-Tao; Li, Yun-Long; Li, Rui

    2010-12-01

    The polymorphism of Interleukin-8 (IL8) gene were investigated for 610 Chinese Holstein cows of 30 bull families from a dairy farm in Shanghai using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) technique with a mixed animal model to verify the effects of the polymorphisms on some milk productive performance, tested day milk yield, tested day fat percentage, tested day milk protein percentage, 305 d corrected milk yield, 305 d milk fat yield, 305 d milk protein yield, and somatic cell score (SCS). The aim was to explore the significant molecular marker in practical dairy production. Three genotypes were identified and the genotypic frequencies of KK, KA, and AA were 0.187, 0.451, and 0.362, respectively. The gene frequencies of K and A were 0.412 and 0.588. The results showed highly significant (P < 0.01) association of IL8 mutations with tested day milk yield, 305 d milk protein yield, 305 d corrected milk yield and 305 d milk fat yield, SCS and tested day milk protein percentage (P < 0.05). However, no association (P > 0.05) with tested day milk fat percentage was recorded. The cows with KK genotype had higher tested day milk yield, 305 d milk protein yield, 305 d corrected milk yield and 305 d milk fat yield than those with AA and KA genotypes (P < 0.01). The least square mean of SCS for KK was significantly lower than that with AA and KA genotypes (P < 0.01). AA genotype was significant lower in tested day milk protein percentage than KK and KA genotypes (P < 0.05). The IL8 gene genetic diversity has a great genetic effect on milk traits and mastitis resistance and could be a useful genetic marker for Chinese Holstein breeding.

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

    PubMed

    Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek; Faber, Rasmus; Lacerda, Evanildo G; Sauer, Stephan P A

    2016-02-05

    Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic 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 four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles with noniterative triple excitations [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 (ZPV) corrections are obtained at the CCSD(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, ZPV, and relativistic corrections for the shieldings and chemical shifts is analyzed. © 2015 Wiley Periodicals, Inc.

  18. Satellite-derived land covers for runoff estimation using SCS-CN method in Chen-You-Lan Watershed, Taiwan

    NASA Astrophysics Data System (ADS)

    Zhang, Wen-Yan; Lin, Chao-Yuan

    2017-04-01

    The Soil Conservation Service Curve Number (SCS-CN) method, which was originally developed by the USDA Natural Resources Conservation Service, is widely used to estimate direct runoff volume from rainfall. The runoff Curve Number (CN) parameter is based on the hydrologic soil group and land use factors. In Taiwan, the national land use maps were interpreted from aerial photos in 1995 and 2008. Rapid updating of post-disaster land use map is limited due to the high cost of production, so the classification of satellite images is the alternative method to obtain the land use map. In this study, Normalized Difference Vegetation Index (NDVI) in Chen-You-Lan Watershed was derived from dry and wet season of Landsat imageries during 2003 - 2008. Land covers were interpreted from mean value and standard deviation of NDVI and were categorized into 4 groups i.e. forest, grassland, agriculture and bare land. Then, the runoff volume of typhoon events during 2005 - 2009 were estimated using SCS-CN method and verified with the measured runoff data. The result showed that the model efficiency coefficient is 90.77%. Therefore, estimating runoff by using the land cover map classified from satellite images is practicable.

  19. Chemical shift assignments of the partially deuterated Fyn SH2-SH3 domain.

    PubMed

    Kieken, Fabien; Loth, Karine; van Nuland, Nico; Tompa, Peter; Lenaerts, Tom

    2018-04-01

    Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1 H, 15 N and 13 C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.

  20. Ab initio 27Al NMR chemical shifts and quadrupolar parameters for Al2O3 phases and their precursors

    NASA Astrophysics Data System (ADS)

    Ferreira, Ary R.; Küçükbenli, Emine; Leitão, Alexandre A.; de Gironcoli, Stefano

    2011-12-01

    The gauge-including projector augmented wave (GIPAW) method, within the density functional theory (DFT) generalized gradient approximation (GGA) framework, is applied to compute solid state NMR parameters for 27Al in the α, θ, and κ aluminium oxide phases and their gibbsite and boehmite precursors. The results for well established crystalline phases compare very well with available experimental data and provide confidence in the accuracy of the method. For γ-alumina, four structural models proposed in the literature are discussed in terms of their ability to reproduce the experimental spectra also reported in the literature. Among the considered models, the Fd3¯m structure proposed by Paglia [Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.71.224115 71, 224115 (2005)] shows the best agreement. We attempt to link the theoretical NMR parameters to the local geometry. Chemical shifts depend on coordination number but no further correlation is found with geometrical parameters. Instead, our calculations reveal that, within a given coordination number, a linear correlation exists between chemical shifts and Born effective charges.

  1. Interaction between repressor Opi1p and ER membrane protein Scs2p facilitates transit of phosphatidic acid from the ER to mitochondria and is essential for INO1 gene expression in the presence of choline

    PubMed Central

    Gaspar, Maria L.; Chang, Yu-Fang; Jesch, Stephen A.; Aregullin, Manuel; Henry, Susan A.

    2017-01-01

    In the yeast Saccharomyces cerevisiae, the Opi1p repressor controls the expression of INO1 via the Opi1p/Ino2p–Ino4p regulatory circuit. Inositol depletion favors Opi1p interaction with both Scs2p and phosphatidic acid at the endoplasmic reticulum (ER) membrane. Inositol supplementation, however, favors the translocation of Opi1p from the ER into the nucleus, where it interacts with the Ino2p–Ino4p complex, attenuating transcription of INO1. A strain devoid of Scs2p (scs2Δ) and a mutant, OPI1FFAT, lacking the ability to interact with Scs2p were utilized to examine the specific role(s) of the Opi1p–Scs2p interaction in the regulation of INO1 expression and overall lipid metabolism. Loss of the Opi1p–Scs2p interaction reduced INO1 expression and conferred inositol auxotrophy. Moreover, inositol depletion in strains lacking this interaction resulted in Opi1p being localized to sites of lipid droplet formation, coincident with increased synthesis of triacylglycerol. Supplementation of choline to inositol-depleted growth medium led to decreased TAG synthesis in all three strains. However, in strains lacking the Opi1p–Scs2p interaction, Opi1p remained in the nucleus, preventing expression of INO1. These data support the conclusion that a specific pool of phosphatidic acid, associated with lipid droplet formation in the perinuclear ER, is responsible for the initial rapid exit of Opi1p from the nucleus to the ER and is required for INO1 expression in the presence of choline. Moreover, the mitochondria-specific phospholipid, cardiolipin, was significantly reduced in both strains compromised for Opi1p–Scs2p interaction, indicating that this interaction is required for the transfer of phosphatidic acid from the ER to the mitochondria for cardiolipin synthesis. PMID:28924045

  2. Interaction between repressor Opi1p and ER membrane protein Scs2p facilitates transit of phosphatidic acid from the ER to mitochondria and is essential for INO1 gene expression in the presence of choline.

    PubMed

    Gaspar, Maria L; Chang, Yu-Fang; Jesch, Stephen A; Aregullin, Manuel; Henry, Susan A

    2017-11-10

    In the yeast Saccharomyces cerevisiae , the Opi1p repressor controls the expression of INO1 via the Opi1p/Ino2p-Ino4p regulatory circuit. Inositol depletion favors Opi1p interaction with both Scs2p and phosphatidic acid at the endoplasmic reticulum (ER) membrane. Inositol supplementation, however, favors the translocation of Opi1p from the ER into the nucleus, where it interacts with the Ino2p-Ino4p complex, attenuating transcription of INO1 A strain devoid of Scs2p ( scs2 Δ) and a mutant, OPI1FFAT , lacking the ability to interact with Scs2p were utilized to examine the specific role(s) of the Opi1p-Scs2p interaction in the regulation of INO1 expression and overall lipid metabolism. Loss of the Opi1p-Scs2p interaction reduced INO1 expression and conferred inositol auxotrophy. Moreover, inositol depletion in strains lacking this interaction resulted in Opi1p being localized to sites of lipid droplet formation, coincident with increased synthesis of triacylglycerol. Supplementation of choline to inositol-depleted growth medium led to decreased TAG synthesis in all three strains. However, in strains lacking the Opi1p-Scs2p interaction, Opi1p remained in the nucleus, preventing expression of INO1 These data support the conclusion that a specific pool of phosphatidic acid, associated with lipid droplet formation in the perinuclear ER, is responsible for the initial rapid exit of Opi1p from the nucleus to the ER and is required for INO1 expression in the presence of choline. Moreover, the mitochondria-specific phospholipid, cardiolipin, was significantly reduced in both strains compromised for Opi1p-Scs2p interaction, indicating that this interaction is required for the transfer of phosphatidic acid from the ER to the mitochondria for cardiolipin synthesis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Rainfall-runoff modeling of the Chapel Branch Creek Watershed using GIS-based rational and SCS-CN methods

    Treesearch

    Elizabeth N. Mihalik; Norm S. Levine; Devendra M. Amatya

    2008-01-01

    Chapel Branch Creek (CBC), located within the Town of Santee adjacent to Lake Marion in Orangeburg County, SC, is listed on the SC 2004 303(d) list of impaired waterbodies due to elevated levels of nitrogen (N), phosphorus (P), chlorophyll-a, and pH. In this study, using a GIS-based approach, two runoff modeling methods, the Rational and SCS-CN methods, have been...

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

    PubMed

    Straka, Michal; Lantto, Perttu; Vaara, Juha

    2008-03-27

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

  5. Chemical Shift MR Imaging Methods for the Quantification of Transcatheter Lipiodol Delivery to the Liver: Preclinical Feasibility Studies in a Rodent Model

    PubMed Central

    Yin, Xiaoming; Guo, Yang; Li, Weiguo; Huo, Eugene; Zhang, Zhuoli; Nicolai, Jodi; Kleps, Robert A.; Hernando, Diego; Katsaggelos, Aggelos K.; Omary, Reed A.

    2012-01-01

    Purpose: To demonstrate the feasibility of using chemical shift magnetic resonance (MR) imaging fat-water separation methods for quantitative estimation of transcatheter lipiodol delivery to liver tissues. Materials and Methods: Studies were performed in accordance with institutional Animal Care and Use Committee guidelines. Proton nuclear MR spectroscopy was first performed to identify lipiodol spectral peaks and relative amplitudes. Next, phantoms were constructed with increasing lipiodol-water volume fractions. A multiecho chemical shift–based fat-water separation method was used to quantify lipiodol concentration within each phantom. Six rats served as controls; 18 rats underwent catheterization with digital subtraction angiography guidance for intraportal infusion of a 15%, 30%, or 50% by volume lipiodol-saline mixture. MR imaging measurements were used to quantify lipiodol delivery to each rat liver. Lipiodol concentration maps were reconstructed by using both single-peak and multipeak chemical shift models. Intraclass and Spearman correlation coefficients were calculated for statistical comparison of MR imaging–based lipiodol concentration and volume measurements to reference standards (known lipiodol phantom compositions and the infused lipiodol dose during rat studies). Results: Both single-peak and multipeak measurements were well correlated to phantom lipiodol concentrations (r2 > 0.99). Lipiodol volume measurements were progressively and significantly higher when comparing between animals receiving different doses (P < .05 for each comparison). MR imaging–based lipiodol volume measurements strongly correlated with infused dose (intraclass correlation coefficients > 0.93, P < .001) with both single- and multipeak approaches. Conclusion: Chemical shift MR imaging fat-water separation methods can be used for quantitative measurements of lipiodol delivery to liver tissues. © RSNA, 2012 PMID:22623693

  6. Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

    PubMed Central

    Schmitz, Christophe; Vernon, Robert; Otting, Gottfried; Baker, David; Huber, Thomas

    2013-01-01

    Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δχ-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δχ-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations. PMID:22285518

  7. Chemical shift and zone-folding effects on the energy gaps of GaAs-AlAs (001) superlattices

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, S.B.; Cohen, M.L.; Louie, S.G.

    1991-04-15

    The chemical shift and zone-folding effects obtained from quasiparticle calculations for ultrathin GaAs-AlAs superlattices are incorporated within a Kronig-Penny model for superlattices of the arbitrary lattice period. We determine that superlattices with lattice periods in the range of 3{times}3 to 9{times}9 have an {ital X}-derived pseudodirect gap. This result explains both the results from first-principles calculations for ultrathin superlattices and those from experiments for a broader lattice period.

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

    PubMed

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

    2017-03-07

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

  9. The shape of the Sc2(μ2-S) unit trapped in C82: crystallographic, computational, and electrochemical studies of the isomers, Sc2(μ2-S)@C(s)(6)-C82 and Sc2(μ2-S)@C(3v)(8)-C82.

    PubMed

    Mercado, Brandon Q; Chen, Ning; Rodríguez-Fortea, Antonio; Mackey, Mary A; Stevenson, Steven; Echegoyen, Luis; Poblet, Josep M; Olmstead, Marilyn M; Balch, Alan L

    2011-05-04

    Single-crystal X-ray diffraction studies of Sc(2)(μ(2)-S)@C(s)(6)-C(82)·Ni(II)(OEP)·2C(6)H(6) and Sc(2)(μ(2)-S)@C(3v)(8)-C(82)·Ni(II)(OEP)·2C(6)H(6) reveal that both contain fully ordered fullerene cages. The crystallographic data for Sc(2)(μ(2)-S)@C(s)(6)-C(82)·Ni(II)(OEP)·2C(6)H(6) show two remarkable features: the presence of two slightly different cage sites and a fully ordered molecule Sc(2)(μ(2)-S)@C(s)(6)-C(82) in one of these sites. The Sc-S-Sc angles in Sc(2)(μ(2)-S)@C(s)(6)-C(82) (113.84(3)°) and Sc(2)(μ(2)-S)@C(3v)(8)-C(82) differ (97.34(13)°). This is the first case where the nature and structure of the fullerene cage isomer exerts a demonstrable effect on the geometry of the cluster contained within. Computational studies have shown that, among the nine isomers that follow the isolated pentagon rule for C(82), the cage stability changes markedly between 0 and 250 K, but the C(s)(6)-C(82) cage is preferred at temperatures ≥250 °C when using the energies obtained with the free encapsulated model (FEM). However, the C(3v)(8)-C(82) cage is preferred at temperatures ≥250 °C using the energies obtained by rigid rotor-harmonic oscillator (RRHO) approximation. These results corroborate the fact that both cages are observed and likely to trap the Sc(2)(μ(2)-S) cluster, whereas earlier FEM and RRHO calculations predicted only the C(s)(6)-C(82) cage is likely to trap the Sc(2)(μ(2)-O) cluster. We also compare the recently published electrochemistry of the sulfide-containing Sc(2)(μ(2)-S)@C(s)(6)-C(82) to that of corresponding oxide-containing Sc(2)(μ(2)-O)@C(s)(6)-C(82). © 2011 American Chemical Society

  10. Earth field NMR with chemical shift spectral resolution: theory and proof of concept.

    PubMed

    Katz, Itai; Shtirberg, Lazar; Shakour, Gubrail; Blank, Aharon

    2012-06-01

    A new method for obtaining an NMR signal in the Earth's magnetic field (EF) is presented. The method makes use of a simple pulse sequence with only DC fields which is much less demanding than previous approaches in terms of the pulses' rise and fall times. Furthermore, it offers the possibility of obtaining NMR data with enough spectral resolution to allow retrieving high resolution molecular chemical shift (CS) information - a capability that was not considered possible in EF NMR until now. Details of the pulse sequence, the experimental system, and our specially tailored EF NMR probe are provided. The experimental results demonstrate the capability to differentiate between three types of samples made of common fluorine compounds, based on their CS data. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. NMR shifts for polycyclic aromatic hydrocarbons from first-principles

    NASA Astrophysics Data System (ADS)

    Thonhauser, T.; Ceresoli, Davide; Marzari, Nicola

    We present first-principles, density-functional theory calculations of the NMR chemical shifts for polycyclic aromatic hydrocarbons, starting with benzene and increasing sizes up to the one- and two-dimensional infinite limits of graphene ribbons and sheets. Our calculations are performed using a combination of the recently developed theory of orbital magnetization in solids, and a novel approach to NMR calculations where chemical shifts are obtained from the derivative of the orbital magnetization with respect to a microscopic, localized magnetic dipole. Using these methods we study on equal footing the 1H and 13 shifts in benzene, pyrene, coronene, in naphthalene, anthracene, naphthacene, and pentacene, and finally in graphene, graphite, and an infinite graphene ribbon. Our results show very good agreement with experiments and allow us to characterize the trends for the chemical shifts as a function of system size.

  12. An analytical solution of Richards' equation providing the physical basis of SCS curve number method and its proportionality relationship

    NASA Astrophysics Data System (ADS)

    Hooshyar, Milad; Wang, Dingbao

    2016-08-01

    The empirical proportionality relationship, which indicates that the ratio of cumulative surface runoff and infiltration to their corresponding potentials are equal, is the basis of the extensively used Soil Conservation Service Curve Number (SCS-CN) method. The objective of this paper is to provide the physical basis of the SCS-CN method and its proportionality hypothesis from the infiltration excess runoff generation perspective. To achieve this purpose, an analytical solution of Richards' equation is derived for ponded infiltration in shallow water table environment under the following boundary conditions: (1) the soil is saturated at the land surface; and (2) there is a no-flux boundary which moves downward. The solution is established based on the assumptions of negligible gravitational effect, constant soil water diffusivity, and hydrostatic soil moisture profile between the no-flux boundary and water table. Based on the derived analytical solution, the proportionality hypothesis is a reasonable approximation for rainfall partitioning at the early stage of ponded infiltration in areas with a shallow water table for coarse textured soils.

  13. Multiparametric fat-water separation method for fast chemical-shift imaging guidance of thermal therapies.

    PubMed

    Lin, Jonathan S; Hwang, Ken-Pin; Jackson, Edward F; Hazle, John D; Stafford, R Jason; Taylor, Brian A

    2013-10-01

    A k-means-based classification algorithm is investigated to assess suitability for rapidly separating and classifying fat/water spectral peaks from a fast chemical shift imaging technique for magnetic resonance temperature imaging. Algorithm testing is performed in simulated mathematical phantoms and agar gel phantoms containing mixed fat/water regions. Proton resonance frequencies (PRFs), apparent spin-spin relaxation (T2*) times, and T1-weighted (T1-W) amplitude values were calculated for each voxel using a single-peak autoregressive moving average (ARMA) signal model. These parameters were then used as criteria for k-means sorting, with the results used to determine PRF ranges of each chemical species cluster for further classification. To detect the presence of secondary chemical species, spectral parameters were recalculated when needed using a two-peak ARMA signal model during the subsequent classification steps. Mathematical phantom simulations involved the modulation of signal-to-noise ratios (SNR), maximum PRF shift (MPS) values, analysis window sizes, and frequency expansion factor sizes in order to characterize the algorithm performance across a variety of conditions. In agar, images were collected on a 1.5T clinical MR scanner using acquisition parameters close to simulation, and algorithm performance was assessed by comparing classification results to manually segmented maps of the fat/water regions. Performance was characterized quantitatively using the Dice Similarity Coefficient (DSC), sensitivity, and specificity. The simulated mathematical phantom experiments demonstrated good fat/water separation depending on conditions, specifically high SNR, moderate MPS value, small analysis window size, and low but nonzero frequency expansion factor size. Physical phantom results demonstrated good identification for both water (0.997 ± 0.001, 0.999 ± 0.001, and 0.986 ± 0.001 for DSC, sensitivity, and specificity, respectively) and fat (0.763 ± 0.006, 0

  14. Evidence of chemical-potential shift with hole doping in Bi2Sr2CaCu2O8+δ

    NASA Astrophysics Data System (ADS)

    Shen, Z.-X.; Dessau, D. S.; Wells, B. O.; Olson, C. G.; Mitzi, D. B.; Lombado, Lou; List, R. S.; Arko, A. J.

    1991-12-01

    We have performed photoemission studies on high-quality Bi2Sr2CaCu2O8+δ samples with various δ. Our results show a clear chemical-potential shift (0.15-0.2 eV) as a function of doping. This result and the existing angle-resolved-photoemission data give a rather standard doping behavior of this compound in its highly doped regime.

  15. Chemical shift magnetic resonance imaging is helpful in detecting hepatic steatosis but not fibrosis in patients with nonalcoholic fatty liver disease (NAFLD).

    PubMed

    Kalra, Naveen; Duseja, Ajay; Das, Ashim; Dhiman, Radha Krishan; Virmani, Vivek; Chawla, Yogesh; Singh, Paramjee; Khandelwal, Niranjan

    2009-01-01

    Imaging modalities have a role in the diagnosis of patients with nonalcoholic fatty liver disease. Aim of the present study was to evaluate the role of chemical shift magnetic resonance imaging in assessing hepatic steatosis and fibrosis in patients with nonalcoholic fatty liver disease. Chemical shift magnetic resonance imaging was done in 10 biopsy proven patients (7 females, mean age 41 +/- 9.2 years) with nonalcoholic fatty liver disease. Objective measurements of signal intensity (SI) were done and a ratio was calculated (SI out-of- phase liver/ SI out-of- phase kidney)/ (SI in- phase liver/ SI in-phase kidney). A lower ratio indicated a higher signal drop and hence higher fat content. The ratio was correlated with hepatic steatosis on histology (< 33% and > 33%). Patients were classified as having histological NASH or no NASH and MRI was assessed in diagnosing hepatic fibrosis as seen on liver histology. Six patients had > 33% hepatic steatosis on histology. Five patients (50%) had evidence of histological NASH. MRI was not helpful in differentiating patients with and without histological NASH. One patient amongst NASH patients did not have fibrosis, one had stage 1, 2 had stage 2 and one had stage 4 fibrosis. SI ratio ranged between 0.35-0.69 in 6 patients with steatosis > 33% and was in the range of 0.69-1.20 in four patients with steatosis < 33% on histology. Fibrotic changes seen in 4 patients on biopsy were not detected on MRI. Chemical shift MRI provides objective data on fat infiltration in patients with NAFLD without giving information about hepatic fibrosis.

  16. Small subsidence of the 660-km discontinuity beneath Japan probed by ScS reverberations

    NASA Astrophysics Data System (ADS)

    Kato, Mamoru; Misawa, Mika; Kawakatsu, Hitoshi

    We investigate layering structure in the mantle beneath Japan using ScS reverberation waveforms of two recent large deep events in the northwest Pacific. We estimate regional variation of the elastic and anelastic structure of the mantle as well as properties of the major velocity discontinuities by modeling broadband seismograms recorded at two dense networks, J-Array and FREESIA. The 660-km discontinuity is the deepest in the region where the stagnant subducting slab in the transition zone is tomographically imaged, but the subsidence is of ∼10 km, much smaller than previous estimates with SS precursors. No significant elevation is detected for the 410-km discontinuity.

  17. Saturated amine oxides: Part 8. Hydroacridines: Part 27. Effects of N-oxidation and of N-quaternization on the 15N NMR chemical shifts of N-methylpiperidine-derived mono-, bi-, and tricycloaliphatic tertiary amines.

    PubMed

    Potmischil, Francisc; Duddeck, Helmut; Nicolescu, Alina; Deleanu, Calin

    2007-03-01

    The (15)N chemical shifts of 13 N-methylpiperidine-derived mono-, bi- and tricycloaliphatic tertiary amines, their methiodides and their N-epimeric pairs of N-oxides were measured, and the contributions of specific structural parameters to the chemical shifts were determined by multilinear regression analysis. Within the examined compounds, the effects of N-oxidation upon the (15)N chemical shifts of the amines vary from +56 ppm to +90 ppm (deshielding), of which approx. +67.7 ppm is due to the inductive effect of the incoming N(+)--O(-) oxygen atom, whereas the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The effects of quaternization vary from -3.1 ppm to +29.3 ppm, of which approx. +8.9 ppm is due to the inductive effect of the incoming N(+)--CH(3) methyl group, and the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The shift effects of the C-alkyl substituents in the amines, the N-oxides and the methiodides are discussed. Copyright (c) 2007 John Wiley & Sons, Ltd.

  18. Correlates to sleepiness on night shift among male workers engaged in three-shift work in a chemical plant: its association with sleep practice and job stress.

    PubMed

    Kageyama, Takayuki; Kobayashi, Toshio; Abe-Gotoh, Ayano

    2011-01-01

    The purpose of this study was to examine the correlation of sleepiness during night shift (SNS) in male shiftworkers with nonpharmacological self-management (nPSM) practices to facilitate good day sleep, and also with job stress. Sleepiness on the job and possible correlates to SNS among 157 male shiftworkers in a rotating three-shift schedule at a chemical plant were cross-sectionally investigated using a self-administered questionnaire. Multivariate analyses revealed that SNS was positively associated with drinking alcoholic beverages before day sleep, but inversely associated with subjective health status, being of the evening type, abstaining from caffeine before day sleep, having a bath before day sleep, job control, reward from work, feeling suited to the job, and support from colleagues. SNS correlated with certain nPSM practices and also with possible modifiers of job stress. These findings provide clues to developing countermeasures against SNS among shiftworkers. The effects of nPSM practices and job stress management on their day sleep and SNS should be examined in detail.

  19. Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide

    NASA Astrophysics Data System (ADS)

    Pichumani, Kumar; George, Gijo; Hebbar, Sankeerth; Chatterjee, Bhaswati; Raghothama, Srinivasarao

    2015-05-01

    Longitudinal relaxation due to cross-correlation between dipolar (1HN-1Hα) and amide-proton chemical shift anisotropy (1HN CSA) has been measured in a model tripeptide Piv-LPro-LPro-LPhe-OMe. The peptide bond across diproline segment is known to undergo cis/trans isomerization and only in the cis form does the lone Phe amide-proton become involved in intramolecular hydrogen bonding. The strength of the cross correlated relaxation interference is found to be significantly different between cis and trans forms, and this difference is shown as an influence of intramolecular hydrogen bonding on the amide-proton CSA.

  20. Matrix fatigue crack development in a notched continuous fiber SCS-6/Ti-15-3 composite

    NASA Technical Reports Server (NTRS)

    Hillberry, B. M.; Johnson, W. S.

    1990-01-01

    In this study the extensive matrix fatigue cracking that has been observed in notched SCS-6/Ti-15-3 composites is investigated. Away from the notch uniform spacing of the fatigue cracks develops. Closer to the notch, fiber-matrix debonding which occurs increases the crack spacing. Crack spacing and debond length determined from shear-lag cylinder models compare favorably with experimental observations. Scanning electron microscope (SEM) fractography showed that the principal fatigue crack initiation occurred around the zero degree fibers. Interface failure in the 90 degree plies does not lead to the development of the primary fatigue cracking.

  1. Matrix fatigue crack development in a notched continuous fiber SCS-6/Ti-15-3 composite

    NASA Technical Reports Server (NTRS)

    Hillberry, B. M.; Johnson, W. S.

    1990-01-01

    In this study the extensive matrix fatigue cracking that has been observed in notched SCS-6/Ti-15-3 composites is investigated. Away from the notch a uniform spacing of the fatigue cracks develops. Closer to the notch, fiber-matrix debonding which occurs increases the crack spacing. Crack spacing and debond length determined from shear-lag cylinder models compare favorably with experimental observations. Scanning electron microscope (SEM) fractography showed that the principal fatigue crack initiation occurred around the zero degree fibers. Interface failure in the 90 degree plies does not lead to the development of the primary fatigue cracking.

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

    DTIC Science & Technology

    2017-12-11

    AFRL-RX-WP-JA-2017-0501 pH- DEPENDENT SPIN STATE POPULATION AND 19F NMR CHEMICAL SHIFT VIA REMOTE LIGAND PROTONATION IN AN IRON(II...From - To) 16 November 2017 Interim 24 January 2014 – 16 October 2017 4. TITLE AND SUBTITLE PH- DEPENDENT SPIN STATE POPULATION AND 19F NMR CHEMICAL...dx.doi.org/10.1039/C7CC08099A 14. ABSTRACT (Maximum 200 words) An FeII complex that features a pH- dependent spin state population, by virtue of a

  3. Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

    PubMed

    Hanni, Matti; Lantto, Perttu; Vaara, Juha

    2011-08-14

    Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

  4. Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

    PubMed

    Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

    2010-03-17

    Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

  5. Fully automatic assignment of small molecules' NMR spectra without relying on chemical shift predictions.

    PubMed

    Castillo, Andrés M; Bernal, Andrés; Patiny, Luc; Wist, Julien

    2015-08-01

    We present a method for the automatic assignment of small molecules' NMR spectra. The method includes an automatic and novel self-consistent peak-picking routine that validates NMR peaks in each spectrum against peaks in the same or other spectra that are due to the same resonances. The auto-assignment routine used is based on branch-and-bound optimization and relies predominantly on integration and correlation data; chemical shift information may be included when available to fasten the search and shorten the list of viable assignments, but in most cases tested, it is not required in order to find the correct assignment. This automatic assignment method is implemented as a web-based tool that runs without any user input other than the acquired spectra. Copyright © 2015 John Wiley & Sons, Ltd.

  6. NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

    PubMed

    Wiedemann, Christoph; Ohlenschläger, Oliver; Mrestani-Klaus, Carmen; Bordusa, Frank

    2017-09-13

    NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual 1 H and 13 C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.

  7. Characterization of SiC Fiber (SCS-6) Reinforced-Reaction-Formed Silicon Carbide Matrix Composites

    NASA Technical Reports Server (NTRS)

    Singh, M.; Dickerson, R. M.

    1996-01-01

    Silicon carbide fiber (SCS-6) reinforced-reaction-formed silicon carbide matrix composites were fabricated using a reaction-forming process. Silicon-2 at.% niobium alloy was used as an infiltrant instead of pure silicon to reduce the amount of free silicon in the matrix after reaction forming. The matrix primarily consists of silicon carbide with a bimodal grain size distribution. Minority phases dispersed within the matrix are niobium disilicide (NbSi2), carbon, and silicon. Fiber pushout tests on these composites determined a debond stress of approximately 67 MPa and a frictional stress of approximately 60 MPa. A typical four-point flexural strength of the composite is 297 MPa (43.1 KSi). This composite shows tough behavior through fiber pullout.

  8. A multicenter retrospective survey of poisoning after consumption of products containing synthetic chemicals in Japan.

    PubMed

    Kamijo, Yoshito; Takai, Michiko; Fujita, Yuji; Hirose, Yasuo; Iwasaki, Yasumasa; Ishihara, Satoshi; Yokoyama, Takashi; Yagi, Keiichi; Sakamoto, Tetsuya

    2014-01-01

    We conducted a multicenter retrospective survey of patients poisoned by synthetic chemicals (SCs) in Japan. Letters were sent to 467 emergency facilities requesting participation in the study, and questionnaires were mailed to facilities that agreed to participate. Patients The study participants were patients who were transported to emergency facilities between January 2006 and December 2012 after consuming SC-containing products. We surveyed 518 patients from 60 (12.8%) facilities. Most patients were male (82.0%), in their 20s or 30s (80.5%), and had inhaled SCs (87.5%) contained in herbal products (86.0%). Harmful behavior was observed at the scene of poisoning for 56 patients (10.8%), including violence to others or things in 32, traffic accidents in seven, and self-injury or suicide attempts in four. Other than physical and neuropsychiatric symptoms, some patients also had physical complications, such as rhabdomyolysis (10.0%). Of the 182 patients (35.1%) admitted to hospitals, including 29 (5.6%) who needed respirators, all of the 21 (4.1%) hospitalized for at least seven days were male, and 20 had physical complications (rhabdomyolysis, 12; liver dysfunction, 5; renal dysfunction, 11; and physical injuries, 3). Most patients (95.6%) completely recovered, although 10 (1.9%) were transferred to a psychiatric department or hospital, and three (0.6%) were handed over to the police due to combative or violent behavior. SCs such as synthetic cannabinoids, synthetic cathinones, or methoxetamine were detected in 20 product samples. Consuming products containing SCs can result in physical complications, including rhabdomyolysis, injuries, and physical or neuropsychiatric symptoms, which may require active interventions, such as respirator use or prolonged hospitalization.

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

    PubMed

    Rozwadowski, Z

    2006-09-01

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

  10. 17O NMR spectroscopy of substituted methyleneindanones: relationship between chemical shift and oxygen atom electron density

    NASA Astrophysics Data System (ADS)

    Kumar, Arvind; Boykin, David W.

    1993-07-01

    17O NMR spectroscopic data for eigth β-substituted methyleneindanones obtained at natural abundance in acetonitrile at 75°C are reported. 17O NMR data for ten para-substituted E-benzalindanones, enriched with 17O, were recorded in acetonitrile at 75°C. The 17O NMR data for the E-benzalindanones gave good correlations with sigma plus values, with literature carbonyl IR stretching frequencies, and with literature 17O NMR carbonyl data of chalcones and 5-aryl-2,3-furandiones. The carbonyl oxygen atom electron density (AM1) gave good correlation with the carbonyl 17O NMR chemical shift of both β-substituted methyleneindanones and the E-benzalindanones.

  11. Improved Algorithm of SCS-CN Model Parameters in Typical Inland River Basin in Central Asia

    NASA Astrophysics Data System (ADS)

    Wang, Jin J.; Ding, Jian L.; Zhang, Zhe; Chen, Wen Q.

    2017-02-01

    Rainfall-runoff relationship is the most important factor for hydrological structures, social and economic development on the background of global warmer, especially in arid regions. The aim of this paper is find the suitable method to simulate the runoff in arid area. The Soil Conservation Service Curve Number (SCS-CN) is the most popular and widely applied model for direct runoff estimation. In this paper, we will focus on Wen-quan Basin in source regions of Boertala River. It is a typical valley of inland in Central Asia. First time to use the 16m resolution remote sensing image about high-definition earth observation satellite “Gaofen-1” to provide a high degree accuracy data for land use classification determine the curve number. Use surface temperature/vegetation index (TS/VI) construct 2D scatter plot combine with the soil moisture absorption balance principle calculate the moisture-holding capacity of soil. Using original and parameter algorithm improved SCS-CN model respectively to simulation the runoff. The simulation results show that the improved model is better than original model. Both of them in calibration and validation periods Nash-Sutcliffe efficiency were 0.79, 0.71 and 0.66,038. And relative error were3%, 12% and 17%, 27%. It shows that the simulation accuracy should be further improved and using remote sensing information technology to improve the basic geographic data for the hydrological model has the following advantages: 1) Remote sensing data having a planar characteristic, comprehensive and representative. 2) To get around the bottleneck about lack of data, provide reference to simulation the runoff in similar basin conditions and data-lacking regions.

  12. In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

    PubMed

    Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

    2016-10-24

    The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Technical Note: Determination of the SCS initial abstraction ratio in an experimental watershed in Greece

    NASA Astrophysics Data System (ADS)

    Baltas, E. A.; Dervos, N. A.; Mimikou, M. A.

    2007-11-01

    The present study was conducted in an experimental watershed in Attica, Greece, using observed rainfall/runoff events. The objective of the study was the determination of the initial abstraction ratio of the watershed. The average ratio (Ia/S) of the entire watershed was equal to 0.014. The corresponding ratio at a subwatershed was 0.037. The difference was attributed to the different spatial distribution of landuses and geological formations at the extent of the watershed. Both of the determined ratios are close to the ratio value of 0.05 that has been suggested from many studies for the improvement of the SCS-CN method.

  14. Progress in Spin Dynamics Solid-State Nuclear Magnetic Resonance with the Application of Floquet-Magnus Expansion to Chemical Shift Anisotropy

    PubMed Central

    Mananga, Eugene Stephane

    2013-01-01

    The purpose of this article is to present an historical overview of theoretical approaches used for describing spin dynamics under static or rotating experiments in solid state nuclear magnetic resonance. The article gives a brief historical overview for major theories in nuclear magnetic resonance and the promising theories. We present the first application of Floquet-Magnus expansion to chemical shift anisotropy when irradiated by BABA pulse sequence. PMID:23711337

  15. Volumetric spiral chemical shift imaging of hyperpolarized [2-(13) c]pyruvate in a rat c6 glioma model.

    PubMed

    Park, Jae Mo; Josan, Sonal; Jang, Taichang; Merchant, Milton; Watkins, Ron; Hurd, Ralph E; Recht, Lawrence D; Mayer, Dirk; Spielman, Daniel M

    2016-03-01

    MRS of hyperpolarized [2-(13)C]pyruvate can be used to assess multiple metabolic pathways within mitochondria as the (13)C label is not lost with the conversion of pyruvate to acetyl-CoA. This study presents the first MR spectroscopic imaging of hyperpolarized [2-(13)C]pyruvate in glioma-bearing brain. Spiral chemical shift imaging with spectrally undersampling scheme (1042 Hz) and a hard-pulse excitation was exploited to simultaneously image [2-(13)C]pyruvate, [2-(13)C]lactate, and [5-(13)C]glutamate, the metabolites known to be produced in brain after an injection of hyperpolarized [2-(13)C]pyruvate, without chemical shift displacement artifacts. A separate undersampling scheme (890 Hz) was also used to image [1-(13)C]acetyl-carnitine. Healthy and C6 glioma-implanted rat brains were imaged at baseline and after dichloroacetate administration, a drug that modulates pyruvate dehydrogenase kinase activity. The baseline metabolite maps showed higher lactate and lower glutamate in tumor as compared to normal-appearing brain. Dichloroacetate led to an increase in glutamate in both tumor and normal-appearing brain. Dichloroacetate-induced %-decrease of lactate/glutamate was comparable to the lactate/bicarbonate decrease from hyperpolarized [1-(13)C]pyruvate studies. Acetyl-carnitine was observed in the muscle/fat tissue surrounding the brain. Robust volumetric imaging with hyperpolarized [2-(13)C]pyruvate and downstream products was performed in glioma-bearing rat brains, demonstrating changes in mitochondrial metabolism with dichloroacetate. © 2015 Wiley Periodicals, Inc.

  16. Characterization of SiC (SCS-6) Fiber Reinforced Reaction-Formed Silicon Carbide Matrix Composites

    NASA Technical Reports Server (NTRS)

    Singh, Mrityunjay; Dickerson, Robert M.

    1995-01-01

    Silicon carbide (SCS-6) fiber reinforced-reaction formed silicon carbide matrix composites were fabricated using NASA's reaction forming process. Silicon-2 at a percent of niobium alloy was used as an infiltrant instead of pure silicon to reduce the amount of free silicon in the matrix after reaction forming. The matrix primarily consists of silicon carbide with a bi-modal grain size distribution. Minority phases dispersed within the matrix are niobium disilicide (NbSi2), carbon and silicon. Fiber push-out tests on these composites determined a debond stress of approx. 67 MPa and a frictional stress of approx. 60 MPa. A typical four point flexural strength of the composite is 297 MPa (43.1 KSi). This composite shows tough behavior through fiber pull out.

  17. Backbone amide 15N chemical shift tensors report on hydrogen bonding interactions in proteins: A magic angle spinning NMR study.

    PubMed

    Paramasivam, Sivakumar; Gronenborn, Angela M; Polenova, Tatyana

    2018-08-01

    Chemical shift tensors (CSTs) are an exquisite probe of local geometric and electronic structure. 15 N CST are very sensitive to hydrogen bonding, yet they have been reported for very few proteins to date. Here we present experimental results and statistical analysis of backbone amide 15 N CSTs for 100 residues of four proteins, two E. coli thioredoxin reassemblies (1-73-(U- 13 C, 15 N)/74-108-(U- 15 N) and 1-73-(U- 15 N)/74-108-(U- 13 C, 15 N)), dynein light chain 8 LC8, and CAP-Gly domain of the mammalian dynactin. The 15 N CSTs were measured by a symmetry-based CSA recoupling method, ROCSA. Our results show that the principal component δ 11 is very sensitive to the presence of hydrogen bonding interactions due to its unique orientation in the molecular frame. The downfield chemical shift change of backbone amide nitrogen nuclei with increasing hydrogen bond strength is manifested in the negative correlation of the principal components with hydrogen bond distance for both α-helical and β-sheet secondary structure elements. Our findings highlight the potential for the use of 15 N CSTs in protein structure refinement. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. Comparison of eight and 12 hour shifts: impacts on health, wellbeing, and alertness during the shift.

    PubMed

    Tucker, P; Barton, J; Folkard, S

    1996-11-01

    The generally agreed view is that there is no ideal shift system, and that most systems will have both advantages and disadvantages. As such, attention has been placed on trying to identify good and bad features of shift systems, with a view to minimising the possible ill health as a consequence of shiftwork. The present study focuses on the duration of the shift and looks at the implications for individual health, wellbeing, and alertness during the shift of extending the shift from the traditional eight hours to 12. Two groups of chemical workers, one working 12 hour shifts and the other working eight hour shifts, took part. All completed a modified version of the standard shiftwork index (SSI), a set of self reported questionnaires related to health and wellbeing. The two groups did not differ on most outcome measures, although the differences that did exist suggested advantages for the 12 hour shift workers over the eight hour shift workers; with the notable exception of rated alertness at certain times of day. The results are explained in terms of the design of the 12 hour shift system and the specific sequencing of shifts that seem to minimise the potential for the build up of fatigue. Although the current data moderately favour 12 hour shifts, a cautionary note is sounded with regard to the implications of the alertness ratings for performance and safety.

  19. Chemical Shift Encoded Water–Fat Separation Using Parallel Imaging and Compressed Sensing

    PubMed Central

    Sharma, Samir D.; Hu, Houchun H.; Nayak, Krishna S.

    2013-01-01

    Chemical shift encoded techniques have received considerable attention recently because they can reliably separate water and fat in the presence of off-resonance. The insensitivity to off-resonance requires that data be acquired at multiple echo times, which increases the scan time as compared to a single echo acquisition. The increased scan time often requires that a compromise be made between the spatial resolution, the volume coverage, and the tolerance to artifacts from subject motion. This work describes a combined parallel imaging and compressed sensing approach for accelerated water–fat separation. In addition, the use of multiscale cubic B-splines for B0 field map estimation is introduced. The water and fat images and the B0 field map are estimated via an alternating minimization. Coil sensitivity information is derived from a calculated k-space convolution kernel and l1-regularization is imposed on the coil-combined water and fat image estimates. Uniform water–fat separation is demonstrated from retrospectively undersampled data in the liver, brachial plexus, ankle, and knee as well as from a prospectively undersampled acquisition of the knee at 8.6x acceleration. PMID:22505285

  20. Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

    PubMed

    Bratholm, Lars A; Jensen, Jan H

    2017-03-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural

  1. Improving the analysis of NMR spectra tracking pH-induced conformational changes: removing artefacts of the electric field on the NMR chemical shift.

    PubMed

    Kukić, Predrag; Farrell, Damien; Søndergaard, Chresten R; Bjarnadottir, Una; Bradley, John; Pollastri, Gianluca; Nielsen, Jens Erik

    2010-03-01

    pH-induced chemical shift perturbations (CSPs) can be used to study pH-dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH-dependent structural transitions in bovine beta-lactoglobulin (betaLG) by analyzing its NMR pH-titration spectra. Here, we augment this analysis method by filtering out changes in the NMR chemical shift that stem from effects that are electrostatic in nature. Specifically, we examine how many CSPs can be explained by purely electrostatic effects arising from titrational events in betaLG. The results show that around 20% of the amide nuclei CSPs in betaLG originate exclusively from "through-space" electric field effects. A PCA of NMR data where electric field artefacts have been removed gives a different picture of the pH-dependent structural transitions in betaLG. The method implemented here is well suited to be applied on a whole range of proteins, which experience at least one pH-dependent conformational change. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

  2. Ab initio/GIAO-CCSD(T) study of structures, energies, and 13C NMR chemical shifts of C4H7(+) and C5H9(+) ions: relative stability and dynamic aspects of the cyclopropylcarbinyl vs bicyclobutonium ions.

    PubMed

    Olah, George A; Surya Prakash, G K; Rasul, Golam

    2008-07-16

    The structures and energies of the carbocations C 4H 7 (+) and C 5H 9 (+) were calculated using the ab initio method. The (13)C NMR chemical shifts of the carbocations were calculated using the GIAO-CCSD(T) method. The pisigma-delocalized bisected cyclopropylcarbinyl cation, 1 and nonclassical bicyclobutonium ion, 2 were found to be the minima for C 4H 7 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level the structure 2 is 0.4 kcal/mol more stable than the structure 1. The (13)C NMR chemical shifts of 1 and 2 were calculated by the GIAO-CCSD(T) method. Based on relative energies and (13)C NMR chemical shift calculations, an equilibrium involving the 1 and 2 in superacid solutions is most likely responsible for the experimentally observed (13)C NMR chemical shifts, with the latter as the predominant equilibrating species. The alpha-methylcyclopropylcarbinyl cation, 4, and nonclassical bicyclobutonium ion, 5, were found to be the minima for C 5H 9 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level ion 5 is 5.9 kcal/mol more stable than the structure 4. The calculated (13)C NMR chemical shifts of 5 agree rather well with the experimental values of C 5H 9 (+).

  3. 13Check_RNA: A tool to evaluate 13C chemical shifts assignments of RNA.

    PubMed

    Icazatti, A A; Martin, O A; Villegas, M; Szleifer, I; Vila, J A

    2018-06-19

    Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for correct assignments of RNA 13C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Based on an existent method we have implemented an open source python module to correct 13C CS (from here on 13Cexp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one. This software is available on GitHub at https://github.com/BIOS-IMASL/13Check_RNA under a MIT license. Supplementary data are available at Bioinformatics online.

  4. Stress/Strain Ratio Effects on Fatigue Response of a SCS-6/Ti-15-3 Metal Matrix Composite at Elevated Temperature.

    DTIC Science & Technology

    1995-12-01

    consisted of a titanium alloy matrix, Figure 1. Turbine Blade Load History [19] Ti-15-3, reinforced with silicon carbide fibers, SCS-6. For this...Composite Science and Technology 1994. 19. Pernot, J. J., Crack Growth Rate Modeling of a Titanium Aluminide Alloy Under Thermal Mechanical Cycling. PhD...Appendix B: Additional Unidirectional, [0]8, Data 102 7. Bibliography 109 8. Vita 112 IV List of Fieures Figure Page 1. Turbine Blade Load

  5. Chemical shift in Lα, Lβ1, Lβ3,4, Lβ2,15, Lγ1 and Lγ2,3 emission lines of 47Ag, 48Cd and 50Sn compounds

    NASA Astrophysics Data System (ADS)

    Singh Kainth, Harpreet; Singh, Ranjit; Singh, Gurjot; Mehta, D.

    2018-01-01

    Positive and negative shifts in L shell emission lines of 47Ag, 48Cd and 50Sn elements in different chemical compounds were determined from their recorded X-ray emission spectra in high resolution wavelength dispersive X-ray fluorescence (WDXRF) spectrometer. In 47Ag compounds, the measured energy shifts in Lα X-ray emission line were in the ranges from (0.12 to 0.40) eV, Lβ1 (0.27 to 0.36) eV, Lβ3,4 (1.10 to 4.89) eV, Lγ1 (-0.09 to 1.13) eV and Lγ2,3 (-2.08 to 0.59) eV. Likewise, for 48Cd compounds, the estimated shifts in Lα X-ray emission lines were in the range (-0.27 to 0.69) eV, Lβ1 (0.50 to 2.06) eV, Lβ2,15 (0.12 to 0.79), Lβ3,4 (-0.62 to 1.79) eV, Lγ1 (0.10 to 1.35) eV and Lγ2,3 (-0.73 to 1.75) eV, while for 50Sn compounds, the measured shifts in Lα X-ray emission lines were in the range of (0.02 to 1.81) eV, Lβ1 (0.11 to 0.78) eV, Lβ2,15 (0.15 to 1.40), Lβ3,4 (0.17 to 2.01) eV, Lγ1 (0.09 to 1.08) eV and Lγ2,3 (0.17 to 1.40) eV respectively. The effective charges (qP, qS, qL and qB) were calculated by four different theoretical methods (Pauling method, Suchet method, Levine method and Batsonav method) and found to be linear dependent with the chemical shift. Further, the measured chemical shifts were correlated with bond length, relative line-width (FWHM), effective charge, electronegativity, number of ligands and Coster-Kronig (CK) transition processes.

  6. Change from an 8-hour shift to a 12-hour shift, attitudes, sleep, sleepiness and performance.

    PubMed

    Lowden, A; Kecklund, G; Axelsson, J; Akerstedt, T

    1998-01-01

    The present study sought to evaluate the effect of a change from a rotating 3-shift (8-hour) to a 2-shift shift (12 hour) schedule on sleep, sleepiness, performance, perceived health, and well-being. Thirty-two shift workers at a chemical plant (control room operators) responded to a questionnaire a few months before a change was made in their shift schedule and 10 months after the change. Fourteen workers also filled out a diary, carried activity loggers, and carried out reaction-time tests (beginning and end of shift). Fourteen day workers served as a reference group for the questionnaires and 9 were intensively studied during a week with workdays and a free weekend. The questionnaire data showed that the shift change increased satisfaction with workhours, sleep, and time for social activities. Health, perceived accident risk, and reaction-time performance were not negatively affected. Alertness improved and subjective recovery time after night work decreased. The quick changes in the 8-hour schedule greatly increased sleep problems and fatigue. Sleepiness integrated across the entire shift cycle showed that the shift workers were less alert than the day workers, across workdays and days off (although alertness increased with the 12-hour shift). The change from 8-hour to 12-hour shifts was positive in most respects, possibly due to the shorter sequences of the workdays, the longer sequences of consecutive days off, the fewer types of shifts (easier planning), and the elimination of quick changes. The results may differ in groups with a higher work load.

  7. Hydrogen bonds in betaine-acid (1:1) crystals revealed by Raman and 13C chemical shift tensors

    NASA Astrophysics Data System (ADS)

    Ilczyszyn, Marek; Ilczyszyn, Maria M.

    2017-06-01

    H-bonds of five betaine-acid (1:1) crystals are considered by analysis of tensors based on the Raman scissoring mode and 13C chemical shift of the betaine -CO1O2- carboxylate group. The leading structural factor in these systems is the strongest H-bond linking the betaine and the acidic moieties, (O1⋯H-O)com. The Raman and NMR tensors are strongly related to its character and to the R(O1⋯O)com distance. Very high molecular polarizability variation due to the scissoring vibration was found for the betaine-selenious acid crystal. The probable reason is modest network of H-bonds in this case and relatively high proton polarizability of these bonds.

  8. The unexpected roles of σ and π orbitals in electron donor and acceptor group effects on the 13C NMR chemical shifts in substituted benzenes† †Electronic supplementary information (ESI) available: Experimental 13C NMR chemical shifts, individual components of the 13C NMR shielding tensor, lists and graphics of NLMO contributions, and tables of NLMO properties. See DOI: 10.1039/c7sc02163a Click here for additional data file.

    PubMed Central

    Viesser, Renan V.

    2017-01-01

    Effects of electron-donating (R = NH2) and electron-withdrawing (R = NO2) groups on 13C NMR chemical shifts in R-substituted benzene are investigated by molecular orbital analyses. The 13C shift substituent effect in ortho, meta, and para position is determined by the σ bonding orbitals in the aryl ring. The π orbitals do not explain the substituent effects in the NMR spectrum as conventionally suggested in textbooks. The familiar electron donating and withdrawing effects on the π system by NH2 and NO2 substituents induce changes in the σ orbital framework, and the 13C chemical shifts follow the trends induced in the σ orbitals. There is an implicit dependence of the σ orbital NMR shift contributions on the π framework, via unoccupied π* orbitals, due to the fact that the nuclear shielding is a response property. PMID:28989684

  9. Anisotropy in the lowermost mantle beneath the Indian Ocean Geoid Low from ScS splitting measurements

    NASA Astrophysics Data System (ADS)

    Padma Rao, B.; Ravi Kumar, M.; Singh, Arun

    2017-02-01

    The Indian Ocean Geoid Low (IOGL) to the south of Indian subcontinent is the world's largest geoid anomaly. In this study, we investigate the seismic anisotropy of the lowermost mantle beneath the IOGL by analyzing splitting of high-quality ScS phases corrected for source and receiver side upper mantle anisotropy. Results reveal significant anisotropy (˜1.01%) in the D'' layer. The observed fast axis polarization azimuths in the ray coordinate system indicate a TTI (transverse isotropy with a tilted axis of symmetry) style of anisotropy. Lattice Preferred Orientation (LPO) deformation of the palaeo-subducted slabs experiencing high shear strain is a plausible explanation for the observed anisotropy beneath the IOGL.

  10. Host shifts and evolutionary radiations of butterflies

    PubMed Central

    Fordyce, James A.

    2010-01-01

    Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today. PMID:20610430

  11. Computation provides chemical insight into the diverse hydride NMR chemical shifts of [Ru(NHC)4(L)H]0/+ species (NHC = N-heterocyclic carbene; L = vacant, H2, N2, CO, MeCN, O2, P4, SO2, H-, F- and Cl-) and their [Ru(R2PCH2CH2PR2)2(L)H]+ congeners.

    PubMed

    Häller, L Jonas L; Mas-Marzá, Elena; Cybulski, Mateusz K; Sanguramath, Rajashekharayya A; Macgregor, Stuart A; Mahon, Mary F; Raynaud, Christophe; Russell, Christopher A; Whittlesey, Michael K

    2017-02-28

    Relativistic density functional theory calculations, both with and without the effects of spin-orbit coupling, have been employed to model hydride NMR chemical shifts for a series of [Ru(NHC) 4 (L)H] 0/+ species (NHC = N-heterocyclic carbene; L = vacant, H 2 , N 2 , CO, MeCN, O 2 , P 4 , SO 2 , H - , F - and Cl - ), as well as selected phosphine analogues [Ru(R 2 PCH 2 CH 2 PR 2 ) 2 (L)H] + (R = i Pr, Cy; L = vacant, O 2 ). Inclusion of spin-orbit coupling provides good agreement with the experimental data. For the NHC systems large variations in hydride chemical shift are shown to arise from the paramagnetic term, with high net shielding (L = vacant, Cl - , F - ) being reinforced by the contribution from spin-orbit coupling. Natural chemical shift analysis highlights the major orbital contributions to the paramagnetic term and rationalizes trends via changes in the energies of the occupied Ru d π orbitals and the unoccupied σ* Ru-H orbital. In [Ru(NHC) 4 (η 2 -O 2 )H] + a δ-interaction with the O 2 ligand results in a low-lying LUMO of d π character. As a result this orbital can no longer contribute to the paramagnetic shielding, but instead provides additional deshielding via overlap with the remaining (occupied) d π orbital under the L z angular momentum operator. These two effects account for the unusual hydride chemical shift of +4.8 ppm observed experimentally for this species. Calculations reproduce hydride chemical shift data observed for [Ru( i Pr 2 PCH 2 CH 2 P i Pr 2 ) 2 (η 2 -O 2 )H] + (δ = -6.2 ppm) and [Ru(R 2 PCH 2 CH 2 PR 2 ) 2 H] + (ca. -32 ppm, R = i Pr, Cy). For the latter, the presence of a weak agostic interaction trans to the hydride ligand is significant, as in its absence (R = Me) calculations predict a chemical shift of -41 ppm, similar to the [Ru(NHC) 4 H] + analogues. Depending on the strength of the agostic interaction a variation of up to 18 ppm in hydride chemical shift is possible and this factor (that is not necessarily

  12. Heterogeneous living donor hepatic fat distribution on MRI chemical shift imaging.

    PubMed

    Choi, YoungRok; Lee, Jeong Min; Yi, Nam-Joon; Kim, Hyeyoung; Park, Min-Su; Hong, Geun; Yoo, Tae; Suh, Suk-Won; Lee, Hae Won; Lee, Kwang-Woong; Suh, Kyung-Suk

    2015-07-01

    We evaluated the heterogeneity of steatosis in living donor livers to determine its regional differences. Between June 2011 and February 2012, 81 liver donors were selected. Fat fraction was estimated using magnetic resonance triple-echo chemical shifting gradient imaging in 13 different regions: segment 1 (S1), S2, S3, and each peripheral and deep region of S4, S5, S6, S7, and S8. There were differences (range, 3.2%-5.3%) in fat fractions between each peripheral and deep region of S4, S6, S7, and S8 (P < 0.001, P = 0.004, P < 0.001, and P = 0.006). Fat deposit amount in S1, S2, S3 and deep regions of S4-S8 were significantly different from one another (F [4.003, 58.032] = 8.684, P < 0.001), while there were no differences among the peripheral regions of S4-S8 (F [2.9, 5.3] = 1.3, P = 0.272) by repeated measure analysis of variance method. And regional differences of the amount of fat deposit in the whole liver increased as a peripheral fat fraction of S5 increased (R(2) = 0.428, P < 0.001). Multifocal fat measurements for the whole liver are needed because a small regional evaluation might not represent the remaining liver completely, especially in patients with severe hepatic steatosis.

  13. Free variable selection QSPR study to predict 19F chemical shifts of some fluorinated organic compounds using Random Forest and RBF-PLS methods

    NASA Astrophysics Data System (ADS)

    Goudarzi, Nasser

    2016-04-01

    In this work, two new and powerful chemometrics methods are applied for the modeling and prediction of the 19F chemical shift values of some fluorinated organic compounds. The radial basis function-partial least square (RBF-PLS) and random forest (RF) are employed to construct the models to predict the 19F chemical shifts. In this study, we didn't used from any variable selection method and RF method can be used as variable selection and modeling technique. Effects of the important parameters affecting the ability of the RF prediction power such as the number of trees (nt) and the number of randomly selected variables to split each node (m) were investigated. The root-mean-square errors of prediction (RMSEP) for the training set and the prediction set for the RBF-PLS and RF models were 44.70, 23.86, 29.77, and 23.69, respectively. Also, the correlation coefficients of the prediction set for the RBF-PLS and RF models were 0.8684 and 0.9313, respectively. The results obtained reveal that the RF model can be used as a powerful chemometrics tool for the quantitative structure-property relationship (QSPR) studies.

  14. Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction

    NASA Astrophysics Data System (ADS)

    Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael

    2015-05-01

    A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100-250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation.

  15. Reliable Resonance Assignments of Selected Residues of Proteins with Known Structure Based on Empirical NMR Chemical Shift Prediction

    PubMed Central

    Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael

    2015-01-01

    A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100 – 250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation. PMID:25863893

  16. Speeding up dynamic spiral chemical shift imaging with incoherent sampling and low-rank matrix completion.

    PubMed

    DeVience, Stephen J; Mayer, Dirk

    2017-03-01

    To improve the temporal and spatial resolution of dynamic 13 C spiral chemical shift imaging via incoherent sampling and low-rank matrix completion (LRMC). Spiral CSI data were both simulated and acquired in rats, and undersampling was implemented retrospectively and prospectively by pseudorandomly omitting a fraction of the spiral interleaves. Undersampled data were reconstructed with both LRMC and a conventional inverse nonuniform fast Fourier transform (iNUFFT) and compared with fully sampled data. Two-fold undersampling with LRMC reconstruction enabled a two-fold improvement in temporal or spatial resolution without significant artifacts or spatiotemporal distortion. Conversely, undersampling with iNUFFT reconstruction created strong artifacts that obscured the image. LRMC performed better at time points with strong metabolite signal. Incoherent undersampling and LRMC provides a way to increase the spatiotemporal resolution of spiral CSI without degrading data integrity. Magn Reson Med 77:951-960, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  17. Runoff potentiality of a watershed through SCS and functional data analysis technique.

    PubMed

    Adham, M I; Shirazi, S M; Othman, F; Rahman, S; Yusop, Z; Ismail, Z

    2014-01-01

    Runoff potentiality of a watershed was assessed based on identifying curve number (CN), soil conservation service (SCS), and functional data analysis (FDA) techniques. Daily discrete rainfall data were collected from weather stations in the study area and analyzed through lowess method for smoothing curve. As runoff data represents a periodic pattern in each watershed, Fourier series was introduced to fit the smooth curve of eight watersheds. Seven terms of Fourier series were introduced for the watersheds 5 and 8, while 8 terms of Fourier series were used for the rest of the watersheds for the best fit of data. Bootstrapping smooth curve analysis reveals that watersheds 1, 2, 3, 6, 7, and 8 are with monthly mean runoffs of 29, 24, 22, 23, 26, and 27 mm, respectively, and these watersheds would likely contribute to surface runoff in the study area. The purpose of this study was to transform runoff data into a smooth curve for representing the surface runoff pattern and mean runoff of each watershed through statistical method. This study provides information of runoff potentiality of each watershed and also provides input data for hydrological modeling.

  18. Runoff Potentiality of a Watershed through SCS and Functional Data Analysis Technique

    PubMed Central

    Adham, M. I.; Shirazi, S. M.; Othman, F.; Rahman, S.; Yusop, Z.; Ismail, Z.

    2014-01-01

    Runoff potentiality of a watershed was assessed based on identifying curve number (CN), soil conservation service (SCS), and functional data analysis (FDA) techniques. Daily discrete rainfall data were collected from weather stations in the study area and analyzed through lowess method for smoothing curve. As runoff data represents a periodic pattern in each watershed, Fourier series was introduced to fit the smooth curve of eight watersheds. Seven terms of Fourier series were introduced for the watersheds 5 and 8, while 8 terms of Fourier series were used for the rest of the watersheds for the best fit of data. Bootstrapping smooth curve analysis reveals that watersheds 1, 2, 3, 6, 7, and 8 are with monthly mean runoffs of 29, 24, 22, 23, 26, and 27 mm, respectively, and these watersheds would likely contribute to surface runoff in the study area. The purpose of this study was to transform runoff data into a smooth curve for representing the surface runoff pattern and mean runoff of each watershed through statistical method. This study provides information of runoff potentiality of each watershed and also provides input data for hydrological modeling. PMID:25152911

  19. The RAMANITA © method for non-destructive and in situ semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts

    NASA Astrophysics Data System (ADS)

    Smith, David C.

    2005-08-01

    The "RAMANITA ©" method, for semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts and mathematical calculation by simultaneous equations, is published here in detail in English for the first time. It was conceived by the present writer 20 years ago for binary and ternary pyroxene and garnet systems. The mathematical description was set out in 1989, but in an abstract in an obscure French special publication. Detailed "step-by-step" calibration of two garnet ternaries, followed by their linking, by M. Pinet and D.C. Smith in the early 1990s provided a hexary garnet database. Much later, using this garnet database, which forms part of his personal database called RAMANITA ©, the present writer began to develop the method by improving the terminology, automating the calculations, discussing problems and experimenting with different real chemical problems in archaeometry. Although this RAMANITA © method has been very briefly mentioned in two recent books, the necessary full mathematical explanation is given only here. The method will find application in any study which requires obtaining a non-destructive semi-quantitative chemical analysis from mineral solid solutions that cannot be analysed by any destructive analytical method, in particular for archaeological, geological or extraterrestrial research projects, e.g. from gemstones or other crystalline artworks of the cultural heritage (especially by Mobile Raman Microscopy (MRM)) in situ in museums or at archaeological sites, including under water for subaquatic archaeometry; from scientifically precious mineral microinclusions (such as garnet or pyroxene within diamond); from minerals in rocks analysed in situ on planetary bodies by a rover (especially "at distance" by telescopy). Recently some other workers have begun deducing chemical compositions from Raman wavenumber shifts in multivariate chemical space, but the philosophical approach is

  20. The HSP90 binding mode of a radicicol-like E-oxime from docking, binding free energy estimations, and NMR 15N chemical shifts

    PubMed Central

    Spichty, Martin; Taly, Antoine; Hagn, Franz; Kessler, Horst; Barluenga, Sofia; Winssinger, Nicolas; Karplus, Martin

    2009-01-01

    We determine the binding mode of a macrocyclic radicicol-like oxime to yeast HSP90 by combining computer simulations and experimental measurements. We sample the macrocyclic scaffold of the unbound ligand by parallel tempering simulations and dock the most populated conformations to yeast HSP90. Docking poses are then evaluated by the use of binding free energy estimations with the linear interaction energy method. Comparison of QM/MM-calculated NMR chemical shifts with experimental shift data for a selective subset of back-bone 15N provides an additional evaluation criteria. As a last test we check the binding modes against available structure-activity-relationships. We find that the most likely binding mode of the oxime to yeast HSP90 is very similar to the known structure of the radicicol-HSP90 complex. PMID:19482409

  1. Comparison of the substituent effects on the (13) C NMR with the (1) H NMR chemical shifts of CH=N in substituted benzylideneanilines.

    PubMed

    Wang, Linyan; Cao, Chaotun; Cao, Chenzhong

    2015-07-01

    Fifty-two samples of substituted benzylideneanilines XPhCH=NPhYs (XBAYs) were synthesized, and their NMR spectra were determined in this paper. Together with the NMR data of other 77 samples of XBAYs quoted from literatures, the (1) H NMR chemical shifts (δH (CH=N)) and (13) C NMR chemical shifts (δC (CH=N)) of the CH=N bridging group were investigated for total of 129 samples of XBAYs. The result shows that the δH (CH=N) and δC (CH=N) have no distinctive linear relationship, which is contrary to the theoretical thought that declared the δH (CH=N) values would increase as the δC (CH=N) values increase. With the in-depth analysis, we found that the effects of σF and σR of X/Y group on the δH (CH=N) and the δC (CH=N) are opposite; the effects of the substituent specific cross-interaction effect between X and Y (Δσ(2) ) on the δH (CH=N) and the δC (CH=N) are different; the contributions of parameters in the regression equations of the δH (CH=N) and the δC (CH=N) [Eqns and 7), respectively] also have an obvious difference. Copyright © 2015 John Wiley & Sons, Ltd.

  2. Arginine Interactions with Anatase TiO2 (100) Surface and the Perturbation of 49Ti NMR Chemical Shifts - A DFT Investigation: Relevance to Renu-Seeram Bio Solar Cell

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Koch, Rainer; Lipton, Andrew S.; Filipek, S.

    2011-06-01

    Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured 49Ti NMR chemical shifts of anatase. Significant binding of arginine through electrostatic interaction and hydrogen bonds of the arginine guanidinium protons to the TiO2 surface oxygen atoms is observed, allowing attachment of proteins to titania surfaces in the construction of bio-sensitized solar cells. GIAO-B3LYP/6-31G(d) NMR calculation of a three-layer model based on the experimental structure of this TiO2 modification gives an excellent reproduction of the experimental value (-927 ppm) within +/- 7more » ppm, however, the change in relative chemical shifts, EFGs and CSA suggest that the effect of the electrostatic arginine binding might be too small for experimental detection.« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sevelsted, Tine F.; Herfort, Duncan; Skibsted, Jørgen, E-mail: jskib@chem.au.dk

    2013-10-15

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

  4. Backbone chemical shift assignments for the sensor domain of the Burkholderia pseudomallei histidine kinase RisS: "missing" resonances at the dimer interface.

    PubMed

    Buchko, Garry W; Edwards, Thomas E; Hewitt, Stephen N; Phan, Isabelle Q H; Van Voorhis, Wesley C; Miller, Samuel I; Myler, Peter J

    2015-10-01

    Using a deuterated sample, all the observable backbone (1)H(N), (15)N, (13)C(a), and (13)C' chemical shifts for the dimeric, periplasmic sensor domain of the Burkholderia pseudomallei histidine kinase RisS were assigned. Approximately one-fifth of the amide resonances are "missing" in the (1)H-(15)N HSQC spectrum and map primarily onto α-helices at the dimer interface observed in a crystal structure suggesting this region either undergoes intermediate timescale motion (μs-ms) and/or is heterogeneous.

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

    PubMed

    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.

  6. Principal component analysis of chemical shift perturbation data of a multiple-ligand-binding system for elucidation of respective binding mechanism.

    PubMed

    Konuma, Tsuyoshi; Lee, Young-Ho; Goto, Yuji; Sakurai, Kazumasa

    2013-01-01

    Chemical shift perturbations (CSPs) in NMR spectra provide useful information about the interaction of a protein with its ligands. However, in a multiple-ligand-binding system, determining quantitative parameters such as a dissociation constant (K(d) ) is difficult. Here, we used a method we named CS-PCA, a principal component analysis (PCA) of chemical shift (CS) data, to analyze the interaction between bovine β-lactoglobulin (βLG) and 1-anilinonaphthalene-8-sulfonate (ANS), which is a multiple-ligand-binding system. The CSP on the binding of ANS involved contributions from two distinct binding sites. PCA of the titration data successfully separated the CSP pattern into contributions from each site. Docking simulations based on the separated CSP patterns provided the structures of βLG-ANS complexes for each binding site. In addition, we determined the K(d) values as 3.42 × 10⁻⁴ M² and 2.51 × 10⁻³ M for Sites 1 and 2, respectively. In contrast, it was difficult to obtain reliable K(d) values for respective sites from the isothermal titration calorimetry experiments. Two ANS molecules were found to bind at Site 1 simultaneously, suggesting that the binding occurs cooperatively with a partial unfolding of the βLG structure. On the other hand, the binding of ANS to Site 2 was a simple attachment without a significant conformational change. From the present results, CS-PCA was confirmed to provide not only the positions and the K(d) values of binding sites but also information about the binding mechanism. Thus, it is anticipated to be a general method to investigate protein-ligand interactions. Copyright © 2012 Wiley Periodicals, Inc.

  7. 1H NMR spectra. Part 30(+): 1H chemical shifts in amides and the magnetic anisotropy, electric field and steric effects of the amide group.

    PubMed

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

    2013-03-01

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

  8. Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

    PubMed

    Estes, Deven P; Gordon, Christopher P; Fedorov, Alexey; Liao, Wei-Chih; Ehrhorn, Henrike; Bittner, Celine; Zier, Manuel Luca; Bockfeld, Dirk; Chan, Ka Wing; Eisenstein, Odile; Raynaud, Christophe; Tamm, Matthias; Copéret, Christophe

    2017-12-06

    Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH 3 ) 3-x (CF 3 ) x } 3 ] (MoF 0 , x = 0; MoF 3 , x = 1; MoF 6 , x = 2; MoF 9 , x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The 13 C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF 0 < MoF 3 < MoF 6 before sharply decreasing for MoF 9 , with a similar effect for the supported systems (MoF 0 ≈ MoF 9 < MoF 6 < MoF 3 ). This is consistent with the different kinetic behavior (zeroth order in alkyne for MoF 9 derivatives instead of first order for the others) and the isolation of stable metallacyclobutadiene intermediates of MoF 9 for both molecular and supported species. Detailed solid-state NMR analysis of molecular and silica-supported metal alkylidyne catalysts coupled with DFT/ZORA calculations rationalize the NMR spectroscopic signatures and discernible activity trends at the frontier orbital level: (1) increasing the number of fluorine atoms lowers the energy of the π*(M≡C) orbital, explaining the more deshielded chemical shift values; it also leads to an increased electrophilicity and higher reactivity for catalysts up to MoF 6 , prior to a sharp decrease in reactivity for MoF 9 due to the formation of stable metallacyclobutadiene intermediates; (2) the silica-supported catalysts are less active than their molecular analogues because they are less electrophilic and dynamic, as revealed by their 13 C NMR chemical shift tensors.

  9. Fatigue Crack Growth and Crack Bridging in SCS-6/Ti-24-11

    NASA Technical Reports Server (NTRS)

    Ghosn, Louis J.; Kantzos, Pete; Telesman, Jack

    1995-01-01

    Interfacial damage induced by relative fiber/matrix sliding was found to occur in the bridged zone of unidirectional SCS-6/Ti-24Al-11Nb intermetallic matrix composite specimens subjected to fatigue crack growth conditions. The degree of interfacial damage was not uniform along the bridged crack wake. Higher damage zones were observed near the machined notch in comparison to the crack tip. The interfacial friction shear strength tau(sub f) measured in the crack wake using pushout testing revealed lower values than the as-received interface. Interfacial wear also reduced the strength of the bridging fibers. The reduction in fiber strength is thought to be a function of the magnitude of relative fiber/matrix displacements ind the degree of interfacial damage. Furthermore, two different fiber bridging models were used to predict the influence of bridging on the fatigue crack driving force. The shear lag model required a variable tau(sub f) in the crack wake (reflecting the degradation of the interface) before its predictions agreed with trends exhibited by the experimental data. The fiber pressure model did an excellent job in predicting both the FCG data and the DeltaCOD in the bridged zone even though it does not require a knowledge of tau(sub f).

  10. Atomic contributions from spin-orbit coupling to 29Si NMR chemical shifts in metallasilatrane complexes.

    PubMed

    Autschbach, Jochen; Sutter, Kiplangat; Truflandier, Lionel A; Brendler, Erica; Wagler, Jörg

    2012-10-01

    New members of a novel class of metallasilatrane complexes [X-Si-(μ-mt)(4)-M-Y], with M=Ni, Pd, Pt, X=F, Cl, Y=Cl, Br, I, and mt=2-mercapto-1-methylimidazolide, have been synthesized and characterized structurally by X-ray diffraction and by (29)Si solid-state NMR. Spin-orbit (SO) effects on the (29)Si chemical shifts induced by the metal, by the sulfur atoms in the ligand, and by heavy halide ligands Y=Cl, Br, I were investigated with the help of relativistic density functional calculations. Operators used in the calculations were constructed such that SO coupling can selectively be switched off for certain atoms. The unexpectedly large SO effects on the (29)Si shielding in the Ni complex with X=Y=Cl reported recently originate directly from the Ni atom, not from other moderately heavy atoms in the complex. With respect to Pd, SO effects are amplified for Ni owing to its smaller ligand-field splitting, despite the smaller nuclear charge. In the X=Cl, Y=Cl, Br, I series of complexes the Y ligand strongly modulates the (29)Si shift by amplifying or suppressing the metal SO effects. The pronounced delocalization of the partially covalent M←Y bond plays an important role in modulating the (29)Si shielding. We also demonstrate an influence from the X ligand on the (29)Si SO shielding contributions originating at Y. The NMR spectra for [X-Si-(μ-mt)(4)-M-Y] must be interpreted mainly based on electronic and relativistic effects, rather than structural differences between the complexes. The results highlight the sometimes unintuitive role of SO coupling in NMR spectra of complexes containing heavy atoms. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed

    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.

  12. Dynamics-based selective 2D 1H/1H chemical shift correlation spectroscopy under ultrafast MAS conditions

    NASA Astrophysics Data System (ADS)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-05-01

    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 1H 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 1H/1H 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.

  13. Inner-shell chemical shift of DNA/RNA bases and inheritance from their parent purine and pyrimidine.

    PubMed

    Wang, Feng; Zhu, Quan; Ivanova, Elena

    2008-11-01

    Inner-shell electronic structures, properties and ionization spectra of DNA/RNA bases are studied with respect to their parent pyrimidine and purine species. Density functional theory B3LYP/aug-cc-pVTZ has been employed to produce the geometries of the bases, whereas LB94/et-pVQZ//B3LYP/aug-cc-pVTZ is used to calculate site-related Hirshfeld charges and core (vertical) ionization energies, as well as inner-shell spectra of C1s, N1s and O1s for DNA/RNA bases and their parent pyrimidine and purine species. The site-dependent variations of properties indicate the changes and inheritance of chemical environment when pyrimidine and purine become substituted. In general, although the changes are site-dependent, they are also ring-dependent. Pyrimidine bases change less significantly with respect to their parent pyrimidine than the purine bases with respect to their parent purine. Pyrimidine bases such as uracil, thymine and cytosine inherit certain properties from their parent pyrimidine, such as the Hirshfeld charge distributions and the order of core ionization energy level etc. No particular sites in the pyrimidine derivatives are engaged with a dramatic chemical shift nor with energy crossings to other sites. For the core shell spectra, the purine bases inherit very little from their parent purine, and guanine exhibits the least similarities to the parent among all the DNA/RNA bases.

  14. Hybrid quantitative MRI using chemical shift displacement and recovery-based simultaneous water and lipid imaging: A preliminary study.

    PubMed

    Ohno, Naoki; Miyati, Tosiaki; Suzuki, Shuto; Kan, Hirohito; Aoki, Toshitaka; Nakamura, Yoshitaka; Hiramatsu, Yuki; Kobayashi, Satoshi; Gabata, Toshifumi

    2018-07-01

    To suppress olefinic signals and enable simultaneous and quantitative estimation of multiple functional parameters associated with water and lipid, we investigated a modified method using chemical shift displacement and recovery-based separation of lipid tissue (SPLIT) involving acquisitions with different inversion times (TIs), echo times (TEs), and b-values. Single-shot diffusion echo-planar imaging (SSD-EPI) with multiple b-values (0-3000 s/mm 2 ) was performed without fat suppression to separate water and lipid images using the chemical shift displacement of lipid signals in the phase-encoding direction. An inversion pulse (TI = 292 ms) was applied to SSD-EPI to remove olefinic signals. Consecutively, SSD-EPI (b = 0 s/mm 2 ) was performed with TI = 0 ms and TE = 31.8 ms for T 1 and T 2 measurements, respectively. Under these conditions, transverse water and lipid images at the maximum diameter of the right calf were obtained in six healthy subjects. T 1 , T 2 , and the apparent diffusion coefficients (ADC) were then calculated for the tibialis anterior (TA), gastrocnemius (GM), and soleus (SL) muscles, tibialis bone marrow (TB), and subcutaneous fat (SF). Perfusion-related (D*) and restricted diffusion coefficients (D) were calculated for the muscles. Lastly, the lipid fractions (LF) of the muscles were determined after T 1 and T 2 corrections. The modified SPLIT method facilitated sufficient separation of water and lipid images of the calf, and the inversion pulse with TI of 292 ms effectively suppressed olefinic signals. All quantitative parameters obtained with the modified SPLIT method were found to be in general agreement with those previously reported in the literature. The modified SPLIT technique enabled sufficient suppression of olefinic signals and simultaneous acquisition of quantitative parameters including diffusion, perfusion, T 1 and T 2 relaxation times, and LF. Copyright © 2018. Published by Elsevier Inc.

  15. Calcium-43 chemical shift and electric field gradient tensor interplay: a sensitive probe of structure, polymorphism, and hydration.

    PubMed

    Widdifield, Cory M; Moudrakovski, Igor; Bryce, David L

    2014-07-14

    Calcium is the 5th most abundant element on earth, and is found in numerous biological tissues, proteins, materials, and increasingly in catalysts. However, due to a number of unfavourable nuclear properties, such as a low magnetogyric ratio, very low natural abundance, and its nuclear electric quadrupole moment, development of solid-state (43)Ca NMR has been constrained relative to similar nuclides. In this study, 12 commonly-available calcium compounds are analyzed via(43)Ca solid-state NMR and the information which may be obtained by the measurement of both the (43)Ca electric field gradient (EFG) and chemical shift tensors (the latter of which are extremely rare with only a handful of literature examples) is discussed. Combined with density functional theory (DFT) computations, this 'tensor interplay' is, for the first time for (43)Ca, illustrated to be diagnostic in distinguishing polymorphs (e.g., calcium formate), and the degree of hydration (e.g., CaCl2·2H2O and calcium tartrate tetrahydrate). For Ca(OH)2, we outline the first example of (1)H to (43)Ca cross-polarization on a sample at natural abundance in (43)Ca. Using prior knowledge of the relationship between the isotropic calcium chemical shift and the calcium quadrupolar coupling constant (CQ) with coordination number, we postulate the coordination number in a sample of calcium levulinate dihydrate, which does not have a known crystal structure. Natural samples of CaCO3 (aragonite polymorph) are used to show that the synthetic structure is present in nature. Gauge-including projector augmented-wave (GIPAW) DFT computations using accepted crystal structures for many of these systems generally result in calculated NMR tensor parameters which are in very good agreement with the experimental observations. This combination of (43)Ca NMR measurements with GIPAW DFT ultimately allows us to establish clear correlations between various solid-state (43)Ca NMR observables and selected structural parameters

  16. Sensitivity of Chemical Shift-Encoded Fat Quantification to Calibration of Fat MR Spectrum

    PubMed Central

    Wang, Xiaoke; Hernando, Diego; Reeder, Scott B.

    2015-01-01

    Purpose To evaluate the impact of different fat spectral models on proton density fat-fraction (PDFF) quantification using chemical shift-encoded (CSE) MRI. Material and Methods Simulations and in vivo imaging were performed. In a simulation study, spectral models of fat were compared pairwise. Comparison of magnitude fitting and mixed fitting was performed over a range of echo times and fat fractions. In vivo acquisitions from 41 patients were reconstructed using 7 published spectral models of fat. T2-corrected STEAM-MRS was used as reference. Results Simulations demonstrate that imperfectly calibrated spectral models of fat result in biases that depend on echo times and fat fraction. Mixed fitting is more robust against this bias than magnitude fitting. Multi-peak spectral models showed much smaller differences among themselves than when compared to the single-peak spectral model. In vivo studies show all multi-peak models agree better (for mixed fitting, slope ranged from 0.967–1.045 using linear regression) with reference standard than the single-peak model (for mixed fitting, slope=0.76). Conclusion It is essential to use a multi-peak fat model for accurate quantification of fat with CSE-MRI. Further, fat quantification techniques using multi-peak fat models are comparable and no specific choice of spectral model is shown to be superior to the rest. PMID:25845713

  17. Understanding and controlling chromaticity shift in LED devices

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Davis, Lynn; Mills, Karmann; Lamvik, Michael

    Chromaticity shift in light-emitting diode (LED) devices arises from multiple mechanisms, and at least five different chromaticity shift modes (CSMs) have been identified to date. This paper focuses on the impacts of irreversible phosphor degradation as a cause of chromaticity shifts in LED devices. The nitride phosphors used to produce warm white LEDs are especially vulnerable to degradation due to thermal and chemical effects such as reactions with oxygen and water. As a result, LED devices utilizing these phosphors were found to undergo either a green shift or, less commonly, a red shift depending on the phosphor mix in themore » LED devices. These types of chromaticity shifts are classified as CSM-2 (green shift) and CSM-5 (red shift). This paper provides an overview of the kinetic processes responsible for green and red chromaticity shifts along with examples from accelerated stress testing of 6” downlights. Both CSMs appear to proceed through analogous mechanisms that are initiated at the surface of the phosphor. A green shift is produced by the surface oxidation of the nitride phosphor that changes the emission profile to lower wavelengths. As the surface oxidation reaction proceeds, reactant limitations slow the rate and bulk oxidation processes become more prevalent. We found that a red chromaticity shift arises from quenching of the green phosphor, also possibly due to surface reactions of oxygen, which shift the emission chromaticity in the red direction. In conclusion, we discuss the implications of these findings on projecting chromaticity.« less

  18. A Long-Gap Peripheral Nerve Injury Therapy Using Human Skeletal Muscle-Derived Stem Cells (Sk-SCs): An Achievement of Significant Morphological, Numerical and Functional Recovery

    PubMed Central

    Hirata, Maki; Nakajima, Nobuyuki; Saito, Kosuke; Hashimoto, Hiroyuki; Soeda, Shuichi; Uchiyama, Yoshiyasu; Watanabe, Masahiko

    2016-01-01

    Losses in vital functions of the somatic motor and sensory nervous system are induced by severe long-gap peripheral nerve transection injury. In such cases, autologous nerve grafts are the gold standard treatment, despite the unavoidable sacrifice of other healthy functions, whereas the prognosis is not always favorable. Here, we use human skeletal muscle-derived stem cells (Sk-SCs) to reconstitute the function after long nerve-gap injury. Muscles samples were obtained from the amputated legs from 9 patients following unforeseen accidents. The Sk-SCs were isolated using conditioned collagenase solution, and sorted as CD34+/45- (Sk-34) and CD34-/45-/29+ (Sk-DN/29+) cells. Cells were separately cultured/expanded under optimal conditions for 2 weeks, then injected into the athymic nude mice sciatic nerve long-gap model (7-mm) bridging an acellular conduit. After 8–12 weeks, active cell engraftment was observed only in the Sk-34 cell transplanted group, showing preferential differentiation into Schwann cells and perineurial/endoneurial cells, as well as formation of the myelin sheath and perineurium/endoneurium surrounding regenerated axons, resulted in 87% of numerical recovery. Differentiation into vascular cell lineage (pericyte and endothelial cells) were also observed. A significant tetanic tension recovery (over 90%) of downstream muscles following electrical stimulation of the sciatic nerve (at upper portion of the gap) was also achieved. In contrast, Sk-DN/29+ cells were completely eliminated during the first 4 weeks, but relatively higher numerical (83% vs. 41% in axon) and functional (80% vs. 60% in tetanus) recovery than control were observed. Noteworthy, significant increase in the formation of vascular networks in the conduit during the early stage (first 2 weeks) of recovery was observed in both groups with the expression of key factors (mRNA and protein levels), suggesting the paracrine effects to angiogenesis. These results suggested that the human Sk-SCs

  19. A Long-Gap Peripheral Nerve Injury Therapy Using Human Skeletal Muscle-Derived Stem Cells (Sk-SCs): An Achievement of Significant Morphological, Numerical and Functional Recovery.

    PubMed

    Tamaki, Tetsuro; Hirata, Maki; Nakajima, Nobuyuki; Saito, Kosuke; Hashimoto, Hiroyuki; Soeda, Shuichi; Uchiyama, Yoshiyasu; Watanabe, Masahiko

    2016-01-01

    Losses in vital functions of the somatic motor and sensory nervous system are induced by severe long-gap peripheral nerve transection injury. In such cases, autologous nerve grafts are the gold standard treatment, despite the unavoidable sacrifice of other healthy functions, whereas the prognosis is not always favorable. Here, we use human skeletal muscle-derived stem cells (Sk-SCs) to reconstitute the function after long nerve-gap injury. Muscles samples were obtained from the amputated legs from 9 patients following unforeseen accidents. The Sk-SCs were isolated using conditioned collagenase solution, and sorted as CD34+/45- (Sk-34) and CD34-/45-/29+ (Sk-DN/29+) cells. Cells were separately cultured/expanded under optimal conditions for 2 weeks, then injected into the athymic nude mice sciatic nerve long-gap model (7-mm) bridging an acellular conduit. After 8-12 weeks, active cell engraftment was observed only in the Sk-34 cell transplanted group, showing preferential differentiation into Schwann cells and perineurial/endoneurial cells, as well as formation of the myelin sheath and perineurium/endoneurium surrounding regenerated axons, resulted in 87% of numerical recovery. Differentiation into vascular cell lineage (pericyte and endothelial cells) were also observed. A significant tetanic tension recovery (over 90%) of downstream muscles following electrical stimulation of the sciatic nerve (at upper portion of the gap) was also achieved. In contrast, Sk-DN/29+ cells were completely eliminated during the first 4 weeks, but relatively higher numerical (83% vs. 41% in axon) and functional (80% vs. 60% in tetanus) recovery than control were observed. Noteworthy, significant increase in the formation of vascular networks in the conduit during the early stage (first 2 weeks) of recovery was observed in both groups with the expression of key factors (mRNA and protein levels), suggesting the paracrine effects to angiogenesis. These results suggested that the human Sk-SCs

  20. The Projection Analysis of NMR Chemical Shifts Reveals Extended EPAC Autoinhibition Determinants

    PubMed Central

    Selvaratnam, Rajeevan; VanSchouwen, Bryan; Fogolari, Federico; Mazhab-Jafari, Mohammad T.; Das, Rahul; Melacini, Giuseppe

    2012-01-01

    EPAC is a cAMP-dependent guanine nucleotide exchange factor that serves as a prototypical molecular switch for the regulation of essential cellular processes. Although EPAC activation by cAMP has been extensively investigated, the mechanism of EPAC autoinhibition is still not fully understood. The steric clash between the side chains of two conserved residues, L273 and F300 in EPAC1, has been previously shown to oppose the inactive-to-active conformational transition in the absence of cAMP. However, it has also been hypothesized that autoinhibition is assisted by entropic losses caused by quenching of dynamics that occurs if the inactive-to-active transition takes place in the absence of cAMP. Here, we test this hypothesis through the comparative NMR analysis of several EPAC1 mutants that target different allosteric sites of the cAMP-binding domain (CBD). Using what to our knowledge is a novel projection analysis of NMR chemical shifts to probe the effect of the mutations on the autoinhibition equilibrium of the CBD, we find that whenever the apo/active state is stabilized relative to the apo/inactive state, dynamics are consistently quenched in a conserved loop (β2-β3) and helix (α5) of the CBD. Overall, our results point to the presence of conserved and nondegenerate determinants of CBD autoinhibition that extends beyond the originally proposed L273/F300 residue pair, suggesting that complete activation necessitates the simultaneous suppression of multiple autoinhibitory mechanisms, which in turn confers added specificity for the cAMP allosteric effector. PMID:22325287

  1. Benchmarking of density functionals for a soft but accurate prediction and assignment of (1) H and (13)C NMR chemical shifts in organic and biological molecules.

    PubMed

    Benassi, Enrico

    2017-01-15

    A number of programs and tools that simulate 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts using empirical approaches are available. These tools are user-friendly, but they provide a very rough (and sometimes misleading) estimation of the NMR properties, especially for complex systems. Rigorous and reliable ways to predict and interpret NMR properties of simple and complex systems are available in many popular computational program packages. Nevertheless, experimentalists keep relying on these "unreliable" tools in their daily work because, to have a sufficiently high accuracy, these rigorous quantum mechanical methods need high levels of theory. An alternative, efficient, semi-empirical approach has been proposed by Bally, Rablen, Tantillo, and coworkers. This idea consists of creating linear calibrations models, on the basis of the application of different combinations of functionals and basis sets. Following this approach, the predictive capability of a wider range of popular functionals was systematically investigated and tested. The NMR chemical shifts were computed in solvated phase at density functional theory level, using 30 different functionals coupled with three different triple-ζ basis sets. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  2. Anxiety about starting three-shift work among female workers: findings from the Female Shift Workers' Health Study.

    PubMed

    Kubo, Tatsuhiko; Maruyama, Takashi; Shirane, Kiyoyumi; Otomo, Hajime; Matsumoto, Tetsuro; Oyama, Ichiro

    2008-03-01

    In 1999, the Japanese Law on Equal Employment Opportunity and Conditions was amended and the previous prohibition of the assignment of female workers to night work was abolished. Subsequently, the number of female shift workers has been increasing in Japan, necessitating greater attention to the health care of this population. The aim of the current study is to evaluate the relationship between anxiety expressed about starting three-shift work and background characteristics among female workers who were being assigned to three-shift work for the first time. The subjects were 38 middle-aged female workers (age range: 44 to 59 years) who were working at a chemical plant. The women completed a self-administered questionnaire before starting three-shift work. Levels of anxiety about starting three-shift work were assessed by the question 'Do you feel anxious about starting three-shift work?' The available responses were: 'Very agree', 'Considerably agree', 'Rather agree', 'Slightly agree' and 'Not agree at all', and 63% of the subjects gave one of the first two answers, which were defined as indicating anxiety. We also acquired information regarding lifestyle and occupation for each subject, including the following factors: frequency of breakfast consumption, subjective sleep insufficiency, previous experience of similar work before beginning shift work, previous experience of two-shift work, and responsibility for household duties. In the study, we found a marginally statistically significant trend association between frequent breakfast consumption and anxiety about starting three-shift work (P(trend) = 0.09). Anxiety was also high among subjects with sleep disorders, especially those suffering from subjective sleep insufficiency (P = 0.08). Due to the small study population, these results should be interpreted with caution and confirmed by future studies.

  3. Understanding the effect of watershed characteristic on the runoff using SCS curve number

    NASA Astrophysics Data System (ADS)

    Damayanti, Frieta; Schneider, Karl

    2015-04-01

    Runoff modeling is a key component in watershed management. The temporal course and amount of runoff is a complex function of a multitude of parameters such as climate, soil, topography, land use, and water management. Against the background of the current rapid environmental change, which is due to both i) man-made changes (e.g. urban development, land use change, water management) as well as ii) changes in the natural systems (e.g. climate change), understanding and predicting the impacts of these changes upon the runoff is very important and affects the wellbeing of many people living in the watershed. A main tool for predictions is hydrologic models. Particularly process based models are the method of choice to assess the impact of land use and climate change. However, many regions which experience large changes in the watersheds can be described as rather data poor, which limits the applicability of such models. This is particularly also true for the Telomoyo Watershed (545 km2) which is located in southern part of Central Java province. The average annual rainfall of the study area reaches 2971 mm. Irrigated paddy field are the dominating land use (35%), followed by built-up area and dry land agriculture. The only available soil map is the FAO soil digital map of the world, which provides rather general soil information. A field survey accompanied by a lab analysis 65 soil samples of was carried out to provide more detailed soil texture information. The soil texture map is a key input in the SCS method to define hydrological soil groups. In the frame of our study on 'Integrated Analysis on Flood Risk of Telomoyo Watershed in Response to the Climate and Land Use Change' funded by the German Academic Exchange service (DAAD) we analyzed the sensitivity of the modeled runoff upon the choice of the method to estimate the CN values using the SCS-CN method. The goal of this study is to analyze the impact of different data sources on the curve numbers and the

  4. Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

    PubMed

    Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

    2016-05-05

    Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes.

  5. Hepatic fat quantification using automated six-point Dixon: Comparison with conventional chemical shift based sequences and computed tomography.

    PubMed

    Shimizu, Kie; Namimoto, Tomohiro; Nakagawa, Masataka; Morita, Kosuke; Oda, Seitaro; Nakaura, Takeshi; Utsunomiya, Daisuke; Yamashita, Yasuyuki

    To compare automated six-point Dixon (6-p-Dixon) MRI comparing with dual-echo chemical-shift-imaging (CSI) and CT for hepatic fat fraction in phantoms and clinical study. Phantoms and fifty-nine patients were examined both MRI and CT for quantitative fat measurements. In phantom study, linear regression between fat concentration and 6-p-Dixon showed good agreement. In clinical study, linear regression between 6-p-Dixon and dual-echo CSI showed good agreement. CT attenuation value was strongly correlated with 6-p-Dixon (R 2 =0.852; P<0.001) and dual-echo CSI (R 2 =0.812; P<0.001). Automated 6-p-Dixon and dual-echo CSI were accurate correlation with CT attenuation value of liver parenchyma. 6-p-Dixon has the potential for automated hepatic fat quantification. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Polyaniline-Modified Oriented Graphene Hydrogel Film as the Free-Standing Electrode for Flexible Solid-State Supercapacitors.

    PubMed

    Du, Pengcheng; Liu, Huckleberry C; Yi, Chao; Wang, Kai; Gong, Xiong

    2015-11-04

    In this study, we report polyaniline (PANI)-modified oriented graphene hydrogel (OGH) films as the free-standing electrode for flexible solid-state supercapacitors (SCs). The OGH films are prepared by a facile filtration method using chemically converted graphene sheets and then introduced to PANI on the surface of OGH films by in situ chemical polymerization. The PANI-modified OGH films possess high flexibility, high electrical conductivity, and mechanical robustness. The flexible solid-state SCs based on the PANI-modified OGH films exhibit a specific capacitance of 530 F/g, keeping 80% of its original value up to 10 000 charge-discharge cycles at the current density of 10 A/g. Remarkably, the flexible solid-state SCs maintain ∼100% capacitance retention bent at 180° for 250 cycles. Moreover, the flexible solid-state SCs are further demonstrated to be able to light up a red-light-emitting diode. These results indicate that the flexible solid-state SCs based on PANI-modified OGH films as the free-standing electrode have potential applications as energy-storage devices.

  7. Bloch-Siegert shift in an interacting Bose-Einstein condensate

    NASA Astrophysics Data System (ADS)

    Zhang, Jinyi; Eigen, Christoph; Lopes, Raphael; Garratt, Sam; Rousso, David; Smith, Robert P.; Hadzibabic, Zoran; Navon, Nir

    2017-04-01

    The Bloch-Siegert shift (BSS) is a paradigmatic frequency shift that arises from the nonlinear response of a two-level system (TLS) subjected to strong driving fields. When a TLS is driven by a linearly polarized field, the co-rotating-wave component leads to the famous Rabi oscillations. By contrast the co-rotating-wave component, whose role is usually neglected in a weak driving, leads to a frequency shift of the TLS resonance frequency. This phenomenon is encountered in various areas, from quantum optics to nuclear magnetic resonance.Here, we investigate the BSS in a box-trapped 87 Rb Bose-Einstein condensate (BEC) driven by a strong oscillating magnetic field gradient. By tuning the chemical potential of the gas, we investigate how the BSS evolves from the ideal shift of the two lowest energy levels of a single particle in a box to the unexplored shift of long-wavelength collective excitations of the interacting BEC.

  8. Metabolites with Gram-negative bacteria quorum sensing inhibitory activity from the marine animal endogenic fungus Penicillium sp. SCS-KFD08.

    PubMed

    Kong, Fan Dong; Zhou, Li Man; Ma, Qing Yun; Huang, Sheng Zhuo; Wang, Pei; Dai, Hao Fu; Zhao, You Xing

    2017-01-01

    Three new compounds named penicitor A, aculene E and penicitor B, as well as four known compounds, were isolated from the fermentation broth of Penicillium sp. SCS-KFD08 associated with a marine animal Sipunculus nudus from the Haikou bay of China. Their planar structures and absolute configurations were unambiguously elucidated by spectroscopic data, Mosher's method, CD spectrum analysis along with quantum ECD calculation. Among them, compounds 2-7 showed quorum sensing inhibitory activity against Chromobacterium violaceum CV026, and could significantly reduce violacein production in N-hexanoyl-l-homoserine lactone (C6-HSL) induced C. violaceum CV026 cultures at sub-inhibitory concentrations.

  9. El Niño-related offshore phytoplankton bloom events around the Spratley Islands in the South China Sea

    NASA Astrophysics Data System (ADS)

    Isoguchi, Osamu; Kawamura, Hiroshi; Ku-Kassim, Ku-Yaacob

    2005-11-01

    Satellite chlorophyll-a (Chl-a) observations reveal offshore phytoplankton bloom events with high Chl-a (>1 mg m-3) spreading over 300 km off the coasts around the Spratley Islands in the South China Sea (SCS) during the spring of 1998. The bloom entails anomalous wind jet and sea surface temperature (SST) cooling, suggesting that the wind jet-induced mixing and/or offshore upwelling bring about the cooling and the bloom through the supply of nutrient-rich waters into the euphotic zone. The strong wind jet is orographically formed responding to shifts in wind direction over the eastern SCS. The wind shift is connected with the Philippine Sea anomalous anticyclone that is established during El Niño, indicating the El Niño-related offshore bloom. The long-term reanalysis winds over the eastern SCS demonstrates that wind jet formation and associated offshore cooling/bloom are expected to occur in most cases of the subsequent El Niño years.

  10. Motor vehicle collisions caused by the 'super-strength' synthetic cannabinoids, MAM-2201, 5F-PB-22, 5F-AB-PINACA, 5F-AMB and 5F-ADB in Japan experienced from 2012 to 2014.

    PubMed

    Kaneko, Shuji

    2017-01-01

    From 2012 to 2014 in Japan, 214 cases of motor vehicle collisions were attributed to the use of illegal drugs. In 93 out of 96 investigated cases, the causative agents were a variety of synthetic cannabinoids (SCs). These SCs can be classified into three groups according to the lineage of the chemical structures: (1) naphthoyl indoles, such as MAM-2201, (2) quinolinyl ester indoles, such as 5F-PB-22, and (3) indazole carboxamides, such as 5F-AB-PINACA, 5F-AMB, and 5F-ADB. These SCs became available sequentially with increasing cannabinoid CB 1 agonist potencies and reached a nationwide outbreak in the summer of 2014. They caused acute intoxication with impaired consciousness, anterograde amnesia (impaired memory), catalepsy with muscle rigidity, tachycardia, and vomiting or drooling soon after smoking. Drivers who had abused one of these SCs might unexpectedly experience the acute intoxication that caused uncontrolled driving. These SCs were generally difficult to detect from body fluid samples. It is thought that the highly lipophilic SCs disappear from the blood via rapid degradation by liver enzymes and selective accumulation into adipose tissues. Thus, much effort should be directed to the development of fast and sensitive chemical detection of the drug usage.

  11. Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate for dual biosensing of pH with chemical exchange saturation transfer (CEST) and biosensor imaging of redundant deviation in shifts (BIRDS).

    PubMed

    Huang, Yuegao; Coman, Daniel; Ali, Meser M; Hyder, Fahmeed

    2015-01-01

    Relaxivity-based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd(3+)) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the nonexchangeable or the exchangeable protons on the lanthanide complexes themselves. The nonexchangeable protons (e.g. -CHx, where 3 ≥ x ≥ 1) are detected using a three-dimensional chemical shift imaging method called biosensor imaging of redundant deviation in shifts (BIRDS), whereas the exchangeable protons (e.g. -OH or -NHy , where 2 ≥ y ≥ 1) are measured with chemical exchange saturation transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP(8-)) chelated with thulium (Tm(3+) ) and ytterbium (Yb(3+)). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e. 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP(5-) than with TmDOTA-4AmP(5-). In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging. Copyright © 2014 John Wiley & Sons, Ltd.

  12. Comment on “Beyond the SCS-CN method: A theoretical framework for spatially lumped rainfall-runoff response” by M.S. Bartlett, A.J. Parolari, J.J. McDonnell and A. Porporato

    USDA-ARS?s Scientific Manuscript database

    Bartlett et al. [2016] performed a re-interpretation and modification of the space-time lumped USDA NRCS (formerly SCS) Curve Number (CN) method to extend its applicability to forested watersheds. We believe that the well documented limitations of the CN method severely constrains the applicability ...

  13. Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel β-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.

    PubMed

    Yazawa, Koji; Suzuki, Furitsu; Nishiyama, Yusuke; Ohata, Takuya; Aoki, Akihiro; Nishimura, Katsuyuki; Kaji, Hironori; Shimizu, Tadashi; Asakura, Tetsuo

    2012-11-25

    The accurate (1)H positions of alanine tripeptide, A(3), with anti-parallel and parallel β-sheet structures could be determined by highly resolved (1)H DQMAS solid-state NMR spectra and (1)H chemical shift calculation with gauge-including projector augmented wave calculations.

  14. Microspectroscopy of spectral biomarkers associated with human corneal stem cells

    PubMed Central

    Nakamura, Takahiro; Kelly, Jemma G.; Trevisan, Júlio; Cooper, Leanne J.; Bentley, Adam J.; Carmichael, Paul L.; Scott, Andrew D.; Cotte, Marine; Susini, Jean; Martin-Hirsch, Pierre L.; Kinoshita, Shigeru; Martin, Francis L.

    2010-01-01

    Purpose Synchrotron-based radiation (SRS) Fourier-transform infrared (FTIR) microspectroscopy potentially provides novel biomarkers of the cell differentiation process. Because such imaging gives a “biochemical-cell fingerprint” through a cell-sized aperture, we set out to determine whether distinguishing chemical entities associated with putative stem cells (SCs), transit-amplifying (TA) cells, or terminally-differentiated (TD) cells could be identified in human corneal epithelium. Methods Desiccated cryosections (10 μm thick) of cornea on barium fluoride infrared transparent windows were interrogated using SRS FTIR microspectroscopy. Infrared analysis was performed through the acquisition of point spectra or image maps. Results Point spectra were subjected to principal component analysis (PCA) to identify distinguishing chemical entities. Spectral image maps to highlight SCs, TA cells, and TD cells of the cornea were then generated. Point spectrum analysis using PCA highlighted remarkable segregation between the three cell classes. Discriminating chemical entities were associated with several spectral differences over the DNA/RNA (1,425–900 cm−1) and protein/lipid (1,800–1480 cm−1) regions. Prominent biomarkers of SCs compared to TA cells and/or TD cells were 1,040 cm−1, 1,080 cm−1, 1,107 cm−1, 1,225 cm−1, 1,400 cm−1, 1,525 cm−1, 1,558 cm−1, and 1,728 cm−1. Chemical entities associated with DNA/RNA conformation (1,080 cm−1 and 1,225 cm−1) were associated with SCs, whereas protein/lipid biochemicals (1,558 cm−1 and 1,728 cm−1) most distinguished TA cells and TD cells. Conclusions SRS FTIR microspectroscopy can be employed to identify differential spectral biomarkers of SCs, TA cells, and/or TD cells in human cornea. This nondestructive imaging technology is a novel approach to characterizing SCs in situ. PMID:20520745

  15. Skin protection by sunscreens is improved by explicit labeling and providing free sunscreen.

    PubMed

    Nicol, Isabelle; Gaudy, Caroline; Gouvernet, Joanny; Richard, Marie A; Grob, Jean J

    2007-01-01

    Whatever the improvement in the protection spectrum of sunscreens (SCs), actual skin protection mainly depends on the way they are used, especially on the quantity applied. This prospective randomized study assessed how much sun protection factor (SPF) labeling, which is hardly understandable by a layman, and high cost account for misuse of SCs. In three beach resorts in France, 364 individuals were blindly randomized during their holidays to three arms (1) free SCs intervention (FS) = four types of SCs with their usual SPF label (60B-A, 20B-A, 12B-A, 6B-3A) at free disposal; (2) same free SCs with an explicit labeling (FNL), including sunburn protection, likely protection against long-term effects of UV, and possibility to get a tan; and (3) no intervention (NI). As compared to FS, FNL increased the quantity of SCs applied, mainly in the minority of people who were not "tan-seekers", reduced sunburns particularly in sun-sensitive individuals (25.6 vs 58.3%, P=0.005), and induced a shift in the level of SCs chosen. Free delivery SCs were associated with a more systematic application of SCs in case of exposure, and a decreased sunburn occurrence, without increase of exposure. These results suggest that a labeling more explicit for the public would result in a better protection in SC users and that cost could be a limiting factor to use SC as often as necessary.

  16. Solid-state (185/187)Re NMR and GIPAW DFT study of perrhenates and Re2(CO)10: chemical shift anisotropy, NMR crystallography, and a metal-metal bond.

    PubMed

    Widdifield, Cory M; Perras, Frédéric A; Bryce, David L

    2015-04-21

    Advances in solid-state nuclear magnetic resonance (SSNMR) methods, such as dynamic nuclear polarization (DNP), intricate pulse sequences, and increased applied magnetic fields, allow for the study of systems which even very recently would be impractical. However, SSNMR methods using certain quadrupolar probe nuclei (i.e., I > 1/2), such as (185/187)Re remain far from fully developed due to the exceedingly strong interaction between the quadrupole moment of these nuclei and local electric field gradients (EFGs). We present a detailed high-field (B0 = 21.1 T) experimental SSNMR study on several perrhenates (KReO4, AgReO4, Ca(ReO4)2·2H2O), as well as ReO3 and Re2(CO)10. We propose solid ReO3 as a new rhenium SSNMR chemical shift standard due to its reproducible and sharp (185/187)Re NMR resonances. We show that for KReO4, previously poorly understood high-order quadrupole-induced effects (HOQIE) on the satellite transitions can be used to measure the EFG tensor asymmetry (i.e., ηQ) to nearly an order-of-magnitude greater precision than competing SSNMR and nuclear quadrupole resonance (NQR) approaches. Samples of AgReO4 and Ca(ReO4)2·2H2O enable us to comment on the effects of counter-ions and hydration upon Re(vii) chemical shifts. Calcium-43 and (185/187)Re NMR tensor parameters allow us to conclude that two proposed crystal structures for Ca(ReO4)2·2H2O, which would be considered as distinct, are in fact the same structure. Study of Re2(CO)10 provides insights into the effects of Re-Re bonding on the rhenium NMR tensor parameters and rhenium oxidation state on the Re chemical shift value. As overtone NQR experiments allowed us to precisely measure the (185/187)Re EFG tensor of Re2(CO)10, we were able to measure rhenium chemical shift anisotropy (CSA) for the first time in a powdered sample. Experimental observations are supported by gauge-including projector augmented-wave (GIPAW) density functional theory (DFT) calculations, with NMR tensor calculations also

  17. Influence of mesh structure on 2D full shallow water equations and SCS Curve Number simulation of rainfall/runoff events

    NASA Astrophysics Data System (ADS)

    Caviedes-Voullième, Daniel; García-Navarro, Pilar; Murillo, Javier

    2012-07-01

    SummaryHydrological simulation of rain-runoff processes is often performed with lumped models which rely on calibration to generate storm hydrographs and study catchment response to rain. In this paper, a distributed, physically-based numerical model is used for runoff simulation in a mountain catchment. This approach offers two advantages. The first is that by using shallow-water equations for runoff flow, there is less freedom to calibrate routing parameters (as compared to, for example, synthetic hydrograph methods). The second, is that spatial distributions of water depth and velocity can be obtained. Furthermore, interactions among the various hydrological processes can be modeled in a physically-based approach which may depend on transient and spatially distributed factors. On the other hand, the undertaken numerical approach relies on accurate terrain representation and mesh selection, which also affects significantly the computational cost of the simulations. Hence, we investigate the response of a gauged catchment with this distributed approach. The methodology consists of analyzing the effects that the mesh has on the simulations by using a range of meshes. Next, friction is applied to the model and the response to variations and interaction with the mesh is studied. Finally, a first approach with the well-known SCS Curve Number method is studied to evaluate its behavior when coupled with a shallow-water model for runoff flow. The results show that mesh selection is of great importance, since it may affect the results in a magnitude as large as physical factors, such as friction. Furthermore, results proved to be less sensitive to roughness spatial distribution than to mesh properties. Finally, the results indicate that SCS-CN may not be suitable for simulating hydrological processes together with a shallow-water model.

  18. Chrodrimanins O-S from the fungus Penicillium sp. SCS-KFD09 isolated from a marine worm, Sipunculusnudus.

    PubMed

    Kong, Fan-Dong; Zhang, Ren-Shuai; Ma, Qing-Yun; Xie, Qing-Yi; Wang, Pei; Chen, Peng-Wei; Zhou, Li-Man; Dai, Hao-Fu; Luo, Du-Qiang; Zhao, You-Xing

    2017-10-01

    Five new meroterpenoids, chrodrimanins O-S (1-5), as well as a known one (6), were isolated from the fermentation broth of Penicillium sp. SCS-KFD09 isolated from a marine worm, Sipunculusnudus, from Haikou Bay, China. The structures including the absolute configurations of the new compounds were unambiguously elucidated by spectroscopic data and ECD spectra analysis along with quantum ECD calculations. Among them, compound 1 represents the first example of an unusual trichlorinated meroterpenoid with an unique dichlorine functionality. Compounds 1 and 4-6 displayed inhibitory activity of protein tyrosine phosphatase 1B (PTP1B) with IC 50 values of 71.6, 62.5, 63.1, and 39.6μM, respectively, and showed no apparent activity against three tumor cell lines (A549, HepG2, and Hela) and human umbilical vein endothelial cells (HUVEC) at 10μM. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Comparison of direct outflow calculated by modified SCS-CN methods for mountainous and highland catchments in upper Vistula Basin, Poland and lowland catchment in South Carolina, U.S.A

    Treesearch

    A. Walega; A. Cupak; D.M. Amatya; E. Drozdzal

    2017-01-01

    The aim of the study is to compare direct outflow from storm events estimated using modifications of original SCS-CN procedure. The study was conducted in a mountainous catchment of Kamienica River and a highland catchment draining Stobnica River located in Upper Vistula water region, both in Poland, and a headwater lowland watershed WS80 located at the Santee...

  20. 1H and 13C NMR Chemical Shift Assignments and Conformational Analysis for the Two Diastereomers of the Vitamin K Epoxide Reductase Inhibitor Brodifacoum

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cort, John R.; Cho, Herman M.

    2009-10-01

    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.

  1. Structural factors affecting 13C NMR chemical shifts of cellulose: a computational study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, Hui; Wang, Tuo; Oehme, Daniel

    Here, the doublet C4 peaks at ~ 85 and ~ 89 ppm in solid-state 13C NMR spectra of native cellulose have been attributed to signals of C4 atoms on the surface (solvent-exposed) and in the interior of microfibrils, designated as sC4 and iC4, respectively. The relative intensity ratios of sC4 and iC4 observed in NMR spectra of cellulose have been used to estimate the degree of crystallinity of cellulose and the number of glucan chains in cellulose microfibrils. However, the molecular structures of cellulose responsible for the specific surface and interior C4 peaks have not been positively confirmed. Using densitymore » functional theory (DFT) methods and structures produced from classical molecular dynamics simulations, we investigated how the following four factors affect 13C NMR chemical shifts in cellulose: conformations of exocyclic groups at C6 ( tg, gt and gg), H 2O molecules H-bonded on the surface of the microfibril, glycosidic bond angles (Φ, Ψ) and the distances between H4 and HO3 atoms. We focus on changes in the δ 13C4 value because it is the most significant observable for the same C atom within the cellulose structure. DFT results indicate that different conformations of the exocyclic groups at C6 have the greatest influence on δ 13C4 peak separation, while the other three factors have secondary effects that increase the spread of the calculated C4 interior and surface peaks.« less

  2. Structural factors affecting 13C NMR chemical shifts of cellulose: a computational study

    DOE PAGES

    Yang, Hui; Wang, Tuo; Oehme, Daniel; ...

    2017-11-02

    Here, the doublet C4 peaks at ~ 85 and ~ 89 ppm in solid-state 13C NMR spectra of native cellulose have been attributed to signals of C4 atoms on the surface (solvent-exposed) and in the interior of microfibrils, designated as sC4 and iC4, respectively. The relative intensity ratios of sC4 and iC4 observed in NMR spectra of cellulose have been used to estimate the degree of crystallinity of cellulose and the number of glucan chains in cellulose microfibrils. However, the molecular structures of cellulose responsible for the specific surface and interior C4 peaks have not been positively confirmed. Using densitymore » functional theory (DFT) methods and structures produced from classical molecular dynamics simulations, we investigated how the following four factors affect 13C NMR chemical shifts in cellulose: conformations of exocyclic groups at C6 ( tg, gt and gg), H 2O molecules H-bonded on the surface of the microfibril, glycosidic bond angles (Φ, Ψ) and the distances between H4 and HO3 atoms. We focus on changes in the δ 13C4 value because it is the most significant observable for the same C atom within the cellulose structure. DFT results indicate that different conformations of the exocyclic groups at C6 have the greatest influence on δ 13C4 peak separation, while the other three factors have secondary effects that increase the spread of the calculated C4 interior and surface peaks.« less

  3. Nuclear field shift in natural environments

    NASA Astrophysics Data System (ADS)

    Moynier, Frédéric; Fujii, Toshiyuki; Brennecka, Gregory A.; Nielsen, Sune G.

    2013-03-01

    The nuclear field shift (NFS) is an isotope shift in atomic energy levels caused by a combination of differences in nuclear size and shape and electron densities at the nucleus. The effect of NFS in isotope fractionation was theoretically established by Bigeleisen in 1996 [Bigeleisen J. (1996) J. Am. Chem. Soc. 118:3676-3680] and has been analytically measured in laboratory chemical exchange reactions. More recently, some isotopic variations of heavy elements (Hg, Tl, U) measured in natural systems as well as isotopic anomalies measured for lower-mass elements in meteorites have been attributed to the NFS effect. These isotopic variations open up new and exciting fields of investigations in Earth sciences. In this paper, we review the different natural systems in which NFS has been proposed to be the origin of isotopic variations.

  4. Quantification of liver fat with respiratory-gated quantitative chemical shift encoded MRI.

    PubMed

    Motosugi, Utaroh; Hernando, Diego; Bannas, Peter; Holmes, James H; Wang, Kang; Shimakawa, Ann; Iwadate, Yuji; Taviani, Valentina; Rehm, Jennifer L; Reeder, Scott B

    2015-11-01

    To evaluate free-breathing chemical shift-encoded (CSE) magnetic resonance imaging (MRI) for quantification of hepatic proton density fat-fraction (PDFF). A secondary purpose was to evaluate hepatic R2* values measured using free-breathing quantitative CSE-MRI. Fifty patients (mean age, 56 years) were prospectively recruited and underwent the following four acquisitions to measure PDFF and R2*; 1) conventional breath-hold CSE-MRI (BH-CSE); 2) respiratory-gated CSE-MRI using respiratory bellows (BL-CSE); 3) respiratory-gated CSE-MRI using navigator echoes (NV-CSE); and 4) single voxel MR spectroscopy (MRS) as the reference standard for PDFF. Image quality was evaluated by two radiologists. MRI-PDFF measured from the three CSE-MRI methods were compared with MRS-PDFF using linear regression. The PDFF and R2* values were compared using two one-sided t-test to evaluate statistical equivalence. There was no significant difference in the image quality scores among the three CSE-MRI methods for either PDFF (P = 1.000) or R2* maps (P = 0.359-1.000). Correlation coefficients (95% confidence interval [CI]) for the PDFF comparisons were 0.98 (0.96-0.99) for BH-, 0.99 (0.97-0.99) for BL-, and 0.99 (0.98-0.99) for NV-CSE. The statistical equivalence test revealed that the mean difference in PDFF and R2* between any two of the three CSE-MRI methods was less than ±1 percentage point (pp) and ±5 s(-1) , respectively (P < 0.046). Respiratory-gated CSE-MRI with respiratory bellows or navigator echo are feasible methods to quantify liver PDFF and R2* and are as valid as the standard breath-hold technique. © 2015 Wiley Periodicals, Inc.

  5. Shifts in priming partly explain impacts of long-term nitrogen input in different chemical forms on soil organic carbon storage.

    PubMed

    Song, Minghua; Guo, Yu; Yu, Feihai; Zhang, Xianzhou; Cao, Guangmin; Cornelissen, Johannes H C

    2018-05-10

    Input of labile organic carbon can enhance decomposition of extant soil organic carbon (SOC) through priming. We hypothesized that long-term nitrogen (N) input in different chemical forms alters SOC pools by altering priming effects associated with N-mediated changes in plants and soil microbes. The hypothesis was tested by integrating field experimental data of plants, soil microbes and two incubation experiments with soils that had experienced 10 years of N enrichment with three chemical forms (ammonium, nitrate and both ammonium and nitrate) in an alpine meadow on the Tibetan Plateau. Incubations with glucose- 13 C addition at three rates were used to quantify effects of exogenous organic carbon input on the priming of SOC. Incubations with microbial inocula extracted from soils that had experienced different long-term N treatments were conducted to detect effects of N-mediated changes in soil microbes on priming effects. We found strong evidence and a mechanistic explanation for alteration of SOC pools following 10 years of N enrichment with different chemical forms. We detected significant negative priming effects both in soils collected from ammonium-addition plots and in sterilized soils inoculated with soil microbes extracted from ammonium-addition plots. In contrast, significant positive priming effects were found both in soils collected from nitrate-addition plots and in sterilized soils inoculated with soil microbes extracted from nitrate-addition plots. Meanwhile, the abundance and richness of graminoids were higher and the abundance of soil microbes was lower in ammonium-addition than in nitrate-addition plots. Our findings provide evidence that shifts toward higher graminoid abundance and changes in soil microbial abundance mediated by N chemical forms are key drivers for priming effects and SOC pool changes, thereby linking human interference with the N cycle to climate change. © 2018 John Wiley & Sons Ltd.

  6. Backbone and sidechain methyl Ile (δ1), Leu and Val chemical shift assignments of RDE-4 (1-243), an RNA interference initiation protein in C. elegans.

    PubMed

    Chiliveri, Sai Chaitanya; Kumar, Sonu; Marelli, Udaya Kiran; Deshmukh, Mandar V

    2012-10-01

    The RNAi pathway of several organisms requires presence of double stranded RNA binding proteins for functioning of Dicer in gene regulation. In C. elegans, a double stranded RNA binding protein, RDE-4 (385 aa, 44 kDa) recognizes long exogenous dsRNA and initiates the RNAi pathway. We have achieved complete backbone and stereospecific methyl sidechain Ile (δ1), Leu and Val chemical shifts of first 243 amino acids of RDE-4, namely RDE-4ΔC.

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

    NASA Astrophysics Data System (ADS)

    Ebel, Andreas; Dreher, Wolfgang; Leibfritz, Dieter

    2000-02-01

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

  8. High intensity low temperature (HILT) performance of space concentrator GaInP/GaInAs/Ge MJ SCs

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shvarts, Maxim Z., E-mail: shvarts@scell.ioffe.ru; Kalyuzhnyy, Nikolay A.; Mintairov, Sergey A.

    2014-09-26

    In the work, the results of an investigation of GaInP/GaInAs/Ge MJ SCs intended for converting concentrated solar radiation, when operating at low temperatures (down to −190 °C) are presented. A kink of the cell I-V characteristic has been observed in the region close to V{sub oc} starting from −20°C at operation under concentrated sunlight. The causes for its occurrence have been analyzed and the reasons for formation of a built-in potential barrier for majority charge carriers at the n-GaInP/n-Ge isotype hetero-interface are discussed. The effect of charge carrier transport in n-GaInP/n-pGe heterostructures on MJ SC output characteristics at low temperaturesmore » has been studied including EL technique.« less

  9. Environmental enrichment accelerates ocular dominance plasticity in mouse visual cortex whereas transfer to standard cages resulted in a rapid loss of increased plasticity.

    PubMed

    Kalogeraki, Evgenia; Pielecka-Fortuna, Justyna; Löwel, Siegrid

    2017-01-01

    In standard cage (SC) raised mice, experience-dependent ocular dominance (OD) plasticity in the primary visual cortex (V1) rapidly declines with age: in postnatal day 25-35 (critical period) mice, 4 days of monocular deprivation (MD) are sufficient to induce OD-shifts towards the open eye; thereafter, 7 days of MD are needed. Beyond postnatal day 110, even 14 days of MD failed to induce OD-plasticity in mouse V1. In contrast, mice raised in a so-called "enriched environment" (EE), exhibit lifelong OD-plasticity. EE-mice have more voluntary physical exercise (running wheels), and experience more social interactions (bigger housing groups) and more cognitive stimulation (regularly changed labyrinths or toys). Whether experience-dependent shifts of V1-activation happen faster in EE-mice and how long the plasticity promoting effect would persist after transferring EE-mice back to SCs has not yet been investigated. To this end, we used intrinsic signal optical imaging to visualize V1-activation i) before and after MD in EE-mice of different age groups (from 1-9 months), and ii) after transferring mice back to SCs after postnatal day 130. Already after 2 days of MD, and thus much faster than in SC-mice, EE-mice of all tested age groups displayed a significant OD-shift towards the open eye. Transfer of EE-mice to SCs immediately abolished OD-plasticity: already after 1 week of SC-housing and MD, OD-shifts could no longer be visualized. In an attempt to rescue abolished OD-plasticity of these mice, we either administered the anti-depressant fluoxetine (in drinking water) or supplied a running wheel in the SCs. OD-plasticity was only rescued for the running wheel- mice. Altogether our results show that raising mice in less deprived environments like large EE-cages strongly accelerates experience-dependent changes in V1-activation compared to the impoverished SC-raising. Furthermore, preventing voluntary physical exercise of EE-mice in adulthood immediately precludes OD-shifts

  10. Environmental enrichment accelerates ocular dominance plasticity in mouse visual cortex whereas transfer to standard cages resulted in a rapid loss of increased plasticity

    PubMed Central

    Pielecka-Fortuna, Justyna; Löwel, Siegrid

    2017-01-01

    In standard cage (SC) raised mice, experience-dependent ocular dominance (OD) plasticity in the primary visual cortex (V1) rapidly declines with age: in postnatal day 25–35 (critical period) mice, 4 days of monocular deprivation (MD) are sufficient to induce OD-shifts towards the open eye; thereafter, 7 days of MD are needed. Beyond postnatal day 110, even 14 days of MD failed to induce OD-plasticity in mouse V1. In contrast, mice raised in a so-called “enriched environment” (EE), exhibit lifelong OD-plasticity. EE-mice have more voluntary physical exercise (running wheels), and experience more social interactions (bigger housing groups) and more cognitive stimulation (regularly changed labyrinths or toys). Whether experience-dependent shifts of V1-activation happen faster in EE-mice and how long the plasticity promoting effect would persist after transferring EE-mice back to SCs has not yet been investigated. To this end, we used intrinsic signal optical imaging to visualize V1-activation i) before and after MD in EE-mice of different age groups (from 1–9 months), and ii) after transferring mice back to SCs after postnatal day 130. Already after 2 days of MD, and thus much faster than in SC-mice, EE-mice of all tested age groups displayed a significant OD-shift towards the open eye. Transfer of EE-mice to SCs immediately abolished OD-plasticity: already after 1 week of SC-housing and MD, OD-shifts could no longer be visualized. In an attempt to rescue abolished OD-plasticity of these mice, we either administered the anti-depressant fluoxetine (in drinking water) or supplied a running wheel in the SCs. OD-plasticity was only rescued for the running wheel- mice. Altogether our results show that raising mice in less deprived environments like large EE-cages strongly accelerates experience-dependent changes in V1-activation compared to the impoverished SC-raising. Furthermore, preventing voluntary physical exercise of EE-mice in adulthood immediately precludes

  11. Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging.

    PubMed

    Dracínský, Martin; Kaminský, Jakub; Bour, Petr

    2009-03-07

    Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in

  12. Investigation of the SCS-CN initial abstraction ratio using a Monte Carlo simulation for the derived flood frequency curves

    NASA Astrophysics Data System (ADS)

    Caporali, E.; Chiarello, V.; Galeati, G.

    2014-12-01

    Peak discharges estimates for a given return period are of primary importance in engineering practice for risk assessment and hydraulic structure design. Different statistical methods are chosen here for the assessment of flood frequency curve: one indirect technique based on the extreme rainfall event analysis, the Peak Over Threshold (POT) model and the Annual Maxima approach as direct techniques using river discharge data. In the framework of the indirect method, a Monte Carlo simulation approach is adopted to determine a derived frequency distribution of peak runoff using a probabilistic formulation of the SCS-CN method as stochastic rainfall-runoff model. A Monte Carlo simulation is used to generate a sample of different runoff events from different stochastic combination of rainfall depth, storm duration, and initial loss inputs. The distribution of the rainfall storm events is assumed to follow the GP law whose parameters are estimated through GEV's parameters of annual maximum data. The evaluation of the initial abstraction ratio is investigated since it is one of the most questionable assumption in the SCS-CN model and plays a key role in river basin characterized by high-permeability soils, mainly governed by infiltration excess mechanism. In order to take into account the uncertainty of the model parameters, this modified approach, that is able to revise and re-evaluate the original value of the initial abstraction ratio, is implemented. In the POT model the choice of the threshold has been an essential issue, mainly based on a compromise between bias and variance. The Generalized Extreme Value (GEV) distribution fitted to the annual maxima discharges is therefore compared with the Pareto distributed peaks to check the suitability of the frequency of occurrence representation. The methodology is applied to a large dam in the Serchio river basin, located in the Tuscany Region. The application has shown as Monte Carlo simulation technique can be a useful

  13. ¹H, ¹³C, ¹⁵N and ³¹P chemical shift assignments of a human Xist RNA A-repeat tetraloop hairpin essential for X-chromosome inactivation.

    PubMed

    Duszczyk, Malgorzata M; Sattler, Michael

    2012-04-01

    Initiation of X-chromosome inactivation in female mammals depends on the non-coding RNA Xist. We have solved the NMR structure of a 14-nucleotide hairpin with a novel AUCG tetraloop fold from a Xist A-repeat that is essential for silencing. The (1)H, (13)C, (15)N and (31)P chemical shift assignments are reported.

  14. FACILITATED CHEMICAL SYNTHESIS UNDER ALTERNATE REACTION CONDITIONS

    EPA Science Inventory

    The chemical research in the late 1990's witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into the atmo...

  15. Speeding Up Sigmatropic Shifts-To Halve or to Hold.

    PubMed

    Tantillo, Dean J

    2016-04-19

    Catalysis is common. Rational catalyst design, however, is at the frontier of chemical science. Although the histories of physical organic and synthetic organic chemistry boast key chapters involving [3s,3s] sigmatropic shifts, catalysis of these reactions is much less common than catalysis of ostensibly more complex processes. The comparative dearth of catalysts for sigmatropic shifts is perhaps a result of the perception that transition state structures for these reactions, like their reactants, are nonpolar and therefore not amenable to selective stabilization and its associated barrier lowering. However, as demonstrated in this Account, transition state structures for [3s,3s] sigmatropic shifts can in fact have charge distributions that differ significantly from those of reactants, even for hydrocarbon substrates, allowing for barriers to be decreased and rates increased. In some cases, differences in charge distribution result from the inclusion of heteroatoms at specific positions in reactants, but in other cases differences are actually induced by catalysts. Perhaps surprisingly, strategies for complexation of transition state structures that remain nonpolar are also possible. In general, the strategies for catalysis employed can be characterized as involving either mechanistic intervention, where a catalyst induces a change from the concerted mechanism expected for a [3s,3s] sigmatropic shift to a multistep process (cutting the transformation into halves or smaller pieces) whose overall barrier is decreased relative to the concerted process, or transition state complexation, where a catalyst simply binds (holds) more tightly to the transition state structure for a [3s,3s] sigmatropic shift than to the reactant, leading to a lower barrier in the presence of the catalyst. Both of these strategies can be considered to be biomimetic in that enzymes frequently induce multistep processes and utilize selective transition state stabilization for the steps involved

  16. SiC (SCS-6) Fiber Reinforced-Reaction Formed SiC Matrix Composites: Microstructure and Interfacial Properties

    NASA Technical Reports Server (NTRS)

    Singh, M.; Dickerson, R. M.; Olmstead, Forrest A.; Eldridge, J. I.

    1997-01-01

    Microstructural and interfacial characterization of unidirectional SiC (SCS-6) fiber reinforced-reaction formed SiC (RFSC) composites has been carried out. Silicon-1.7 at.% molybdenum alloy was used as the melt infiltrant, instead of pure silicon, to reduce the activity of silicon in the melt as well as to reduce the amount of free silicon in the matrix. Electron microprobe analysis was used to evaluate the microstructure and phase distribution in these composites. The matrix is SiC with a bi-modal grain-size distribution and small amounts of MoSi2, silicon, and carbon. Fiber push-outs tests on these composites showed that a desirably low interfacial shear strength was achieved. The average debond shear stress at room temperature varied with specimen thickness from 29 to 64 MPa, with higher values observed for thinner specimens. Initial frictional sliding stresses showed little thickness dependence with values generally close to 30 MPa. Push-out test results showed very little change when the test temperature was increased to 800 C from room temperature, indicating an absence of significant residual stresses in the composite.

  17. Comparison of qualitative and quantitative evaluation of diffusion-weighted MRI and chemical-shift imaging in the differentiation of benign and malignant vertebral body fractures.

    PubMed

    Geith, Tobias; Schmidt, Gerwin; Biffar, Andreas; Dietrich, Olaf; Dürr, Hans Roland; Reiser, Maximilian; Baur-Melnyk, Andrea

    2012-11-01

    The objective of our study was to compare the diagnostic value of qualitative diffusion-weighted imaging (DWI), quantitative DWI, and chemical-shift imaging in a single prospective cohort of patients with acute osteoporotic and malignant vertebral fractures. The study group was composed of patients with 26 osteoporotic vertebral fractures (18 women, eight men; mean age, 69 years; age range, 31 years 6 months to 86 years 2 months) and 20 malignant vertebral fractures (nine women, 11 men; mean age, 63.4 years; age range, 24 years 8 months to 86 years 4 months). T1-weighted, STIR, and T2-weighted sequences were acquired at 1.5 T. A DW reverse fast imaging with steady-state free precession (PSIF) sequence at different delta values was evaluated qualitatively. A DW echo-planar imaging (EPI) sequence and a DW single-shot turbo spin-echo (TSE) sequence at different b values were evaluated qualitatively and quantitatively using the apparent diffusion coefficient. Opposed-phase sequences were used to assess signal intensity qualitatively. The signal loss between in- and opposed-phase images was determined quantitatively. Two-tailed Fisher exact test, Mann-Whitney test, and receiver operating characteristic analysis were performed. Sensitivities, specificities, and accuracies were determined. Qualitative DW-PSIF imaging (delta = 3 ms) showed the best performance for distinguishing between benign and malignant fractures (sensitivity, 100%; specificity, 88.5%; accuracy, 93.5%). Qualitative DW-EPI (b = 50 s/mm(2) [p = 1.00]; b = 250 s/mm(2) [p = 0.50]) and DW single-shot TSE imaging (b = 100 s/mm(2) [p = 1.00]; b = 250 s/mm(2) [p = 0.18]; b = 400 s/mm(2) [p = 0.18]; b = 600 s/mm(2) [p = 0.39]) did not indicate significant differences between benign and malignant fractures. DW-EPI using a b value of 500 s/mm(2) (p = 0.01) indicated significant differences between benign and malignant vertebral fractures. Quantitative DW-EPI (p = 0.09) and qualitative opposed-phase imaging (p = 0

  18. Dynamical patterns and regime shifts in the nonlinear model of soil microorganisms growth

    NASA Astrophysics Data System (ADS)

    Zaitseva, Maria; Vladimirov, Artem; Winter, Anna-Marie; Vasilyeva, Nadezda

    2017-04-01

    Dynamical model of soil microorganisms growth and turnover is formulated as a system of nonlinear partial differential equations of reaction-diffusion type. We consider spatial distributions of concentrations of several substrates and microorganisms. Biochemical reactions are modelled by chemical kinetic equations. Transport is modelled by simple linear diffusion for all chemical substances, while for microorganisms we use different transport functions, e.g. some of them can actively move along gradient of substrate concentration, while others cannot move. We solve our model in two dimensions, starting from uniform state with small initial perturbations for various parameters and find parameter range, where small initial perturbations grow and evolve. We search for bifurcation points and critical regime shifts in our model and analyze time-space profile and phase portraits of these solutions approaching critical regime shifts in the system, exploring possibility to detect such shifts in advance. This work is supported by NordForsk, project #81513.

  19. Job Relocation is High in Chemical Industry.

    ERIC Educational Resources Information Center

    Chemical and Engineering News, 1979

    1979-01-01

    The chances of an employee being relocated are higher in the chemical and plastics industries than in U.S. business as a whole. But the benefits provided by chemical and plastics companies to employees shifted to other locations are generally better than average. (Author/BB)

  20. Potentiation of Chemical Ototoxicity by Noise

    PubMed Central

    Steyger, Peter S.

    2010-01-01

    High-intensity and/or prolonged exposure to noise causes temporary or permanent threshold shifts in auditory perception. Occupational exposure to solvents or administration of clinically important drugs, such as aminoglycoside antibiotics and cisplatin, also can induce permanent hearing loss. The mechanisms by which these ototoxic insults cause auditory dysfunction are still being unraveled, yet they share common sequelae, particularly generation of reactive oxygen species, that ultimately lead to hearing loss and deafness. Individuals are frequently exposed to ototoxic chemical contaminants (e.g., fuel) and noise simultaneously in a variety of work and recreational environments. Does simultaneous exposure to chemical ototoxins and noise potentiate auditory dysfunction? Exposure to solvent vapor in noisy environments potentiates the permanent threshold shifts induced by noise alone. Moderate noise levels potentiate both aminoglycoside- and cisplatin-induced ototoxicity in both rate of onset and in severity of auditory dysfunction. Thus, simultaneous exposure to chemical ototoxins and moderate levels of noise can potentiate auditory dysfunction. Preventing the ototoxic synergy of noise and chemical ototoxins requires removing exposure to ototoxins and/or attenuating noise exposure levels when chemical ototoxins are present. PMID:20523755

  1. Shape-shifting colloids via stimulated dewetting

    NASA Astrophysics Data System (ADS)

    Youssef, Mena; Hueckel, Theodore; Yi, Gi-Ra; Sacanna, Stefano

    2016-07-01

    The ability to reconfigure elementary building blocks from one structure to another is key to many biological systems. Bringing the intrinsic adaptability of biological systems to traditional synthetic materials is currently one of the biggest scientific challenges in material engineering. Here we introduce a new design concept for the experimental realization of self-assembling systems with built-in shape-shifting elements. We demonstrate that dewetting forces between an oil phase and solid colloidal substrates can be exploited to engineer shape-shifting particles whose geometry can be changed on demand by a chemical or optical signal. We find this approach to be quite general and applicable to a broad spectrum of materials, including polymers, semiconductors and magnetic materials. This synthetic methodology can be further adopted as a new experimental platform for designing and rapidly prototyping functional colloids, such as reconfigurable micro swimmers, colloidal surfactants and switchable building blocks for self-assembly.

  2. Animal-Free Chemical Safety Assessment

    PubMed Central

    Loizou, George D.

    2016-01-01

    The exponential growth of the Internet of Things and the global popularity and remarkable decline in cost of the mobile phone is driving the digital transformation of medical practice. The rapidly maturing digital, non-medical world of mobile (wireless) devices, cloud computing and social networking is coalescing with the emerging digital medical world of omics data, biosensors and advanced imaging which offers the increasingly realistic prospect of personalized medicine. Described as a potential “seismic” shift from the current “healthcare” model to a “wellness” paradigm that is predictive, preventative, personalized and participatory, this change is based on the development of increasingly sophisticated biosensors which can track and measure key biochemical variables in people. Additional key drivers in this shift are metabolomic and proteomic signatures, which are increasingly being reported as pre-symptomatic, diagnostic and prognostic of toxicity and disease. These advancements also have profound implications for toxicological evaluation and safety assessment of pharmaceuticals and environmental chemicals. An approach based primarily on human in vivo and high-throughput in vitro human cell-line data is a distinct possibility. This would transform current chemical safety assessment practice which operates in a human “data poor” to a human “data rich” environment. This could also lead to a seismic shift from the current animal-based to an animal-free chemical safety assessment paradigm. PMID:27493630

  3. Interspecies chemical communication in bacterial development.

    PubMed

    Straight, Paul D; Kolter, Roberto

    2009-01-01

    Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

  4. A retrospective cohort study of shift work and risk of cancer-specific mortality in German male chemical workers.

    PubMed

    Yong, Mei; Nasterlack, Michael; Messerer, Peter; Oberlinner, Christoph; Lang, Stefan

    2014-02-01

    Human evidence of carcinogenicity concerning shift work is inconsistent. In a previous study, we observed no elevated risk of total mortality in shift workers followed up until the end of 2006. The present study aimed to investigate cancer-specific mortality, relative to shift work. The cohort consisted of male production workers (14,038 shift work and 17,105 day work), employed at BASF Ludwigshafen for at least 1 year between 1995 and 2005. Vital status was followed from 2000 to 2009. Cause-specific mortality was obtained from death certificates. Exposure to shift work was measured both as a dichotomous and continuous variable. While lifetime job history was not available, job duration in the company was derived from personal data, which was then categorized at the quartiles. Cox proportional hazard model was used to adjust for potential confounders, in which job duration was treated as a time-dependent covariate. Between 2000 and 2009, there were 513 and 549 deaths among rotating shift and day work employees, respectively. Risks of total and cancer-specific mortalities were marginally lower among shift workers when taking age at entry and job level into consideration and were statistically significantly lower when cigarette smoking, alcohol intake, job duration, and chronic disease prevalence at entry to follow-up were included as explanatory factors. With respect to mortality risks in relation to exposure duration, no increased risks were found in any of the exposure groups after full adjustment and there was no apparent trend suggesting an exposure-response relation with duration of shift work. The present analysis extends and confirms our previous finding of no excess risk of mortality associated with work in the shift system employed at BASF Ludwigshafen. More specifically, there is also no indication of an increased risk of mortality due to cancer.

  5. Primary selection into shift work and change of cardiovascular risk profile.

    PubMed

    Yong, Mei; Germann, Christina; Lang, Stefan; Oberlinner, Christoph

    2015-05-01

    A potential "healthy shift worker effect" may bias the studied effect of shift work on health. The observed differences among shift and day workers in health behavior and health outcomes can be caused by: (i) primary selection, (ii) the influence from the shift work-related environment, and (iii) the impact of shift work. We aimed to study these potential sources. A cohort of 4754 male trainees who had finished their professional training and started their career in production in a chemical company between 1995 and 2012 was identified. Among them, 1348 (28%) were involved in rotating shift work and 3406 (72%) in day work. Information on health behavior and risk factors for cardiovascular diseases was retrieved from the medical examinations. This information was then compared (i) at the beginning of training, (ii) at the end of training, and (iii) 3 years after the employment, in relation to the working time. At the beginning of the training, the prevalence of smokers was higher among future shift workers (26% versus 21%), from 1995 to 2012. During the training and the first three years of employment, a marginal decline of systolic blood pressure and an elevation of triglyceride were related with shift work. No difference was found with respect to other risk factors for cardiovascular diseases. Our findings do not support a primary selection in favor of shift workers. An impact of shift work on the risk profile of cardiovascular diseases was not indicated in the observation period.

  6. A Novel View of the Adult Stem Cell Compartment From the Perspective of a Quiescent Population of Very Small Embryonic-Like Stem Cells.

    PubMed

    Ratajczak, Mariusz Z; Ratajczak, Janina; Suszynska, Malwina; Miller, Donald M; Kucia, Magda; Shin, Dong-Myung

    2017-01-06

    Evidence has accumulated that adult hematopoietic tissues and other organs contain a population of dormant stem cells (SCs) that are more primitive than other, already restricted, monopotent tissue-committed SCs (TCSCs). These observations raise several questions, such as the developmental origin of these cells, their true pluripotent or multipotent nature, which surface markers they express, how they can be efficiently isolated from adult tissues, and what role they play in the adult organism. The phenotype of these cells and expression of some genes characteristic of embryonic SCs, epiblast SCs, and primordial germ cells suggests their early-embryonic deposition in developing tissues as precursors of adult SCs. In this review, we will critically discuss all these questions and the concept that small dormant SCs related to migratory primordial germ cells, described as very small embryonic-like SCs, are deposited during embryogenesis in bone marrow and other organs as a backup population for adult tissue-committed SCs and are involved in several processes related to tissue or organ rejuvenation, aging, and cancerogenesis. The most recent results on successful ex vivo expansion of human very small embryonic-like SC in chemically defined media free from feeder-layer cells open up new and exciting possibilities for their application in regenerative medicine. © 2017 American Heart Association, Inc.

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

    USGS Publications Warehouse

    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

  8. Infrared transient-liquid-phase joining of SCS-6/ β21S titanium matrix composite

    NASA Astrophysics Data System (ADS)

    Blue, Craig A.; Sikka, Vinod K.; Blue, Randall A.; Lin, Ray Y.

    1996-12-01

    Fiber-reinforced titanium matrix composites (TMCs) are among the advanced materials being considered for use in the aerospace industry due to their light weight, high strength, and high modulus. A rapid infrared joining process has been developed for the joining of composites and advanced materials. Rapid infrared joining has been shown not to have many of the problems associated with conventional joining methods. Two models were utilized to predict the joint evolution and fiber reaction zone growth. Titanium matrix composite, 16-ply SCS-6/ β21S, has been successfully joined with total processing times of approximately 2 minutes, utilizing the rapid infrared joining technique. The process utilizes a 50 °C/s ramping rate, 17- µm Ti-15Cu-15Ni wt pct filler material between the faying surfaces; a joining temperature of 1100 °C; and 120 seconds of time to join the composite material. Joint shear-strength testing of the rapid infrared joints at temperatures as high as 800 °C has revealed no joint failures. Also, due to the rapid cooling of the process, no poststabilization of the matrix material is necessary to prevent the formation of a brittle omega phase during subsequent use of the TMC at intermediate temperatures, 270 °C to 430 °C, for up to 20 hours.

  9. Shape-shifting colloids via stimulated dewetting

    PubMed Central

    Youssef, Mena; Hueckel, Theodore; Yi, Gi-Ra; Sacanna, Stefano

    2016-01-01

    The ability to reconfigure elementary building blocks from one structure to another is key to many biological systems. Bringing the intrinsic adaptability of biological systems to traditional synthetic materials is currently one of the biggest scientific challenges in material engineering. Here we introduce a new design concept for the experimental realization of self-assembling systems with built-in shape-shifting elements. We demonstrate that dewetting forces between an oil phase and solid colloidal substrates can be exploited to engineer shape-shifting particles whose geometry can be changed on demand by a chemical or optical signal. We find this approach to be quite general and applicable to a broad spectrum of materials, including polymers, semiconductors and magnetic materials. This synthetic methodology can be further adopted as a new experimental platform for designing and rapidly prototyping functional colloids, such as reconfigurable micro swimmers, colloidal surfactants and switchable building blocks for self-assembly. PMID:27426418

  10. Thermomechanical testing techniques for high-temparature composites: TMF behavior of SiC(SCS-6)/Ti-15-3

    NASA Technical Reports Server (NTRS)

    Castelli, Michael G.; Ellis, J. Rodney; Bartolotta, Paul A.

    1990-01-01

    Thermomechanical testing techniques recently developed for monolithic structural alloys were successfully extended to continuous fiber reinforced composite materials in plate form. The success of this adaptation was verified on a model metal matrix composite (MMC) material, namely SiC(SCS-6)/Ti-15V-3Cr-3Al-3Sn. Effects of heating system type and specimen preparation are also addressed. Cyclic lives determined under full thermo-mechanical conditions were shown to be significantly reduced from those obtained under comparable isothermal and in-phase bi-thermal conditions. Fractography and metallography from specimens subjected to isothermal, out-of-phase and in-phase conditions reveal distinct differences in damage-failure modes. Isothermal metallography revealed extensive matrix cracking associated with fiber damage throughout the entire cross-section of the specimen. Out-of-phase metallography revealed extensive matrix damage associated with minimal (if any) fiber cracking. However, the damage was located exclusively at surface and near-surface locations. In-phase conditions produced extensive fiber cracking throughout the entire cross-section, associated with minimal (if any) matrix damage.

  11. Enhancing Thai Students' Learning of Chemical Kinetics

    ERIC Educational Resources Information Center

    Chairam, Sanoe; Somsook, Ekasith; Coll, Richard K.

    2009-01-01

    Chemical kinetics is an extremely important concept for introductory chemistry courses. The literature suggests that instruction in chemical kinetics is often teacher-dominated at both the secondary school and tertiary levels, and this is the case in Thailand--the educational context for this inquiry. The work reported here seeks to shift students…

  12. Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP8−) for dual biosensing of pH with CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts)

    PubMed Central

    Huang, Yuegao; Coman, Daniel; Ali, Meser M.; Hyder, Fahmeed

    2014-01-01

    Relaxivity based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd3+) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the non-exchangeable or the exchangeable protons on the lanthanide complexes themselves. The non-exchangeable protons (e.g., –CHx, where 3≥x≥1) are detected using a three-dimensional chemical shift imaging method called Biosensor Imaging of Redundant Deviation in Shifts (BIRDS), whereas the exchangeable protons (e.g., –OH or –NHy, where 2≥y≥1) are measured with Chemical Exchange Saturation Transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP8−) chelated with thulium (Tm3+) and ytterbium (Yb3+). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs. using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e., 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP5− than with TmDOTA-4AmP5−. In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging. PMID:24801742

  13. CHEMICAL SYNTHESIS USING 'GREENER' ALTERNATIVE REACTION CONDITIONS AND MEDIA

    EPA Science Inventory

    The chemical research during the last decade has witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into ...

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

    PubMed Central

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

    2014-01-01

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

  15. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shi, Pan; School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026; Xi, Zhaoyong

    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at threemore » different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.« less

  16. Neuromodulation therapy does not influence blood flow distribution or left-ventricular dynamics during acute myocardial ischemia.

    PubMed

    Kingma, J G; Linderoth, B; Ardell, J L; Armour, J A; DeJongste, M J; Foreman, R D

    2001-08-13

    Electrical stimulation of the dorsal aspect of the upper thoracic spinal cord is used increasingly to treat patients with angina pectoris refractory to conventional therapeutic strategies. The purpose of this study was to determine whether spinal cord stimulation (SCS) in dogs affects regional myocardial blood flow and left-ventricular (LV) function before and during transient obstruction of the left anterior descending coronary artery (LAD). In anesthetized dogs, regional myocardial blood flow distribution was determined using radiolabeled microspheres and left-ventricular function was measured by impedance-derived pressure-volume loops. SCS was accomplished by stimulating the dorsal T1-T2 segments of the spinal cord using epidural bipolar electrodes at 90% of motor threshold (MT) (50 Hz, 0.2-ms duration). Effects of 5-min SCS were assessed under basal conditions and during 4-min occlusion of the LAD. SCS alone evoked no change in regional myocardial blood flow or cardiovascular indices. Transient LAD occlusion significantly diminished blood flow within ischemic, but not in non-ischemic myocardial tissue. Left ventricular pressure-volume loops were shifted rightward during LAD occlusion. Cardiac indices were altered similarly during LAD occlusion and concurrent SCS. SCS does not influence the distribution of blood flow within the non-ischemic or ischemic myocardium. Nor does it modify LV pressure-volume dynamics in the anesthetized experimental preparation.

  17. Measurements of relative chemical shift tensor orientations in solid-state NMR: new slow magic angle spinning dipolar recoupling experiments.

    PubMed

    Jurd, Andrew P S; Titman, Jeremy J

    2009-08-28

    Solid-state NMR experiments can be used to determine conformational parameters, such as interatomic distances and torsion angles. The latter can be obtained from measurements of the relative orientation of two chemical shift tensors, if the orientation of these with respect to the surrounding bonds is known. In this paper, a new rotor-synchronized magic angle spinning (MAS) dipolar correlation experiment is described which can be used in this way. Because the experiment requires slow MAS rates, a novel recoupling sequence, designed using symmetry principles, is incorporated into the mixing period. This recoupling sequence is based in turn on a new composite cyclic pulse referred to as COAST (for combined offset and anisotropy stabilization). The new COAST-C7(2)(1) sequence is shown to give good theoretical and experimental recoupling efficiency, even when the CSA far exceeds the MAS rate. In this regime, previous recoupling sequences, such as POST-C7(2)(1), exhibit poor recoupling performance. The effectiveness of the new method has been explored by a study of the dipeptide L-phenylalanyl-L-phenylalanine.

  18. Is there substituent cross-interaction effect in all the conjugated systems containing Cdbnd N polar bond? The substituent effects on the NMR chemical shifts of 2,5-disubstituted pyrimidines

    NASA Astrophysics Data System (ADS)

    Yuan, Hua; Zhang, Yan; Chen, Chun-Ni; Li, Meng-Yang

    2018-03-01

    The substituent cross-interaction effect in the substituted benzylidene anilines (p-Xsbnd C6H4sbnd CHdbnd Nsbnd C6H4sbnd Y-p) has been observed and widely investigated. In order to investigate whether the substituent cross-interaction effect exist in all the conjugated systems containing Cdbnd N polar bond, this paper employed 2-X-5-Y pyrimidines as the model compounds for study. The influences of substituents X and Y on the 1H NMR and 13C NMR chemical shifts of 2, 5-disubsitituted pyrimidines have been systematically investigated. Quantitative structure-chemical shifts relationship models have been built for δ(H4,6), δ(C2), δ(C4,6) and δ(C5) with four to six molecular descriptors. These models were confirmed of good stability and predictive performances by leave-one-out cross validation. This study indicates that the substituent effects of 2,5-disubstituted pyrimidines are much more complex than that of the substituted benzylidene anilines. More structural factors besides of Hammett parameter should be taken into consideration. Different from the substituted benzylidene anilines, the cross-interaction effect (Δσ2) of substituents X and Y has little contribution to δ(H4,6), δ(C2), δ(C5) and δ(C4,6) of 2,5-disubstituted pyrimidines.

  19. Shifts in fisheries management: adapting to regime shifts

    PubMed Central

    King, Jacquelynne R.; McFarlane, Gordon A.; Punt, André E.

    2015-01-01

    For many years, fisheries management was based on optimizing yield and maintaining a target biomass, with little regard given to low-frequency environmental forcing. However, this policy was often unsuccessful. In the last two to three decades, fisheries science and management have undergone a shift towards balancing sustainable yield with conservation, with the goal of including ecosystem considerations in decision-making frameworks. Scientific understanding of low-frequency climate–ocean variability, which is manifested as ecosystem regime shifts and states, has led to attempts to incorporate these shifts and states into fisheries assessment and management. To date, operationalizing these attempts to provide tactical advice has met with limited success. We review efforts to incorporate regime shifts and states into the assessment and management of fisheries resources, propose directions for future investigation and outline a potential framework to include regime shifts and changes in ecosystem states into fisheries management.

  20. Thermomechanical testing of high-temperature composites - Thermomechanical fatigue (TMF) behavior of SiC(SCS-6)/Ti-15-3

    NASA Technical Reports Server (NTRS)

    Castelli, Michael G.; Bartolotta, Paul; Ellis, John R.

    1992-01-01

    Thermomechanical testing techniques recently developed for monolithic structural alloys were successfully extended to continuous fiber reinforced composite materials in plate form. The success of this adaptation was verified on a model metal matrix composite (MMC) material, namely SiC(SCS-6)/Ti-15V-3Cr-3Al-3Sn. Effects of heating system type and specimen preparation are also addressed. Cyclic lives determined under full thermomechanical conditions were shown to be significantly reduced from those obtained under comparable isothermal and in-phase bi-thermal conditions. Fractography and metallography from specimens subjected to isothermal, out-of-phase and in-phase conditions reveal distinct differences in damage-failure modes. Isothermal metallography revealed extensive matrix cracking associated with fiber damage throughout the entire cross-section of the specimen. Out-of-phase metallography revealed extensive matrix damage associated with minimal (if any) fiber cracking. However, the damage was located exclusively at surface and near-surface locations. In-phase conditions produced extensive fiber cracking throughout the entire cross-section, associated with minimal (if any) matrix damage.

  1. NMR Spectroscopy Using a Chiral Lanthanide Shift Reagent to Assess the Optical Purity of 1-Phenylethylamine

    NASA Astrophysics Data System (ADS)

    Viswanathan, Tito; Toland, Alan

    1995-10-01

    Enantiomeric forms of 1-phenylethylamine cannot be distinguished by 1H or 13C-NMR because the groups attached to the stereocenter are in an enantiopic environment. However, the chemical shifts of the protons in the groups attached to the stereocenter can be differentially altered to appear as distinct peaks in the NMR spectrum. This is accomplished by the use of a commercially available chiral lanthanide shift reagent, Yb(tfC)3. The NMR spectrum after the addition of a chiral shift reagent allows one to assess the optical purity of the sample.

  2. Ab Initio Theory of Nuclear Magnetic Resonance Shifts in Metals

    NASA Astrophysics Data System (ADS)

    D'Avezac, Mayeul; Marzari, Nicola; Mauri, Francesco

    2005-03-01

    A comprehensive approach for the first-principles determination of all-electron NMR shifts in metallic systems is presented. Our formulation is based on a combination of density-functional perturbation theory and all-electron wavefunction reconstruction, starting from periodic-boundary calculations in the pseudopotential approximation. The orbital contribution to the NMR shift (the chemical shift) is obtained by combining the gauge-including projector augmented-wave approach (GIPAW), originally developed for the case of insulatorsootnotetextC. J. Pickard, Francesco Mauri, Phys. Rev. B, 63, 245101(2001), with the extension of linear-response theory to the case of metallic systemsootnotetextS. de Gironcoli, Phys. Rev. B, 51, 6773(1995). The spin contribution (the Knight shift) is obtained as a response to a finite uniform magnetic field, and through reconstructing the hyperfine interaction between the electron-spin density and the nuclear spins with the projector augmented-wave method (PAWootnotetextC. G. Van de Walle, P. E. Blöchl, Phys. Rev. B, 47, 4244(1993)). Our method is validated with applications to the case of the homogeneous electron gas and of simple metals. (Work supported by MURI grant DAAD 19-03-1-0169 and MIT-France)

  3. Has Chemical Education Reached Equilibrium?

    NASA Astrophysics Data System (ADS)

    Moore, John W.

    1997-06-01

    The other day I got to thinking about whether something akin to Le Chatelier's principle operates in chemical education. That is, whenever someone alters the conditions under which we interact with students, there is a shift in the system that attempts to minimize or counteract the change.

  4. Shift Work and Shift Work Sleep Disorder: Clinical and Organizational Perspectives.

    PubMed

    Wickwire, Emerson M; Geiger-Brown, Jeanne; Scharf, Steven M; Drake, Christopher L

    2017-05-01

    Throughout the industrialized world, nearly one in five employees works some form of nontraditional shift. Such shift work is associated with numerous negative health consequences, ranging from cognitive complaints to cancer, as well as diminished quality of life. Furthermore, a substantial percentage of shift workers develop shift work disorder, a circadian rhythm sleep disorder characterized by excessive sleepiness, insomnia, or both as a result of shift work. In addition to adverse health consequences and diminished quality of life at the individual level, shift work disorder incurs significant costs to employers through diminished workplace performance and increased accidents and errors. Nonetheless, shift work will remain a vital component of the modern economy. This article reviews seminal and recent literature regarding shift work, with an eye toward real-world application in clinical and organizational settings. Copyright © 2016 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

  5. Hydrodynamic fluctuations, nonequilibrium equations of state, and the shift of the spinodal line in polymer solutions under flow

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Criado-Sancho, M.; Casas-Vazquez, J.; Jou, D.

    1997-08-01

    In the literature, the shift of the spinodal line of polymer solutions under flow is attributed either to an actual shift of the spinodal due to a nonequilibrium modification of the equation of state for the chemical potential, or to an apparent shift due to an increase of hydrodynamic fluctuations owing to the flow. Here we see that both approaches are compatible and that both effects add up. {copyright} {ital 1997} {ital The American Physical Society}

  6. Cortico-pontine theta carrier frequency phase shift across sleep/wake states following monoaminergic lesion in rat.

    PubMed

    Kalauzi, Aleksandar; Spasic, Sladjana; Petrovic, Jelena; Ciric, Jelena; Saponjic, Jelena

    2012-06-01

    This study was aimed to explore the sleep/wake states related cortico-pontine theta carrier frequency phase shift following a systemically induced chemical axotomy of the monoaminergic afferents within a brain of the freely moving rats. Our experiments were performed in 14 adult, male Sprague Dawley rats, chronically implanted for sleep recording. We recorded sleep during baseline condition, following sham injection (saline i.p. 1 ml/kg), and every week for 5 weeks following injection of the systemic neurotoxins (DSP-4 or PCA; 1 ml/kg, i.p.) for chemical axotomy of the locus coeruleus (LC) and dorsal raphe (DR) axon terminals. After sleep/wake states identification, FFT analysis was performed on 5 s epochs. Theta carrier frequency phase shift (∆Φ) was calculated for each epoch by averaging theta Fourier component phase shifts, and the ∆Φ values were plotted for each rat in control condition and 28 days following the monoaminergic lesions, as a time for permanently established DR or LC chemical axotomy. Calculated group averages have shown that ∆Φ increased between pons and cortex significantly in all sleep/wake states (Wake, NREM and REM) following the monoaminergic lesions, with respect to controls. Monoaminergic lesions established the pontine leading role in the brain theta oscillations during all sleep/wake states.

  7. Identifying Chemical Groups for Biomonitoring

    PubMed Central

    Krowech, Gail; Hoover, Sara; Plummer, Laurel; Sandy, Martha; Zeise, Lauren; Solomon, Gina

    2016-01-01

    Summary: Regulatory agencies face daunting challenges identifying emerging chemical hazards because of the large number of chemicals in commerce and limited data on exposure and toxicology. Evaluating one chemical at a time is inefficient and can lead to replacement with uncharacterized chemicals or chemicals with structural features already linked to toxicity. The Office of Environmental Health Hazard Assessment (OEHHA) has developed a process for constructing and assessing chemical groups for potential biomonitoring in California. We screen for chemicals with significant exposure potential and propose possible chemical groups, based on structure and function. To support formal consideration of these groups by Biomonitoring California’s Scientific Guidance Panel, we conduct a detailed review of exposure and toxicity data and examine the likelihood of detection in biological samples. To date, 12 chemical groups have been constructed and added to the pool of chemicals that can be selected for Biomonitoring California studies, including p,p´-bisphenols, brominated and chlorinated organic compounds used as flame retardants, non-halogenated aromatic phosphates, and synthetic polycyclic musks. Evaluating chemical groups, rather than individual chemicals, is an efficient way to respond to shifts in chemical use and the emergence of new chemicals. This strategy can enable earlier identification of important chemicals for monitoring and intervention. PMID:27905275

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

    USGS Publications Warehouse

    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.

  9. Shift work and the assessment and management of shift work disorder (SWD).

    PubMed

    Wright, Kenneth P; Bogan, Richard K; Wyatt, James K

    2013-02-01

    Nearly 20% of the labor force worldwide, work shifts that include work hours outside 07:00 h to 18:00 h. Shift work is common in many occupations that directly affect the health and safety of others (e.g., protective services, transportation, healthcare), whereas quality of life, health, and safety during shift work and the commute home can affect workers in any field. Increasing evidence indicates that shift-work schedules negatively influence worker physiology, health, and safety. Shift work disrupts circadian sleep and alerting cycles, resulting in disturbed daytime sleep and excessive sleepiness during the work shift. Moreover, shift workers are at risk for shift work disorder (SWD). This review focuses on shift work and the assessment and management of sleepiness and sleep disruption associated with shift work schedules and SWD. Management strategies include approaches to promote sleep, wakefulness, and adaptation of the circadian clock to the imposed work schedule. Additional studies are needed to further our understanding of the mechanisms underlying the health risks of shift work, understanding which shift workers are at most risk of SWD, to investigate treatment options that address the health and safety burdens associated with shift work and SWD, and to further develop and assess the comparative effectiveness of countermeasures and treatment options. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Doubly Selective Multiple Quantum Chemical Shift Imaging and T1 Relaxation Time Measurement of Glutathione (GSH) in the Human Brain In Vivo

    PubMed Central

    Choi, In-Young; Lee, Phil

    2012-01-01

    Mapping of a major antioxidant, glutathione (GSH), was achieved in the human brain in vivo using a doubly selective multiple quantum filtering based chemical shift imaging (CSI) of GSH at 3 T. Both in vivo and phantom tests in CSI and single voxel measurements were consistent with excellent suppression of overlapping signals from creatine, γ-Amino butyric acid (GABA) and macromolecules. The GSH concentration in the fronto-parietal region was 1.20 ± 0.16 µmol/g (mean ± SD, n = 7). The longitudinal relaxation time (T1) of GSH in the human brain was 397 ± 44 ms (mean ± SD, n = 5), which was substantially shorter than those of other metabolites. This GSH CSI method permits us to address regional differences of GSH in the human brain with conditions where oxidative stress has been implicated, including multiple sclerosis, aging and neurodegenerative diseases. PMID:22730142

  11. New S control chart using skewness correction method for monitoring process dispersion of skewed distributions

    NASA Astrophysics Data System (ADS)

    Atta, Abdu; Yahaya, Sharipah; Zain, Zakiyah; Ahmed, Zalikha

    2017-11-01

    Control chart is established as one of the most powerful tools in Statistical Process Control (SPC) and is widely used in industries. The conventional control charts rely on normality assumption, which is not always the case for industrial data. This paper proposes a new S control chart for monitoring process dispersion using skewness correction method for skewed distributions, named as SC-S control chart. Its performance in terms of false alarm rate is compared with various existing control charts for monitoring process dispersion, such as scaled weighted variance S chart (SWV-S); skewness correction R chart (SC-R); weighted variance R chart (WV-R); weighted variance S chart (WV-S); and standard S chart (STD-S). Comparison with exact S control chart with regards to the probability of out-of-control detections is also accomplished. The Weibull and gamma distributions adopted in this study are assessed along with the normal distribution. Simulation study shows that the proposed SC-S control chart provides good performance of in-control probabilities (Type I error) in almost all the skewness levels and sample sizes, n. In the case of probability of detection shift the proposed SC-S chart is closer to the exact S control chart than the existing charts for skewed distributions, except for the SC-R control chart. In general, the performance of the proposed SC-S control chart is better than all the existing control charts for monitoring process dispersion in the cases of Type I error and probability of detection shift.

  12. Change from slowly rotating 8-hour shifts to rapidly rotating 8-hour and 12-hour shifts using participative shift roster design.

    PubMed

    Smith, P A; Wright, B M; Mackey, R W; Milsop, H W; Yates, S C

    1998-01-01

    The study examined the impact of change, from slowly rotating continuous 8-hour shifts to more rapidly rotating continuous 8-hour and 12-hour shifts, on the health and quality of life of shift workers. Self-report survey data were collected from 72 shift workers at 3 sewage treatment plants before and several months after roster change. After the change 1 plant first worked a rapidly rotating, 8-hour shift roster and then worked a 12-hour shift roster, and the other 2 plants worked continuous 12-hour shift rosters. After the change the shift workers at each plant reported increased satisfaction with roster design, a decrease in physical and psychological circadian malaise associated with shift work, improved day sleep quality, less tiredness, and improvements in the quality of home, social and work life. A between-plant comparison of the rapidly rotating 8-hour and 12-hour shift rosters showed greater improvements had been obtained with the 12-hour shift roster, and no significant differences in tiredness or sleep quality between the redesigned 8- and 12-hour shift rosters. However, a within-plant matched-pairs comparison at the 1st plant of the rapidly rotating 8-hour shift roster and the 12-hour shift roster showed no significant differences. The results show that the prior level of support for change may best explain the impact of roster redesign on individual well-being. They lend further support to shift worker participation in roster design.

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

    PubMed

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

    2001-01-01

    The purpose of this work was to explore the reproducibility of fat-fraction measurements using Dixon quantitative chemical shift imaging (QCSI) in the lumbar spine (L3, L4, and L5) of healthy volunteers. Sixteen healthy volunteers were examined at 1.5 T two times to obtain a repeated measurement in the same slice and a third time in three parallel slices. Single slice, two point Dixon SE (TR/TE 2,500/22.3) sequences were used, from which fat-fraction images were calculated. The fat-fraction results are presented as averages over regions of interest, which were derived from the contours of the vertebrae. Reproducibility measures related to repeated measurements on different days, slice position, and contour drawing were calculated. The mean fat fraction was 0.37 (SD 0.08). The SD due to repeated measurement was small (sigmaR = 0.013-0.032), almost all of which can be explained by slice-(re)-positioning errors. When used to evaluate the same person longitudinally in time, Dixon QCSI fat-fraction measurement has an excellent reproducibility. It is a powerful noninvasive tool in the evaluation of bone marrow composition.

  14. Repeatability of two-dimensional chemical shift imaging multivoxel proton magnetic resonance spectroscopy for measuring human cerebral choline-containing compounds.

    PubMed

    Puri, Basant K; Egan, Mary; Wallis, Fintan; Jakeman, Philip

    2018-03-22

    To investigate the repeatability of proton magnetic resonance spectroscopy in the in vivo measurement of human cerebral levels of choline-containing compounds (Cho). Two consecutive scans were carried out in six healthy resting subjects at a magnetic field strength of 1.5 T. On each occasion, neurospectroscopy data were collected from 64 voxels using the same 2D chemical shift imaging (CSI) sequence. The data were analyzed in the same way, using the same software, to obtain the values for each voxel of the ratio of Cho to creatine. The Wilcoxon related-samples signed-rank test, coefficient of variation (CV), repeatability coefficient (RC), and intraclass correlation coefficient (ICC) were used to assess the repeatability. The CV ranged from 2.75% to 33.99%, while the minimum RC was 5.68%. There was excellent reproducibility, as judged by significant ICC values, in 26 voxels. Just three voxels showed significant differences according to the Wilcoxon related-samples signed-rank test. It is therefore concluded that when CSI multivoxel proton neurospectroscopy is used to measure cerebral choline-containing compounds at 1.5 T, the reproducibility is highly acceptable.

  15. Non-occupational physical activity levels of shift workers compared with non-shift workers

    PubMed Central

    Loef, Bette; Hulsegge, Gerben; Wendel-Vos, G C Wanda; Verschuren, W M Monique; Bakker, Marije F; van der Beek, Allard J; Proper, Karin I

    2017-01-01

    Objectives Lack of physical activity (PA) has been hypothesised as an underlying mechanism in the adverse health effects of shift work. Therefore, our aim was to compare non-occupational PA levels between shift workers and non-shift workers. Furthermore, exposure–response relationships for frequency of night shifts and years of shift work regarding non-occupational PA levels were studied. Methods Data of 5980 non-shift workers and 532 shift workers from the European Prospective Investigation into Cancer and Nutrition-Netherlands (EPIC-NL) were used in these cross-sectional analyses. Time spent (hours/week) in different PA types (walking/cycling/exercise/chores) and intensities (moderate/vigorous) were calculated based on self-reported PA. Furthermore, sports were operationalised as: playing sports (no/yes), individual versus non-individual sports, and non-vigorous-intensity versus vigorous-intensity sports. PA levels were compared between shift workers and non-shift workers using Generalized Estimating Equations and logistic regression. Results Shift workers reported spending more time walking than non-shift workers (B=2.3 (95% CI 1.2 to 3.4)), but shift work was not associated with other PA types and any of the sports activities. Shift workers who worked 1–4 night shifts/month (B=2.4 (95% CI 0.6 to 4.3)) and ≥5 night shifts/month (B=3.7 (95% CI 1.8 to 5.6)) spent more time walking than non-shift workers. No exposure–response relationships were found between years of shift work and PA levels. Conclusions Shift workers spent more time walking than non-shift workers, but we observed no differences in other non-occupational PA levels. To better understand if and how PA plays a role in the negative health consequences of shift work, our findings need to be confirmed in future studies. PMID:27872151

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

    PubMed

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

    2013-11-12

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

  17. Reduced Tolerance to Night Shift in Chronic Shift Workers: Insight From Fractal Regulation.

    PubMed

    Li, Peng; Morris, Christopher J; Patxot, Melissa; Yugay, Tatiana; Mistretta, Joseph; Purvis, Taylor E; Scheer, Frank A J L; Hu, Kun

    2017-07-01

    Healthy physiology is characterized by fractal regulation (FR) that generates similar structures in the fluctuations of physiological outputs at different time scales. Perturbed FR is associated with aging and age-related pathological conditions. Shift work, involving repeated and chronic exposure to misaligned environmental and behavioral cycles, disrupts circadian coordination. We tested whether night shifts perturb FR in motor activity and whether night shifts affect FR in chronic shift workers and non-shift workers differently. We studied 13 chronic shift workers and 14 non-shift workers as controls using both field and in-laboratory experiments. In the in-laboratory study, simulated night shifts were used to induce a misalignment between the endogenous circadian pacemaker and the sleep-wake cycles (ie, circadian misalignment) while environmental conditions and food intake were controlled. In the field study, we found that FR was robust in controls but broke down in shift workers during night shifts, leading to more random activity fluctuations as observed in patients with dementia. The night shift effect was present even 2 days after ending night shifts. The in-laboratory study confirmed that night shifts perturbed FR in chronic shift workers and showed that FR in controls was more resilience to the circadian misalignment. Moreover, FR during real and simulated night shifts was more perturbed in those who started shift work at older ages. Chronic shift work causes night shift intolerance, which is probably linked to the degraded plasticity of the circadian control system. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

  18. Spinal cord stimulation (SCS) in conjunction with peripheral nerve field stimulation (PNfS) for the treatment of complex pain in failed back surgery syndrome (FBSS).

    PubMed

    Reverberi, Claudio; Dario, Alessandro; Barolat, Giancarlo

    2013-01-01

    Failed back surgery syndrome (FBSS) is a well-defined pathologic condition observed over many years. We have investigated the effect of spinal cord stimulation (SCS) with peripheral nerve field stimulation (PNfS) in eight patients with FBSS. The following parameters were collected and analyzed: The pain intensity score on a 0-10 numbering rating scale (NRS), the psychologic profile with Beck Depression Inventory (BDI), the pain quality with McGill Pain Questionnaire-short form (MGPQ-sf), the back pain with Oswestry scale score (OS), and the health general quality pattern with QualityMetric's SF-36v2(®) Health Survey. Eight patients with low back and radicular pain in FBSS are reported. The mean duration of pain was 6.7 months, and the mean NRS score was 9.5, BDI 28.8, MGPQ-sf 16.8, OS 44.5, and SF-36 score was 72.8. The average drug intake of opioids was 250 mg/day. In six patients, two octopolar leads were placed in epidural space at D7-D8 and D8-D9, in conjunction with two octopolar leads placed in lumbar-sacral subcutaneous space (Precision System, Boston Scientific, Valencia, CA, USA), and in two patients, a two tetrapolar leads was placed in epidural space at D8-D9 with two tetrapolar leads (Pisces Quad, Plus, Medtronic Inc., Minneapolis, MN, USA) placed in lumbar-sacral subcutaneous space (Restore Ultra, Medtronic Inc., Minneapolis, MN, USA). After one year mean of follow-up, the mean NRS score was 4, BDI 8, MGPQ-sf 5, OS 21, and the SF-36 score was increased at 108.5. The mean drug intake of opioids was decreased at 20 mg/day. The combination of SCS and PNfS, using the latest rechargeable systems, may be a valid therapeutic strategy in FBSS. © 2012 International Neuromodulation Society.

  19. FunShift: a database of function shift analysis on protein subfamilies

    PubMed Central

    Abhiman, Saraswathi; Sonnhammer, Erik L. L.

    2005-01-01

    Members of a protein family normally have a general biochemical function in common, but frequently one or more subgroups have evolved a slightly different function, such as different substrate specificity. It is important to detect such function shifts for a more accurate functional annotation. The FunShift database described here is a compilation of function shift analysis performed between subfamilies in protein families. It consists of two main components: (i) subfamilies derived from protein domain families and (ii) pairwise subfamily comparisons analyzed for function shift. The present release, FunShift 12, was derived from Pfam 12 and consists of 151 934 subfamilies derived from 7300 families. We carried out function shift analysis by two complementary methods on families with up to 500 members. From a total of 179 210 subfamily pairs, 62 384 were predicted to be functionally shifted in 2881 families. Each subfamily pair is provided with a markup of probable functional specificity-determining sites. Tools for searching and exploring the data are provided to make this database a valuable resource for protein function annotation. Knowledge of these functionally important sites will be useful for experimental biologists performing functional mutation studies. FunShift is available at http://FunShift.cgb.ki.se. PMID:15608176

  20. TIPS (trigger an IIF paradigm shift).

    PubMed

    Kilcup P E, Glen; Hickox, Dick; Reynaga, Adolfo

    2007-04-11

    ) injuries. Biggest total injury type was ergonomic. Biggest recordable injury type (58%) was cuts/lacerations. Chemical exposure and inhalations resulted in no recordables. Biggest root cause category was behavioral. Biggest behavioral root cause was "Failure to Evaluate Hazards". Biggest administrative controls root cause was "Inadequate Procedures". Biggest engineering controls root cause was "Unrecognized Workplace Hazard". Majority of injuries occurred in Spring/Summer which accounted for 86% of recordables. Response was inadequate or poor for 25% of injuries. Number of injuries by workgroup were about equal. Work area injuries were mostly in the CUB and Subfab but CUB injuries favored cuts/lacerations while Subfab favored ergonomic injuries. These learnings and gaps were used to develop our New Mexico Site Safety Action Plan for 2005. It has also been used by individual managers and supervisors in their day-to-day business meetings, activities, and communications, for a more focused IIF message and effort. [graph: see text]. Challenges are different amongst shifts. Shift culture may be stronger than workgroup culture. Work areas pose different challenges that all should be aware of and prepared for. We should prepare ourselves for challenges posed by the Spring and Summer seasons as well. We should be aware of and prepare for the different challenges and cultures characteristic of each shift. Supervisors need to spend more time in the field with their people to help them address safety issues and help make IIF a more consistent component of daily workgroup culture. Each site should analyze their data and look for their unique safety challenges. This will allow customized, focused action plans that meet the unique needs of each site.

  1. Non-occupational physical activity levels of shift workers compared with non-shift workers.

    PubMed

    Loef, Bette; Hulsegge, Gerben; Wendel-Vos, G C Wanda; Verschuren, W M Monique; Vermeulen, Roel C H; Bakker, Marije F; van der Beek, Allard J; Proper, Karin I

    2017-05-01

    Lack of physical activity (PA) has been hypothesised as an underlying mechanism in the adverse health effects of shift work. Therefore, our aim was to compare non-occupational PA levels between shift workers and non-shift workers. Furthermore, exposure-response relationships for frequency of night shifts and years of shift work regarding non-occupational PA levels were studied. Data of 5980 non-shift workers and 532 shift workers from the European Prospective Investigation into Cancer and Nutrition-Netherlands (EPIC-NL) were used in these cross-sectional analyses. Time spent (hours/week) in different PA types (walking/cycling/exercise/chores) and intensities (moderate/vigorous) were calculated based on self-reported PA. Furthermore, sports were operationalised as: playing sports (no/yes), individual versus non-individual sports, and non-vigorous-intensity versus vigorous-intensity sports. PA levels were compared between shift workers and non-shift workers using Generalized Estimating Equations and logistic regression. Shift workers reported spending more time walking than non-shift workers (B=2.3 (95% CI 1.2 to 3.4)), but shift work was not associated with other PA types and any of the sports activities. Shift workers who worked 1-4 night shifts/month (B=2.4 (95% CI 0.6 to 4.3)) and ≥5 night shifts/month (B=3.7 (95% CI 1.8 to 5.6)) spent more time walking than non-shift workers. No exposure-response relationships were found between years of shift work and PA levels. Shift workers spent more time walking than non-shift workers, but we observed no differences in other non-occupational PA levels. To better understand if and how PA plays a role in the negative health consequences of shift work, our findings need to be confirmed in future studies. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  2. Is there a shift to "active nanostructures"?

    NASA Astrophysics Data System (ADS)

    Subramanian, Vrishali; Youtie, Jan; Porter, Alan L.; Shapira, Philip

    2010-01-01

    It has been suggested that an important transition in the long-run trajectory of nanotechnology development is a shift from passive to active nanostructures. Such a shift could present different or increased societal impacts and require new approaches for risk assessment. An active nanostructure "changes or evolves its state during its operation," according to the National Science Foundation's (2006) Active Nanostructures and Nanosystems grant solicitation. Active nanostructure examples include nanoelectromechanical systems (NEMS), nanomachines, self-healing materials, targeted drugs and chemicals, energy storage devices, and sensors. This article considers two questions: (a) Is there a "shift" to active nanostructures? (b) How can we characterize the prototypical areas into which active nanostructures may emerge? We build upon the NSF definition of active nanostructures to develop a research publication search strategy, with a particular intent to distinguish between passive and active nanotechnologies. We perform bibliometric analyses and describe the main publication trends from 1995 to 2008. We then describe the prototypes of research that emerge based on reading the abstracts and review papers encountered in our search. Preliminary results suggest that there is a sharp rise in active nanostructures publications in 2006, and this rise is maintained in 2007 and through to early 2008. We present a typology that can be used to describe the kind of active nanostructures that may be commercialized and regulated in the future.

  3. Origin of the blue shift of the CH stretching band for 2-butoxyethanol in water.

    PubMed

    Katsumoto, Yukiteru; Komatsu, Hiroyuki; Ohno, Keiichi

    2006-07-26

    The blue shift of the isolated CD stretching band of 2-butoxyethanol (C4E1), which is observed for the aqueous solution during the dilution process, has been investigated by infrared (IR) spectroscopy and quantum chemical calculations. Mono-deuterium-labeled C4E1's were employed to remove the severe overlapping among the CH stretching bands. The isolated CD stretching mode of the alpha-methylene in the butoxy group shows a large blue shift, while those of the beta-methylene and methyl groups are not largely shifted. The spectral simulation results for the C4E1/H2O complexes indicate that the large blue shift of the CD stretching band of the butoxy group arises mainly from the hydration of the ether oxygen atom.

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

    PubMed

    Bültmann, Eva; Nägele, Thomas; Lanfermann, Heinrich; Klose, Uwe

    2017-01-01

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

  5. Protein structure refinement using a quantum mechanics-based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

    PubMed Central

    2017-01-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1–0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large

  6. New perspectives in the PAW/GIPAW approach: J(P-O-Si) coupling constants, antisymmetric parts of shift tensors and NQR predictions.

    PubMed

    Bonhomme, Christian; Gervais, Christel; Coelho, Cristina; Pourpoint, Frédérique; Azaïs, Thierry; Bonhomme-Coury, Laure; Babonneau, Florence; Jacob, Guy; Ferrari, Maude; Canet, Daniel; Yates, Jonathan R; Pickard, Chris J; Joyce, Siân A; Mauri, Francesco; Massiot, Dominique

    2010-12-01

    In 2001, Pickard and Mauri implemented the gauge including projected augmented wave (GIPAW) protocol for first-principles calculations of NMR parameters using periodic boundary conditions (chemical shift anisotropy and electric field gradient tensors). In this paper, three potentially interesting perspectives in connection with PAW/GIPAW in solid-state NMR and pure nuclear quadrupole resonance (NQR) are presented: (i) the calculation of J coupling tensors in inorganic solids; (ii) the calculation of the antisymmetric part of chemical shift tensors and (iii) the prediction of (14)N and (35)Cl pure NQR resonances including dynamics. We believe that these topics should open new insights in the combination of GIPAW, NMR/NQR crystallography, temperature effects and dynamics. Points (i), (ii) and (iii) will be illustrated by selected examples: (i) chemical shift tensors and heteronuclear (2)J(P-O-Si) coupling constants in the case of silicophosphates and calcium phosphates [Si(5)O(PO(4))(6), SiP(2)O(7) polymorphs and α-Ca(PO(3))(2)]; (ii) antisymmetric chemical shift tensors in cyclopropene derivatives, C(3)X(4) (X = H, Cl, F) and (iii) (14)N and (35)Cl NQR predictions in the case of RDX (C(3)H(6)N(6)O(6)), β-HMX (C(4)H(8)N(8)O(8)), α-NTO (C(2)H(2)N(4)O(3)) and AlOPCl(6). RDX, β-HMX and α-NTO are explosive compounds. Copyright © 2010 John Wiley & Sons, Ltd.

  7. Blue and red shifted temperature dependence of implicit phonon shifts in graphene

    NASA Astrophysics Data System (ADS)

    Mann, Sarita; Jindal, V. K.

    2017-07-01

    We have calculated the implicit shift for various modes of frequency in a pure graphene sheet. Thermal expansion and Grüneisen parameter which are required for implicit shift calculation have already been studied and reported. For this calculation, phonon frequencies are obtained using force constants derived from dynamical matrix calculated using VASP code where the density functional perturbation theory (DFPT) is used in interface with phonopy software. The implicit phonon shift shows an unusual behavior as compared to the bulk materials. The frequency shift is large negative (red shift) for ZA and ZO modes and the value of negative shift increases with increase in temperature. On the other hand, blue shift arises for all other longitudinal and transverse modes with a similar trend of increase with increase in temperature. The q dependence of phonon shifts has also been studied. Such simultaneous red and blue shifts in transverse or out plane modes and surface modes, respectively leads to speculation of surface softening in out of plane direction in preference to surface melting.

  8. Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory.

    PubMed

    Kussmann, Jörg; Ochsenfeld, Christian

    2007-08-07

    Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.

  9. Deprotonation/protonation of coordinated secondary thioamide units of pincer ruthenium complexes: modulation of voltammetric and spectroscopic characterization of the pincer complexes.

    PubMed

    Teratani, Takuya; Koizumi, Take-aki; Yamamoto, Takakazu; Tanaka, Koji; Kanbara, Takaki

    2011-09-21

    New pincer ruthenium complexes, [Ru(SCS)(tpy)]PF(6) (1) (SCS = 2,6-bis(benzylaminothiocarbonyl)phenyl), tpy = 2,2':6',2''-terpyridyl) and [Ru(SNS)(tpy)]PF(6) (2) (SNS = 2,5-bis(benzylaminothiocarbonyl)pyrrolyl), having κ(3)SCS and κ(3)SNS pincer ligands with two secondary thioamide units were synthesized by the reactions of [RuCl(3)(tpy)] with N,N'-dibenzyl-1,3-benzenedicarbothioamide (L1) and N,N'-dibenzyl-2,5-1H-pyrroledicarbothioamide (L2), respectively, and their chemical and electrochemical properties were elucidated. The structure of 1 was determined by X-ray crystallography. The complexes 1 and 2 showed a two-step deprotonation reaction by treatment with 1,8-diazabicyclo[5,4,0]undec-7-ene (DBU), and the addition of DBU led to a shift of the metal-centered redox couples to a lower potential by 720 and 550 mV, respectively. The di-deprotonated complexes were also studied by (1)H-NMR and UV-vis spectroscopy. The addition of methanesulfonic acid (MSA) to the di-deprotonated complexes enabled the recovery of 1 and 2, indicating that the thioamide moiety underwent a reversible deprotonation-protonation process, which resulted in regulating the redox potentials of the metal center. The Pourbaix diagram of 1 revealed that 1 underwent a one-proton/one-electron transfer process in the pH range of 5.83-10.35, and a two-proton/one-electron process at a pH of over 10.35, indicating that the deprotonation/protonation process of the complexes is related to proton-coupled electron transfer (PCET). This journal is © The Royal Society of Chemistry 2011

  10. Contributors to shift work tolerance in South Korean nurses working rotating shift.

    PubMed

    Jung, Hye-Sun; Lee, Bokim

    2015-05-01

    Shift workers have rapidly increased in South Korea; however, there is no published research exploring shift work tolerance among South Korean workers. This study aimed to investigate factors related to shift work tolerance in South Korean nurses. The sample comprised of 660 nurses who worked shifts in a large hospital in South Korea. A structured questionnaire included following comprehensive variables: demographic (age and number of children), individual (morningness and self-esteem), psychosocial (social support and job stress), lifestyle (alcohol consumption, physical activity, and BMI), and working condition factors (number of night shifts and working hours). Shift work tolerance was measured in terms of insomnia, fatigue, and depression. The results of hierarchical regressions indicate that all variables, except for three, number of children, BMI, and working hours, were related to at least one of the symptoms associated with shift work tolerance. Based on these results, we offer some practical implications to help improve shift work tolerance of workers. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Sleep Loss and Fatigue in Shift Work and Shift Work Disorder

    PubMed Central

    Åkerstedt, Torbjörn; Wright, Kenneth P.

    2010-01-01

    Shift work is highly prevalent in industrialized societies (>20%) but, when it includes night work, it has pronounced negative effects on sleep, subjective and physiological sleepiness, performance, accident risk, as well as on health outcomes such as cardiovascular disease and certain forms of cancer. The reason is the conflict between the day oriented circadian physiology and the requirement for work and sleep at the “wrong” biological time of day. Other factors that negatively impact work shift sleepiness and accident risk include long duration shifts greater than 12 hours and individual vulnerability for phase intolerance that may lead to a diagnosis of shift work disorder; i.e., those shift workers with the greatest sleepiness and performance impairment during the biological night and insomnia during the biological day. Whereas some countermeasures may be used to ameliorate the negative impact of shift work on nighttime sleepiness and daytime insomnia (combined countermeasures may be the best available), there seems at present to be no way to eliminate most of the negative effects of shift work on human physiology and cognition. PMID:20640236

  12. Expert system application for prioritizing preventive actions for shift work: shift expert.

    PubMed

    Esen, Hatice; Hatipoğlu, Tuğçen; Cihan, Ahmet; Fiğlali, Nilgün

    2017-09-19

    Shift patterns, work hours, work arrangements and worker motivations have increasingly become key factors for job performance. The main objective of this article is to design an expert system that identifies the negative effects of shift work and prioritizes mitigation efforts according to their importance in preventing these negative effects. The proposed expert system will be referred to as the shift expert. A thorough literature review is conducted to determine the effects of shift work on workers. Our work indicates that shift work is linked to demographic variables, sleepiness and fatigue, health and well-being, and social and domestic conditions. These parameters constitute the sections of a questionnaire designed to focus on 26 important issues related to shift work. The shift expert is then constructed to provide prevention advice at the individual and organizational levels, and it prioritizes this advice using a fuzzy analytic hierarchy process model, which considers comparison matrices provided by users during the prioritization process. An empirical study of 61 workers working on three rotating shifts is performed. After administering the questionnaires, the collected data are analyzed statistically, and then the shift expert produces individual and organizational recommendations for these workers.

  13. Characterization Data Package for Containerized Sludge Samples Collected from Engineered Container SCS-CON-210

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fountain, Matthew S.; Fiskum, Sandra K.; Baldwin, David L.

    This data package contains the K Basin sludge characterization results obtained by Pacific Northwest National Laboratory during processing and analysis of four sludge core samples collected from Engineered Container SCS-CON-210 in 2010 as requested by CH2M Hill Plateau Remediation Company. Sample processing requirements, analytes of interest, detection limits, and quality control sample requirements are defined in the KBC-33786, Rev. 2. The core processing scope included reconstitution of a sludge core sample distributed among four to six 4-L polypropylene bottles into a single container. The reconstituted core sample was then mixed and subsampled to support a variety of characterization activities. Additionalmore » core sludge subsamples were combined to prepare a container composite. The container composite was fractionated by wet sieving through a 2,000 micron mesh and a 500-micron mesh sieve. Each sieve fraction was sampled to support a suite of analyses. The core composite analysis scope included density determination, radioisotope analysis, and metals analysis, including the Waste Isolation Pilot Plant Hazardous Waste Facility Permit metals (with the exception of mercury). The container composite analysis included most of the core composite analysis scope plus particle size distribution, particle density, rheology, and crystalline phase identification. A summary of the received samples, core sample reconstitution and subsampling activities, container composite preparation and subsampling activities, physical properties, and analytical results are presented. Supporting data and documentation are provided in the appendices. There were no cases of sample or data loss and all of the available samples and data are reported as required by the Quality Assurance Project Plan/Sampling and Analysis Plan.« less

  14. Alginate-cellulose sulphate-oligocation microcapsules: optimization of mass transport and mechanical properties.

    PubMed

    Schuldt, U; Hunkeler, D

    2007-02-01

    Microcapsules based on polyelectrolyte complexation, where the inner phase involves a blend of alginate and sodium cellulose sulphate (SCS), have mechanical and transport properties which are relatively insensitive to the chemical composition of the rigid polyanion. Specifically, the bursting force of 400- and 1000 microm microcapsules increase slightly with the degree of substitution of the SCS, though the molar mass of the SCS appears to influence the transport properties more strongly than its composition. The concentration of the sodium chloride in the gelling batch can be varied rather extensively, with optimum properties at approximately half (i.e. 0.5 M) the level typically employed for the formation of cell-containing microcapsules. This indicates that the microcapsule properties can be tuned for biocompatability, without concern that changes to the polymer microstructure or reaction process conditions would adversely influence the bursting force or molar mass cut-off of the capsules. The alginate-SCS blend, which is typical equimass, can be slightly increased in favour of the SCS (to 55 wt%) if one seeks to mechanically optimize the system. The substitution of the oligocation polymethylene-co-guanidine with pDADMAC seems strongly undesirable. Similarly, the replacement of SCS with sulphoethylcellulose, while possible, offers no important advantages. The overall optimum conditions appear to be for a SCS with a DS of 2, prepared at 1.2 wt% of total cation with alginate. The ideal ratio, for mechanical and transport properties, of SCS to alginate is 55:45 (wt:wt), which represents a subtle modification from the classical formulation with very good biocompatability.

  15. Chrodrimanins K-N and Related Meroterpenoids from the Fungus Penicillium sp. SCS-KFD09 Isolated from a Marine Worm, Sipunculus nudus.

    PubMed

    Kong, Fan-Dong; Ma, Qing-Yun; Huang, Sheng-Zhuo; Wang, Pei; Wang, Jun-Feng; Zhou, Li-Man; Yuan, Jing-Zhe; Dai, Hao-Fu; Zhao, You-Xing

    2017-04-28

    Six new meroterpenoids, chrodrimanins K-N (1-4), including two uncommon chlorinated ones (1 and 2), and verruculides B2 (5) and B3 (6), as well as seven known ones (7-13), were isolated from the fermentation broth of Penicillium sp. SCS-KFD09 isolated from a marine worm, Sipunculus nudus, from Haikou Bay, China. The structures including the absolute configurations of the new compounds were unambiguously elucidated by spectroscopic data, X-ray diffraction analysis, and ECD spectra analysis along with quantum ECD calculations. In addition, the X-ray crystal structures and absolute configurations of two previously reported meroterpenoids, chrodrimanins F (9) and A (11), are described for the first time. Compounds 1, 4, and 7 displayed anti-H1N1 activity with IC 50 values of 74, 58, and 34 μM, respectively, while compound 5 showed weak inhibitory activity against Staphylococcus aureus with an MIC of 32 μg/mL.

  16. Modeling nuclear field shift isotope fractionation in crystals

    NASA Astrophysics Data System (ADS)

    Schauble, E. A.

    2013-12-01

    In this study nuclear field shift fractionations in solids (and chemically similar liquids) are estimated using calibrated density functional theory calculations. The nuclear field shift effect is a potential driver of mass independent isotope fractionation(1,2), especially for elements with high atomic number such as Hg, Tl and U. This effect is caused by the different shapes and volumes of isotopic nuclei, and their interactions with electronic structures and energies. Nuclear field shift isotope fractionations can be estimated with first principles methods, but the calculations are computationally difficult, limiting most theoretical studies so far to small gas-phase molecules and molecular clusters. Many natural materials of interest are more complex, and it is important to develop ways to estimate field shift effects that can be applied to minerals, solutions, in biomolecules, and at mineral-solution interfaces. Plane-wave density functional theory, in combination with the projector augmented wave method (DFT-PAW), is much more readily adapted to complex materials than the relativistic all-electron calculations that have been the focus of most previous studies. DFT-PAW is a particularly effective tool for studying crystals with periodic boundary conditions, and may also be incorporated into molecular dynamics simulations of solutions and other disordered phases. Initial calibrations of DFT-PAW calculations against high-level all-electron models of field shift fractionation suggest that there may be broad applicability of this method to a variety of elements and types of materials. In addition, the close relationship between the isomer shift of Mössbauer spectroscopy and the nuclear field shift isotope effect makes it possible, at least in principle, to estimate the volume component of field shift fractionations in some species that are too complex even for DFT-PAW models, so long as there is a Mössbauer isotope for the element of interest. Initial results

  17. Measuring (19)F shift anisotropies and (1)H-(19)F dipolar interactions with ultrafast MAS NMR.

    PubMed

    Martini, Francesca; Miah, Habeeba K; Iuga, Dinu; Geppi, Marco; Titman, Jeremy J

    2015-10-01

    A new (19)F anisotropic-isotropic shift correlation experiment is described that operates with ultrafast MAS, resulting in good resolution of isotropic (19)F shifts in the detection dimension. The new experiment makes use of a recoupling sequence designed using symmetry principles that reintroduces the (19)F chemical shift anisotropy in the indirect dimension. The situations in which the new experiment is appropriate are discussed, and the (19)F shift anisotropy parameters in poly(difluoroethylene) (PVDF) are measured. In addition, similar recoupling sequences are shown to be effective for measuring (1)H-(19)F distances via the heteronuclear dipolar interaction. This is demonstrated by application to a recently synthesized zirconium phosphonate material that contains one-dimensional chains linked by H-F hydrogen bonds. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    NASA Technical Reports Server (NTRS)

    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.

  19. Theoretical Modeling of (99)Tc NMR Chemical Shifts.

    PubMed

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

    2016-09-06

    Technetium-99 (Tc) displays a rich chemistry due to its wide range of accessible oxidation states (from -I to +VII) and ability to form coordination compounds. Determination of Tc speciation in complex mixtures is a major challenge, and (99)Tc nuclear magnetic resonance (NMR) spectroscopy is widely used to probe chemical environments of Tc in odd oxidation states. However, interpretation of (99)Tc NMR data is hindered by the lack of reference compounds. Density functional theory (DFT) calculations can help to fill this gap, but to date few computational studies have focused on (99)Tc NMR of compounds and complexes. This work evaluates the effectiveness of both pure generalized gradient approximation and their corresponding hybrid functionals, both with and without the inclusion of scalar relativistic effects, to model the (99)Tc NMR spectra of Tc(I) carbonyl compounds. With the exception of BLYP, which performed exceptionally well overall, hybrid functionals with inclusion of scalar relativistic effects are found to be necessary to accurately calculate (99)Tc NMR spectra. The computational method developed was used to tentatively assign an experimentally observed (99)Tc NMR peak at -1204 ppm to fac-Tc(CO)3(OH)3(2-). This study examines the effectiveness of DFT computations for interpretation of the (99)Tc NMR spectra of Tc(I) coordination compounds in high salt alkaline solutions.

  20. Shifting schedules: the health effects of reorganizing shift work.

    PubMed

    Bambra, Clare L; Whitehead, Margaret M; Sowden, Amanda J; Akers, Joanne; Petticrew, Mark P

    2008-05-01

    Approximately one fifth of workers are engaged in some kind of shift work. The harmful effects of shift work on the health and work-life balance of employees are well known. A range of organizational interventions has been suggested to address these negative effects. This study undertook the systematic review (following Quality Of Reporting Of Meta [QUORUM] analyses guidelines) of experimental and quasi-experimental studies, from any country (in any language) that evaluated the effects on health and work-life balance of organizational-level interventions that redesign shift work schedules. Twenty-seven electronic databases (medical, social science, economic) were searched. Data extraction and quality appraisal were carried out by two independent reviewers. Narrative synthesis was performed. The review was conducted between October 2005 and November 2006. Twenty-six studies were found relating to a variety of organizational interventions. No one type of intervention was found to be consistently harmful to workers. However, three types were found to have beneficial effects on health and work-life balance: (1) switching from slow to fast rotation, (2) changing from backward to forward rotation, and (3) self-scheduling of shifts. Improvements were usually at little or no direct organizational cost. However, there were concerns about the generalizability of the evidence, and no studies reported on impacts on health inequalities. This review reinforces the findings of epidemiologic and laboratory-based research by suggesting that certain organizational-level interventions can improve the health of shift workers, their work-life balance, or both. This evidence could be useful when designing interventions to improve the experience of shift work.

  1. Fatigue crack growth in unidirectional and cross-ply SCS-6/Timetal 21S titanium matrix composite

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Herrmann, D.J.

    1994-01-01

    Fatigue crack growth in unidirectional and cross-ply SCS-6/ Timetal(R) 21S titanium matrix composite was investigated. Fatigue crack growth tests were performed on (0){sub 4}, (90){sub 4}, and (0/90){sub s} center notch specimens. The (0){sub 4} and (0/90){sub s} fatigue crack growth rates decreased initially. Specimens removed prior to failure were polished to the first row of fibers and intact fibers in the wake of the matrix crack were observed. These bridging fibers reduced the stress intensity range that the matrix material was subjected to, thus reducing the crack growth rate. The crack growth rate eventually increased as fibers failed inmore » the crack wake but the fatigue crack growth rate was still much slower than that of unreinforced Timetal(R) 21S. A model was developed to study the mechanics of a cracked unidirectional composite with any combination of intact and broken fibers in the wake of a matrix crack. The model was correlated to fatigue crack growth rate tests. The model was verified by comparing predicted displacements near the crack surface with Elber gage (1.5 mm gage length extensometer) measurements. The fatigue crack growth rate for the (90){sub 4} specimens was faster than that of unreinforced Timetal(registered trademark) 21S. Elber gage displacement measurements were in agreement with linear elastic fracture mechanics predictions, suggesting that linear elastic fracture mechanics may be applicable to transversely loaded titanium matrix composites.« less

  2. Assigning the stereochemistry of syn and anti β-trimethylsiloxy-α-trimethylsilyl alkanoic acid silyl esters using GIAO 1H NMR chemical shift calculations

    NASA Astrophysics Data System (ADS)

    Hadj Mohamed, Slim; Trabelsi, Mahmoud; Champagne, Benoît

    2017-08-01

    The stereostructure of β-trimethylsiloxy-α-trimethylsilyl alkanoic acid silyl esters synthesized by Bellassoued et al. [J. Org. Chem. 2001, 66, 5054-5057] using Mukaiyama aldol reaction has been reassigned using density functional theory NMR 1H chemical shifts calculations. It is now concluded that the major diastereoisomer is syn and the minor is anti. Within this assignment, for all silyl esters, δHa(anti) > δHa(syn), δHb(anti) < δHb(syn), and 3JHa-Hb (anti) > 3JHa-Hb (syn). Since the experimental assignment was based on the stereostructure (E/Z) of the cinnamic acid obtained by elimination of trimethylsilyl 3-phenyl-3-(trimethylsiloxy)-2-(trimethylsilyl)propanoate in the presence of TiCl4 and on the assumption that this elimination is anti stereospecific in acidic medium, one arrives at the conclusion that the elimination of syn and anti β-trimethylsiloxy-α-trimethylsilyl alkanoic acid silyl esters is not anti stereospecific.

  3. 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

    NASA Astrophysics Data System (ADS)

    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.

  4. Correlation between the Temperature Dependence of Intrsinsic Mr Parameters and Thermal Dose Measured by a Rapid Chemical Shift Imaging Technique

    PubMed Central

    Taylor, Brian A.; Elliott, Andrew M.; Hwang, Ken-Pin; Hazle, John D.; Stafford, R. Jason

    2011-01-01

    In order to investigate simultaneous MR temperature imaging and direct validation of tissue damage during thermal therapy, temperature-dependent signal changes in proton resonance frequency (PRF) shifts, R2* values, and T1-weighted amplitudes are measured from one technique in ex vivo tissue heated with a 980-nm laser at 1.5T and 3.0T. Using a multi-gradient echo acquisition and signal modeling with the Stieglitz-McBride algorithm, the temperature sensitivity coefficient (TSC) values of these parameters are measured in each tissue at high spatiotemporal resolutions (1.6×1.6×4mm3,≤5sec) at the range of 25-61 °C. Non-linear changes in MR parameters are examined and correlated with an Arrhenius rate dose model of thermal damage. Using logistic regression, the probability of changes in these parameters is calculated as a function of thermal dose to determine if changes correspond to thermal damage. Temperature calibrations demonstrate TSC values which are consistent with previous studies. Temperature sensitivity of R2* and, in some cases, T1-weighted amplitudes are statistically different before and after thermal damage occurred. Significant changes in the slopes of R2* as a function of temperature are observed. Logistic regression analysis shows that these changes could be accurately predicted using the Arrhenius rate dose model (Ω=1.01±0.03), thereby showing that the changes in R2* could be direct markers of protein denaturation. Overall, by using a chemical shift imaging technique with simultaneous temperature estimation, R2* mapping and T1-W imaging, it is shown that changes in the sensitivity of R2* and, to a lesser degree, T1-W amplitudes are measured in ex vivo tissue when thermal damage is expected to occur according to Arrhenius rate dose models. These changes could possibly be used for direct validation of thermal damage in contrast to model-based predictions. PMID:21721063

  5. Improving chemical shift encoding‐based water–fat separation based on a detailed consideration of magnetic field contributions

    PubMed Central

    Ruschke, Stefan; Eggers, Holger; Meineke, Jakob; Rummeny, Ernst J.; Karampinos, Dimitrios C.

    2018-01-01

    Purpose To improve the robustness of existing chemical shift encoding‐based water–fat separation methods by incorporating a priori information of the magnetic field distortions in complex‐based water–fat separation. Methods Four major field contributions are considered: inhomogeneities of the scanner magnet, the shim field, an object‐based field map estimate, and a residual field. The former two are completely determined by spherical harmonic expansion coefficients directly available from the magnetic resonance (MR) scanner. The object‐based field map is forward simulated from air–tissue interfaces inside the field of view (FOV). The missing residual field originates from the object outside the FOV and is investigated by magnetic field simulations on a numerical whole body phantom. In vivo the spatially linear first‐order component of the residual field is estimated by measuring echo misalignments after demodulation of other field contributions resulting in a linear residual field. Gradient echo datasets of the cervical and the ankle region without and with shimming were acquired, where all four contributions were incorporated in the water–fat separation with two algorithms from the ISMRM water–fat toolbox and compared to water–fat separation with less incorporated field contributions. Results Incorporating all four field contributions as demodulation steps resulted in reduced temporal and spatial phase wraps leading to almost swap‐free water–fat separation results in all datasets. Conclusion Demodulating estimates of major field contributions reduces the phase evolution to be driven by only small differences in local tissue susceptibility, which supports the field smoothness assumption of existing water–fat separation techniques. PMID:29424458

  6. Correlation of the bond-length change and vibrational frequency shift in model hydrogen-bonded complexes of pyrrole

    NASA Astrophysics Data System (ADS)

    McDowell, Sean A. C.

    2017-04-01

    An MP2 computational study of model hydrogen-bonded pyrrole⋯YZ (YZ = NH3, NCH, BF, CO, N2, OC, FB) complexes was undertaken in order to examine the variation of the Nsbnd H bond length change and its associated vibrational frequency shift. The chemical hardness of Y, as well as the YZ dipole moment, were found to be important parameters in modifying the bond length change/frequency shift. The basis set effect on the computed properties was also assessed. A perturbative model, which accurately reproduced the ab initio Nsbnd H bond length changes and frequency shifts, was useful in rationalizing the observed trends.

  7. Effect of substrate bias voltage on tensile properties of single crystal silicon microstructure fully coated with plasma CVD diamond-like carbon film

    NASA Astrophysics Data System (ADS)

    Zhang, Wenlei; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Tabata, Osamu

    2018-06-01

    Tensile strength and strength distribution in a microstructure of single crystal silicon (SCS) were improved significantly by coating the surface with a diamond-like carbon (DLC) film. To explore the influence of coating parameters and the mechanism of film fracture, SCS microstructure surfaces (120 × 4 × 5 μm3) were fully coated by plasma enhanced chemical vapor deposition (PECVD) of a DLC at five different bias voltages. After the depositions, Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), thermal desorption spectrometry (TDS), surface profilometry, atomic force microscope (AFM) measurement, and nanoindentation methods were used to study the chemical and mechanical properties of the deposited DLC films. Tensile test indicated that the average strength of coated samples was 13.2-29.6% higher than that of the SCS sample, and samples fabricated with a -400 V bias voltage were strongest. The fracture toughness of the DLC film was the dominant factor in the observed tensile strength. Deviations in strength were reduced with increasingly negative bias voltage. The effect of residual stress on the tensile properties is discussed in detail.

  8. Determination of the three-dimensional structure of oligosaccharides in the solid state from experimental 13C NMR data and ab initio chemical shift surfaces.

    PubMed

    Sergeyev, Ivan; Moyna, Guillermo

    2005-05-02

    A novel method for the determination of the three-dimensional (3D) structure of oligosaccharides in the solid state using experimental 13C NMR data is presented. The approach employs this information, combined with 13C chemical shift surfaces (CSSs) for the glycosidic bond carbons in the generation of NMR pseudopotential energy functions suitable for use as constraints in molecular modeling simulations. Application of the method to trehalose, cellobiose, and cellotetraose produces 3D models that agree remarkably well with the reported X-ray structures, with phi and psi dihedral angles that are within 10 degrees from the ones observed in the crystals. The usefulness of the approach is further demonstrated in the determination of the 3D structure of the cellohexaose, an hexasaccharide for which no X-ray data has been reported, as well as in the generation of accurate structural models for cellulose II and amylose V6.

  9. Merlin controls the repair capacity of Schwann cells after injury by regulating Hippo/YAP activity

    PubMed Central

    Doddrell, Robin D.S.; Edwards, Philip; Morrison, Helen

    2017-01-01

    Loss of the Merlin tumor suppressor and activation of the Hippo signaling pathway play major roles in the control of cell proliferation and tumorigenesis. We have identified completely novel roles for Merlin and the Hippo pathway effector Yes-associated protein (YAP) in the control of Schwann cell (SC) plasticity and peripheral nerve repair after injury. Injury to the peripheral nervous system (PNS) causes a dramatic shift in SC molecular phenotype and the generation of repair-competent SCs, which direct functional repair. We find that loss of Merlin in these cells causes a catastrophic failure of axonal regeneration and remyelination in the PNS. This effect is mediated by activation of YAP expression in Merlin-null SCs, and loss of YAP restores axonal regrowth and functional repair. This work identifies new mechanisms that control the regenerative potential of SCs and gives new insight into understanding the correct control of functional nerve repair in the PNS. PMID:28137778

  10. A unique, fast-forwards rotating schedule with 12-h long shifts prevents chronic sleep debt.

    PubMed

    Fischer, Dorothee; Vetter, Céline; Oberlinner, Christoph; Wegener, Sven; Roenneberg, Till

    2016-01-01

    Sleep debt--together with circadian misalignment--is considered a central factor for adverse health outcomes associated with shift work. Here, we describe in detail sleep-wake behavior in a fast-forward rotating 12-h shift schedule, which involves at least 24 hours off after each shift and thus allows examining the role of immediate recovery after shift-specific sleep debt. Thirty-five participants at two chemical plants in Germany were chronotyped using the Munich ChronoType Questionnaire for Shift-Workers (MCTQ(Shift)) and wore actimeters throughout the two-week study period. From these actimetry recordings, we computed sleep and nap duration, social jetlag (a measure of circadian misalignment), and the daily timing of activity and sleep (center of gravity and mid-sleep, respectively). We observed that the long off-work periods between each shift create a fast alternation between shortened (mean ± standard deviation, 5h 17min ± 56min) and extended (8h 25min ± 72min) sleep episodes resulting in immanent reductions of sleep debt. Additionally, extensive napping of early chronotypes (up to 3 hours before the night shift) statistically compensated short sleep durations after the night shift. Partial rank correlations showed chronotype-dependent patterns of sleep and activity that were similar to those previously described in 8-h schedules; however, sleep before the day shift did not differ between chronotypes. Our findings indicate that schedules preventing a build-up of chronic sleep debt may reduce detrimental effects of shift work irrespective of shift duration. Prospective studies are needed to further elucidate the relationship between sleep, the circadian system, and health and safety hazards.

  11. Integrated ecological and chemical food web accumulation modeling explains PAH temporal trends during regime shifts in a shallow lake.

    PubMed

    Kong, Xiangzhen; He, Wei; Qin, Ning; Liu, Wenxiu; Yang, Bin; Yang, Chen; Xu, Fuliu; Mooij, Wolf M; Koelmans, Albert A

    2017-08-01

    Shallow lakes can switch suddenly from a turbid situation with high concentrations of phytoplankton and other suspended solids to a vegetated state with clear water, and vice versa. These alternative stable states may have a substantial impact on the fate of hydrophobic organic compounds (HOCs). Models that are fit to simulate impacts from these complex interactions are scarce. We developed a contaminant fate model which is linked to an ecosystem model (PCLake) for shallow lakes. This integrated model was successful in simulating long-term dynamics (1953-2012) of representative polycyclic aromatic hydrocarbons (PAHs) in the main biotic and abiotic components in a large shallow lake (Chaohu in China), which has undergone regime shifts in this period. Historical records from sediment cores were used to evaluate the model. The model revealed that regime shifts in shallow lakes had a strong impact on the fate of less hydrophobic compounds due to the large storage capacity of macrophytes, which accumulated up to 55.6% of phenanthrene in the clear state. The abrupt disappearance of macrophytes after the regime shift resulted in a sudden change in phenanthrene distribution, as the sediment became the major sink. For more hydrophobic compounds such as benzo(a)pyrene, the modeled impact of the regime shift was negligible for the whole environment, yet large for biotic compartments. This study is the first to provide a full mechanistic analysis of the impact of regime shifts on the fate of PAHs in a real lake ecosystem. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

    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. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M. B.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Laurie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Lui, J.; hide

    2015-01-01

    INTRODUCTION: Mechanisms responsible for the ocular structural and functional changes that characterize the visual impairment and intracranial pressure (ICP) syndrome (VIIP) are unclear, but hypothesized to be secondary to the cephalad fluid shift experienced in spaceflight. This study will relate the fluid distribution and compartmentalization associated with long-duration spaceflight with VIIP symptoms. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, can be predicted preflight with acute hemodynamic manipulations, and also if lower body negative pressure (LBNP) can reverse the VIIP effects. METHODS: Physiologic variables will be examined pre-, in- and post-flight in 10 International Space Station crewmembers including: fluid compartmentalization (D2O and NaBr dilution); interstitial tissue thickness (ultrasound); vascular dimensions and dynamics (ultrasound and MRI (including cerebrospinal fluid pulsatility)); ocular measures (optical coherence tomography, intraocular pressure, ultrasound); and ICP measures (tympanic membrane displacement, otoacoustic emissions). Pre- and post-flight measures will be assessed while upright, supine and during 15 deg head-down tilt (HDT). In-flight measures will occur early and late during 6 or 12 month missions. LBNP will be evaluated as a countermeasure during HDT and during spaceflight. RESULTS: The first two crewmembers are in the preflight testing phase. Preliminary results characterize the acute fluid shifts experienced from upright, to supine and HDT postures (increased stroke volume, jugular dimensions and measures of ICP) which are reversed with 25 millimeters Hg LBNP. DISCUSSION: Initial results indicate that acute cephalad fluid shifts may be related to VIIP symptoms, but also may be reversible by LBNP. The effect of a chronic fluid shift has yet to be evaluated. Learning Objectives: Current spaceflight VIIP research is described

  14. Risk of emergency medical treatment following consumption of cannabis or synthetic cannabinoids in a large global sample.

    PubMed

    Winstock, Adam; Lynskey, Michael; Borschmann, Rohan; Waldron, Jon

    2015-06-01

    Synthetic cannabinoids (SCs) have become increasingly popular in recent years. Diverse in chemical structure, many have been subjected to legislative regulation, but their availability and use persists. Often marketed to reflect their similar effects to cannabis, their use has been associated with a range of negative health effects. We sought to determine the relative risk of seeking emergency medical treatment (EMT) following use of SCs and natural cannabis. We utilized an anonymous online survey of drug use, obtaining data from 22,289 respondents. We calculated the relative risk of seeking EMT between the two substances using an estimate for days used in the past year. Thirty-seven cannabis users (0.2%) and 21 SC users (1.0%) had sought EMT during the past year following use. The relative risk associated with the use of SCs was 30 (95% CI 17.5-51.2) times higher than that associated with cannabis. Significantly more symptoms (p=0.03) were reported by respondents seeking treatment for SCs than for cannabis. Whilst these findings must be treated with caution, SCs potentially pose a greater risk to users' health than natural forms of cannabis. Regulation is unlikely to remove SCs from the market, so well-informed user-focused health promotion messages need to be crafted to discourage their use. © The Author(s) 2015.

  15. Chemical shift magnetic resonance imaging for distinguishing minimal-fat renal angiomyolipoma from renal cell carcinoma: a meta-analysis.

    PubMed

    Chen, Ling-Shan; Zhu, Zheng-Qiu; Wang, Zhi-Tao; Li, Jing; Liang, Li-Feng; Jin, Ji-Yang; Wang, Zhong-Qiu

    2018-05-01

    To determine the performance of chemical shift signal intensity index (CS-SII) values for distinguishing minimal-fat renal angiomyolipoma (mfAML) from renal cell carcinoma (RCC) and to assess RCC subtype characterisation. We identified eligible studies on CS magnetic resonance imaging (CS-MRI) of focal renal lesions via PubMed, Embase, and the Cochrane Library. CS-SII values were extracted by lesion type and evaluated using linear mixed model-based meta-regression. RCC subtypes were analysed. Two-sided p value <0.05 indicated statistical significance. Methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 tool. Eleven articles involving 850 patients were included. Minimal-fat AML had significantly higher CS-SII value than RCC (p < 0.05); there were no significant differences between mfAML and clear cell RCC (cc-RCC) (p = 0.112). Clear cell RCC had a significantly higher CS-SII value than papillary RCC (p-RCC) (p < 0.001) and chromophobe RCC (ch-RCC) (p = 0.045). The methodological quality was relatively high, and Begg's test data points indicated no obvious publication bias. The CS-SII value for differentiating mfAML from cc-RCC remains unproven, but is a promising method for differentiating cc-RCC from p-RCC and ch-RCC. • RCC CS-SII values are significantly lower than those of mfAML overall. • CS-SII values cannot aid differentiation between mfAML and cc-RCC. • CS-SII values might help characterise RCC subtypes.

  16. Comparison of brown and white adipose tissues in infants and children with chemical-shift-encoded water-fat MRI.

    PubMed

    Hu, Houchun H; Yin, Larry; Aggabao, Patricia C; Perkins, Thomas G; Chia, Jonathan M; Gilsanz, Vicente

    2013-10-01

    To compare fat-signal fractions (FFs) and T2* values between brown (BAT) and white (WAT) adipose tissue located within the supraclavicular fossa and subcutaneous depots, respectively. Twelve infants and 39 children were studied. Children were divided into lean and overweight/obese subgroups. Chemical-shift-encoded water-fat magnetic resonance imaging (MRI) was used to quantify FFs and T2* metrics in the supraclavicular and adjacent subcutaneous adipose tissue depots. Linear regression and t-tests were performed. Infants had lower supraclavicular FFs than children (P < 0.01) but T2* values were similar (P = 0.5). Lean children exhibited lower supraclavicular FFs and T2* values than overweight children (P < 0.01). In each individual infant and child, supraclavicular FFs were consistently lower than adjacent subcutaneous FFs. Supraclavicular T2* values were consistently lower than subcutaneous T2* values in children, but not in infants. FFs in both depots were positively correlated with age and weight in infants (P < 0.01). In children, they were correlated with weight and body mass index (BMI) (P < 0.01), but not age. Correlations between T2* and anthropometric variables existed in children (P < 0.01), but were absent in infants. Cross-sectional comparisons suggest variations in FF and T2* values in the supraclavicular and subcutaneous depots of infants and children, which are potentially indicative of physiological differences in adipose tissue fat content, amount, and metabolic activity. Copyright © 2013 Wiley Periodicals, Inc.

  17. Shifting Attention

    ERIC Educational Resources Information Center

    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…

  18. A storm-based CSLE incorporating the modified SCS-CN method for soil loss prediction on the Chinese Loess Plateau

    NASA Astrophysics Data System (ADS)

    Shi, Wenhai; Huang, Mingbin

    2017-04-01

    the storm-based CSLE. In addition, the surface runoff used by the storm-based CSLE was either obtained from measurements or from the values predicted by the modified Soil Conservation Service Curve Number (SCS-CN) method. When using the measured runoff, the storm-based CSLE had an E of 76.6%, whereas the use of the predicted runoff gave an E of 76.4%. The high E values indicated that the storm-based CSLE incorporating the modified SCS-CN method could accurately predict storm-event-based soil losses resulting from both sheet and rill erosion at the field scale on the Chinese Loess Plateau. This approach could be applicable to other areas of the world once the model parameters have been suitably calibrated.

  19. Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.

    PubMed

    Kobayashi, Ayaho; Kanaba, Teppei; Satoh, Ryosuke; Ito, Yutaka; Sugiura, Reiko; Mishima, Masaki

    2017-10-01

    Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1. Phosphorylation significantly reduces RNA-binding activity and likely modulates Nrd1 function. To reveal the relationship between the structure and function of Nrd1 and how phosphorylation affects structure, we used heteronuclear NMR techniques to investigate the three-dimensional structure of Nrd1. Here we report the 1 H, 13 C, and 15 N resonance assignments of RRM1-RRM2 (residues 108-284) comprising the first and second RRMs obtained using heteronuclear NMR techniques. Secondary structures derived from the chemical shifts are reported. These data should contribute to the understanding of the three-dimensional structure of the RRM1-RRM2 region of Nrd1 and the perturbation caused by phosphorylation.

  20. Work shift duration: a review comparing eight hour and 12 hour shift systems.

    PubMed

    Smith, L; Folkard, S; Tucker, P; Macdonald, I

    1998-04-01

    Shiftwork is now a major feature of working life across a broad range of industries. The features of the shift systems operated can impact on the wellbeing, performance, and sleep of shiftworkers. This paper reviews the current state of knowledge on one major characteristic of shift rotas-namely, shift duration. Evidence comparing the relative effects of eight hour and 12 hour shifts on fatigue and job performance, safety, sleep, and physical and psychological health are considered. At the organisational level, factors such as the mode of system implementation, attitudes towards shift rotas, sickness absence and turnover, overtime, and moonlighting are discussed. Manual and electronic searches of the shiftwork research literature were conducted to obtain information on comparisons between eight hour and 12 hour shifts. The research findings are largely equivocal. The bulk of the evidence suggests few differences between eight and 12 hour shifts in the way they affect people. There may even be advantages to 12 hour shifts in terms of lower stress levels, better physical and psychological wellbeing, improved durations and quality of off duty sleep as well as improvements in family relations. On the negative side, the main concerns are fatigue and safety. It is noted that a 12 hour shift does not equate with being active for only 12 hours. There can be considerable extension of the person's time awake either side of the shift. However, the effects of longer term exposure to extended work days have been relatively uncharted in any systematic way. Longitudinal comparative research into the chronic impact of the compressed working week is needed.

  1. Insomnia in shift work.

    PubMed

    Vallières, Annie; Azaiez, Aïda; Moreau, Vincent; LeBlanc, Mélanie; Morin, Charles M

    2014-12-01

    Shift work disorder involves insomnia and/or excessive sleepiness associated with the work schedule. The present study examined the impact of insomnia on the perceived physical and psychological health of adults working on night and rotating shift schedules compared to day workers. A total of 418 adults (51% women, mean age 41.4 years), including 51 night workers, 158 rotating shift workers, and 209 day workers were selected from an epidemiological study. An algorithm was used to classify each participant of the two groups (working night or rotating shifts) according to the presence or absence of insomnia symptoms. Each of these individuals was paired with a day worker according to gender, age, and income. Participants completed several questionnaires measuring sleep, health, and psychological variables. Night and rotating shift workers with insomnia presented a sleep profile similar to that of day workers with insomnia. Sleep time was more strongly related to insomnia than to shift work per se. Participants with insomnia in the three groups complained of anxiety, depression, and fatigue, and reported consuming equal amounts of sleep-aid medication. Insomnia also contributed to chronic pain and otorhinolaryngology problems, especially among rotating shift workers. Work productivity and absenteeism were more strongly related to insomnia. The present study highlights insomnia as an important component of the sleep difficulties experienced by shift workers. Insomnia may exacerbate certain physical and mental health problems of shift workers, and impair their quality of life. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Effects of extended work shifts and shift work on patient safety, productivity, and employee health.

    PubMed

    Keller, Simone M

    2009-12-01

    It is estimated 1.3 million health care errors occur each year and of those errors 48,000 to 98,000 result in the deaths of patients (Barger et al., 2006). Errors occur for a variety of reasons, including the effects of extended work hours and shift work. The need for around-the-clock staff coverage has resulted in creative ways to maintain quality patient care, keep health care errors or adverse events to a minimum, and still meet the needs of the organization. One way organizations have attempted to alleviate staff shortages is to create extended work shifts. Instead of the standard 8-hour shift, workers are now working 10, 12, 16, or more hours to provide continuous patient care. Although literature does support these staffing patterns, it cannot be denied that shifts beyond the traditional 8 hours increase staff fatigue, health care errors, and adverse events and outcomes and decrease alertness and productivity. This article includes a review of current literature on shift work, the definition of shift work, error rates and adverse outcomes related to shift work, health effects on shift workers, shift work effects on older workers, recommended optimal shift length, positive and negative effects of shift work on the shift worker, hazards associated with driving after extended shifts, and implications for occupational health nurses. Copyright 2009, SLACK Incorporated.

  3. Facilitated ion transport in all-solid-state flexible supercapacitors.

    PubMed

    Choi, Bong Gill; Hong, Jinkee; Hong, Won Hi; Hammond, Paula T; Park, HoSeok

    2011-09-27

    The realization of highly flexible and all-solid-state energy-storage devices strongly depends on both the electrical properties and mechanical integrity of the constitutive materials and the controlled assembly of electrode and solid electrolyte. Herein we report the preparation of all-solid-state flexible supercapacitors (SCs) through the easy assembly of functionalized reduced graphene oxide (f-RGO) thin films (as electrode) and solvent-cast Nafion electrolyte membranes (as electrolyte and separator). In particular, the f-RGO-based SCs (f-RGO-SCs) showed a 2-fold higher specific capacitance (118.5 F/g at 1 A/g) and rate capability (90% retention at 30 A/g) compared to those of all-solid-state graphene SCs (62.3 F/g at 1A/g and 48% retention at 30 A/g). As proven by the 4-fold faster relaxation of the f-RGO-SCs than that of the RGO-SCs and more capacitive behavior of the former at the low-frequency region, these results were attributed to the facilitated ionic transport at the electrical double layer by means of the interfacial engineering of RGO by Nafion. Moreover, the superiority of all-solid-state flexible f-RGO-SCs was demonstrated by the good performance durability under the 1000 cycles of charging and discharging due to the mechanical integrity as a consequence of the interconnected networking structures. Therefore, this research provides new insight into the rational design and fabrication of all-solid-state flexible energy-storage devices as well as the fundamental understanding of ion and charge transport at the interface. © 2011 American Chemical Society

  4. Spinal cord activation differentially modulates ischaemic electrical responses to different stressors in canine ventricles.

    PubMed

    Cardinal, René; Ardell, Jeffrey L; Linderoth, Bengt; Vermeulen, Michel; Foreman, Robert D; Armour, J Andrew

    2004-03-31

    Spinal cord stimulation (SCS) represents an acceptable treatment modality for patients with chronic angina pectoris refractory to standard therapy, but its mechanism of action remains unclear. To develop an experimental paradigm to study this issue, ameroid (AM) constrictors were implanted around the left circumflex coronary artery (LCx) in canines. Six weeks later, unipolar electrograms were recorded from 191 sites in the LCx territory in the open-chest, anesthetized state under basal pacing at 150 beats/min. We investigated the effect of SCS on ST segment displacements induced in the collateral-dependent myocardium in response to two stressors: (i) transient bouts of rapid ventricular pacing (TRP: 240/min for 1 min) and (ii) angiotensin II administered to right atrial neurons via their coronary artery blood supply. ST segment responses to TRP consisted of ST segment elevation in central areas of the LCx territory and ST depression at more peripheral areas. Such responses were unchanged when TRP was applied under SCS. Shortening of repolarization intervals in the metabolically compromised myocardium in response to TRP was also unaffected by SCS. In contrast, ST segment responses to intracoronary angiotensin II, which consisted of increased ST elevation, were attenuated by SCS in 6/8 preparations. The modulator effects of SCS were greatest at sites at which the greatest responses to angiotensin II occurred in the absence of SCS. These data indicate that spinal cord stimulation may attenuate the deleterious effects that stressors exert on the myocardium with reduced coronary reserve, particularly stressors associated with chemical activation of the intrinsic cardiac nervous system. Copyright 2004 Elsevier B.V.

  5. FTIR and 1H MAS NMR investigations on the correlation between the frequency of stretching vibration and the chemical shift of surface OH groups of solids

    NASA Astrophysics Data System (ADS)

    Brunner, Eike; Karge, H. G.; Pfeifer, H.

    1992-03-01

    The study of surface hydroxyl groups of solids, especially of zeolites, belongs to the 'classical' topics of IR spectroscopy since physico-chemical information may be derived from the wavenumber (nu) OH of the stretching vibration of the different hydroxyls. On the other hand, the last decade has seen the development of high resolution solid-state NMR spectroscopy and through the use of the so-called magic-angle-spinning technique (MAS) the signals of different hydroxyl species can be resolved in the 1H NMR spectra of solids. The chemical shift (delta) H describing the position of these lines may be used as well as (nu) OH to characterize quantitatively the strength of acidity of surface OH groups of solids. In a first comparison of (nu) OH with (delta) H for several types of surface OH groups, a linear correlation between them could be found. The aim of this paper was to prove the validity of this correlation for a wide variety of hydroxyls. The IR measurements were carried out on a Perkin-Elmer FTIR spectrometer 1800 at the Fritz Haber Institute of the Max Planck Society, Berlin, and the 1H MAS NMR spectra were recorded on a Bruker MSL- 300 at the University of Leipzig.

  6. E-2-Benzylidenebenzocycloalkanones. IV. Studies on transmission of substituent effects on 13C NMR chemical shifts of E-2-(X-benzylidene)-1-tetralones, and -benzosuberones. Comparison with the 13C NMR data of chalcones and E-2-(X-benzylidene)-1-indanones

    NASA Astrophysics Data System (ADS)

    Perjési, Pál; Linnanto, Juha; Kolehmainen, Erkki; Ősz, Erzsébet; Virtanen, Elina

    2005-04-01

    Single substituent parameter (SSP) and dual substituent parameter (DSP) analyses were applied to study the transmission of substituent effects on selected 13C NMR chemical shifts of the cyclic chalcone analogues, E-2-(4'-X-benzylidene)-1-tetralones ( 2) and E-2-(4'-X-benzylidene)-1-benzosuberones ( 3). In order to study how the geometry of the cyclic chalcone analogues affects the transmission of substituent effects similar investigations with the respective chalcones ( 4) were also performed. The results obtained earlier with the five-membered analogue E-2-(4'-X-benzylidene)-1-indanones ( 1) were also involved in the comparisons. Geometry optimization of the unsubstituted 1a, 2a, 3a and 4a as well as the substituted 2 and 3 was performed by ab initio quantum chemical calculations. Both SSP and DSP analyses reflected that resonance effects contribute more to the chemical shift of C-α (C2), while inductive effects primarily affect that of C-β (C10) of the enone moiety of all the four series. This latter effect, however, is far not as pronounced as that of the former one. It was found that DSP analysis data ( ρF and ρR values) of transmission of substituent effects on the δC2 data can serve as a measure of choice to study the conformation (planarity) of the investigated enones in the four series.

  7. Spinal cord stimulation modulates intraspinal colorectal visceroreceptive transmission in rats

    PubMed Central

    Qin, C.; Lehew, R.T.; Khan, K.A.; Wienecke, G.M.; Foreman, R.D.

    2007-01-01

    Previous studies have shown that spinal cord stimulation (SCS) of upper lumbar segments decreases visceromotor responses to mechanical stimuli in a sensitized rat colon and reduces symptoms of irritable bowel syndrome in patients. SCS applied to the upper cervical spinal dorsal column reduces pain of chronic refractory angina. Further, chemical stimulation of C1-C2 propriospinal neurons in rats modulates the responses of lumbosacral spinal neurons to colorectal distension. The present study was designed to compare the effects of upper cervical and lumbar SCS on activity of lumbosacral neurons receiving noxious colorectal input. Extracellular potentials of L6-S2 spinal neurons were recorded in pentobarbital anesthetized, paralyzed and ventilated male rats. SCS (50 Hz, 0.2 ms) at low intensity (90% of motor threshold) was applied to the dorsal column of upper cervical (C1-C2) or upper lumbar (L2-L3) ipsilateral spinal segments. Colorectal distension (CRD, 20, 40, 60 mmHg, 20 s) was produced by air inflation of a latex balloon. Results showed that SCS applied to L2-L3 and C1-C2 segments significantly reduced the excitatory responses to noxious CRD from 417.6±68.0 imp to 296.3±53.6 imp (P<0.05, n=24) and from 336.2±64.5 imp to 225.0±73.3 imp (P<0.05, n= 18), respectively. Effects of L2-L3 and C1-C2 SCS lasted 10.2±1.9 min and 8.0±0.9 min after offset of CRD. Effects of SCS were observed on spinal neurons with either high or low threshold excitatory responses to CRD. However, L2-L3 or C1-C2 SCS did not significantly affect inhibitory neuronal responses to CRD. C1-C2 SCS-induced effects were abolished by cutting the C7-C8 dorsal column but not by spinal transection at cervicomedullary junction. These data demonstrated that upper cervical or lumbar SCS modulated responses of lumbosacral spinal neurons to noxious mechanical stimulation of the colon, thereby, proved two loci for a potential therapeutic effect of SCS in patients with irritable bowel syndrome and other

  8. Large-Scale Computation of Nuclear Magnetic Resonance Shifts for Paramagnetic Solids Using CP2K.

    PubMed

    Mondal, Arobendo; Gaultois, Michael W; Pell, Andrew J; Iannuzzi, Marcella; Grey, Clare P; Hutter, Jürg; Kaupp, Martin

    2018-01-09

    Large-scale computations of nuclear magnetic resonance (NMR) shifts for extended paramagnetic solids (pNMR) are reported using the highly efficient Gaussian-augmented plane-wave implementation of the CP2K code. Combining hyperfine couplings obtained with hybrid functionals with g-tensors and orbital shieldings computed using gradient-corrected functionals, contact, pseudocontact, and orbital-shift contributions to pNMR shifts are accessible. Due to the efficient and highly parallel performance of CP2K, a wide variety of materials with large unit cells can be studied with extended Gaussian basis sets. Validation of various approaches for the different contributions to pNMR shifts is done first for molecules in a large supercell in comparison with typical quantum-chemical codes. This is then extended to a detailed study of g-tensors for extended solid transition-metal fluorides and for a series of complex lithium vanadium phosphates. Finally, lithium pNMR shifts are computed for Li 3 V 2 (PO 4 ) 3 , for which detailed experimental data are available. This has allowed an in-depth study of different approaches (e.g., full periodic versus incremental cluster computations of g-tensors and different functionals and basis sets for hyperfine computations) as well as a thorough analysis of the different contributions to the pNMR shifts. This study paves the way for a more-widespread computational treatment of NMR shifts for paramagnetic materials.

  9. Work shift duration: a review comparing eight hour and 12 hour shift systems

    PubMed Central

    Smith, L.; Folkard, S.; Tucker, P.; Macdonald, I.

    1998-01-01

    OBJECTIVES: Shiftwork is now a major feature of working life across a broad range of industries. The features of the shift systems operated can impact on the wellbeing, performance, and sleep of shiftworkers. This paper reviews the current state of knowledge on one major characteristic of shift rotas-namely, shift duration. Evidence comparing the relative effects of eight hour and 12 hour shifts on fatigue and job performance, safety, sleep, and physical and psychological health are considered. At the organisational level, factors such as the mode of system implementation, attitudes towards shift rotas, sickness absence and turnover, overtime, and moonlighting are discussed. METHODS: Manual and electronic searches of the shiftwork research literature were conducted to obtain information on comparisons between eight hour and 12 hour shifts. RESULTS: The research findings are largely equivocal. The bulk of the evidence suggests few differences between eight and 12 hour shifts in the way they affect people. There may even be advantages to 12 hour shifts in terms of lower stress levels, better physical and psychological wellbeing, improved durations and quality of off duty sleep as well as improvements in family relations. On the negative side, the main concerns are fatigue and safety. It is noted that a 12 hour shift does not equate with being active for only 12 hours. CONCLUSIONS: There can be considerable extension of the person's time awake either side of the shift. However, the effects of longer term exposure to extended work days have been relatively uncharted in any systematic way. Longitudinal comparative research into the chronic impact of the compressed working week is needed.   PMID:9624275

  10. Effect of a Perturbation on the Chemical Equilibrium: Comparison with Le Chatelier's Principle

    ERIC Educational Resources Information Center

    Torres, Emilio Martinez

    2007-01-01

    This article develops a general thermodynamic treatment to predict the direction of shift in a chemical equilibrium when it is subjected to a stress. This treatment gives an inequality that relates the change in the perturbed variable and the change that the equilibrium shift produces in the conjugated variable. To illustrate the generality of…

  11. Comparison of the quantitative determination of soil organic carbon in coastal wetlands containing reduced forms of Fe and S

    NASA Astrophysics Data System (ADS)

    Passos, Tassia R. G.; Artur, Adriana G.; Nóbrega, Gabriel N.; Otero, Xosé L.; Ferreira, Tiago O.

    2016-06-01

    The performance of the Walkley-Black wet oxidation chemical method for soil organic carbon (SOC) determination in coastal wetland soils (mangroves, coastal lagoons, and hypersaline tidal flats) was evaluated in the state of Ceará along the semiarid coast of Brazil, assessing pyrite oxidation and its effects on soil C stock (SCS) quantification. SOC determined by the chemical oxidation method (CWB) was compared to that assessed by means of a standard elemental analyzer (CEA) for surficial samples (<30 cm depth) from the three wetland settings. The pyrite fraction was quantified in various steps of the chemical oxidation method, evaluating the effects of pyrite oxidation. Regardless of the method used, and consistent with site-specific physicochemical conditions, higher pyrite and SOC contents were recorded in the mangroves, whereas lower values were found in the other settings. CWB values were higher than CEA values. Significant differences in SCS calculations based on CWB and CEA were recorded for the coastal lagoons and hypersaline tidal flats. Nevertheless, the CWB and CEA values were strongly correlated, indicating that the wet oxidation chemical method can be used in such settings. In contrast, the absence of correlation for the mangroves provides evidence of the inadequacy of this method for these soils. Air drying and oxidation decrease the pyrite content, with larger effects rooted in oxidation. Thus, the wet oxidation chemical method is not recommended for mangrove soils, but seems appropriate for SOC/SCS quantification in hypersaline tidal flat and coastal lagoon soils characterized by lower pyrite contents.

  12. Impulsive Raman spectroscopy via precision measurement of frequency shift with low energy excitation.

    PubMed

    Raanan, Dekel; Ren, Liqing; Oron, Dan; Silberberg, Yaron

    2018-02-01

    Stimulated Raman scattering (SRS) has recently become useful for chemically selective bioimaging. It is usually measured via modulation transfer from the pump beam to the Stokes beam. Impulsive stimulated Raman spectroscopy, on the other hand, relies on the spectral shift of ultrashort pulses as they propagate in a Raman active sample. This method was considered impractical with low energy pulses since the observed shifts are very small compared to the excitation pulse bandwidth, spanning many terahertz. Here we present a new apparatus, using tools borrowed from the field of precision measurement, for the detection of low-frequency Raman lines via stimulated-Raman-scattering-induced spectral shifts. This method does not require any spectral filtration and is therefore an excellent candidate to resolve low-lying Raman lines (<200  cm -1 ), which are commonly masked by the strong Rayleigh scattering peak. Having the advantage of the high repetition rate of the ultrafast oscillator, we reduce the noise level by implementing a lock-in detection scheme with a wavelength shift sensitivity well below 100 fm. This is demonstrated by the measurement of low-frequency Raman lines of various liquid samples.

  13. Calcium-43 chemical shift tensors as probes of calcium binding environments. Insight into the structure of the vaterite CaCO3 polymorph by 43Ca solid-state NMR spectroscopy.

    PubMed

    Bryce, David L; Bultz, Elijah B; Aebi, Dominic

    2008-07-23

    Natural-abundance (43)Ca solid-state NMR spectroscopy at 21.1 T and gauge-including projector-augmented-wave (GIPAW) DFT calculations are developed as tools to provide insight into calcium binding environments, with special emphasis on the calcium chemical shift (CS) tensor. The first complete analysis of a (43)Ca solid-state NMR spectrum, including the relative orientation of the CS and electric field gradient (EFG) tensors, is reported for calcite. GIPAW calculations of the (43)Ca CS and EFG tensors for a series of small molecules are shown to reproduce experimental trends; for example, the trend in available solid-state chemical shifts is reproduced with a correlation coefficient of 0.983. The results strongly suggest the utility of the calcium CS tensor as a novel probe of calcium binding environments in a range of calcium-containing materials. For example, for three polymorphs of CaCO3 the CS tensor span ranges from 8 to 70 ppm and the symmetry around calcium is manifested differently in the CS tensor as compared with the EFG tensor. The advantages of characterizing the CS tensor are particularly evident in very high magnetic fields where the effect of calcium CS anisotropy is augmented in hertz while the effect of second-order quadrupolar broadening is often obscured for (43)Ca because of its small quadrupole moment. Finally, as an application of the combined experimental-theoretical approach, the solid-state structure of the vaterite polymorph of calcium carbonate is probed and we conclude that the hexagonal P6(3)/mmc space group provides a better representation of the structure than does the orthorhombic Pbnm space group, thereby demonstrating the utility of (43)Ca solid-state NMR as a complementary tool to X-ray crystallographic methods.

  14. [The productivity of female shift workers].

    PubMed

    Vidacek, S; Radosević-Vidacek, B; Kaliterna, L; Prizmić, Z

    1990-12-01

    The productivity of female shift workers, working on a weekly rotating three-shift system, was examined. The afternoon shift was found to be the most productive and the night shift the least productive one. The greatest difference in productivity between shifts was found in the first two days of the week, when the productivity on night shift was significantly lower than that on the other two shifts. From the third day on there were no longer significant differences in productivity between shifts. The most productive and the least productive workers on night shift did not significantly differ in extraversion or in sleep duration after the night shift. Family responsibility was found to be associated with the duration of sleep after the night shift: married women slept significantly shorter after the night shift than unmarried women. However, this difference in sleep duration was not associated with productivity on night shift. Sleep duration after the afternoon shift (8 hours 40 minutes) was on average two hours longer than after the other two shifts. The difference in sleep duration after different shifts, along with circadian variations in alertness, readiness for work and performance efficiency, could be responsible for differences in productivity between shifts.

  15. [Sleep quality of nurses working in shifts - Hungarian adaptation of the Bergen Shift Work Sleep Questionnaire].

    PubMed

    Fusz, Katalin; Tóth, Ákos; Fullér, Noémi; Müller, Ágnes; Oláh, András

    2015-12-06

    Sleep disorders among shift workers are common problems due to the disturbed circadian rhythm. The Bergen Shift Work Sleep Questionnaire assesses discrete sleep problems related to work shifts (day, evening and night shifts) and rest days. The aim of the study was to develop the Hungarian version of this questionnaire and to compare the sleep quality of nurses in different work schedules. 326 nurses working in shifts filled in the questionnaire. The authors made convergent and discriminant validation of the questionnaire with the Athens Insomnia Scale and the Perceived Stress Questionnaire. The questionnaire based on psychometric characteristics was suitable to assess sleep disorders associated with shift work in a Hungarian sample. The frequency of discrete symptoms significantly (p<0.001) differed with the shifts. Nurses experienced the worst sleep quality and daytime fatigue after the night shift. Nurses working in irregular shift system had worse sleep quality than nurses working in regular and flexible shift system (p<0.001). The sleep disorder of nurses working in shifts should be assessed with the Hungarian version of the Bergen Shift Work Sleep Questionnaire on a nationally representative sample, and the least burdensome shift system could be established.

  16. Age differences in strategy shift: retrieval avoidance or general shift reluctance?

    PubMed

    Frank, David J; Touron, Dayna R; Hertzog, Christopher

    2013-09-01

    Previous studies of metacognitive age differences in skill acquisition strategies have relied exclusively on tasks with a processing shift from an algorithm to retrieval strategy. Older adults' demonstrated reluctance to shift strategies in such tasks could reflect either a specific aversion to a memory retrieval strategy or a general, inertial resistance to strategy change. Haider and Frensch's (1999) alphabet verification task (AVT) affords a non-retrieval-based strategy shift. Participants verify the continuation of alphabet strings such as D E F G [4] L, with the bracketed digit indicating a number of letters to be skipped. When all deviations are restricted to the letter-digit-letter portion, participants can speed their responses by selectively attending to only that part of the stimulus. We adapted the AVT to include conditions that promoted shift to a retrieval strategy, a selective attention strategy, or both strategies. Item-level strategy reports were validated by eye movement data. Older adults shifted more slowly to the retrieval strategy but more quickly to the selective attention strategy than young adults, indicating a retrieval-strategy avoidance. Strategy confidence and perceived strategy difficulty correlated with shift to the two strategies in both age groups. Perceived speed of responses with each strategy specifically correlated with older adults' strategy choices, suggesting that some older adults avoid retrieval because they do not appreciate its efficiency benefits.

  17. Age Differences in Strategy Shift: Retrieval Avoidance or General Shift Reluctance?

    PubMed Central

    Frank, David J.; Touron, Dayna R.; Hertzog, Christopher

    2013-01-01

    Previous studies of metacognitive age differences in skill acquisition strategies have relied exclusively on tasks with a processing shift from an algorithm to retrieval strategy. Older adults’ demonstrated reluctance to shift strategies in such tasks could reflect either a specific aversion to a memory retrieval strategy or a general, inertial resistance to strategy change. Haider and Frensch’s (1999) alphabet verification task (AVT) affords a non-retrieval-based strategy shift. Participants verify the continuation of alphabet strings such as D E F G [4] L, with the bracketed digit indicating a number of letters to be skipped. When all deviations are restricted to the letter-digit-letter portion, participants can speed their responses by selectively attend only to that part of the stimulus. We adapted the AVT to include conditions which promoted shift to a retrieval strategy, a selective attention strategy, or both strategies. Item-level strategy reports were validated by eye movement data. Older adults shifted more slowly to the retrieval strategy but more quickly to the selective attention strategy than young adults, indicating a retrieval-strategy avoidance. Strategy confidence and perceived strategy difficulty correlated with shift to the two strategies in both age groups. Perceived speed of responses with each strategy specifically correlated with older adults’ strategy choices, suggesting that some older adults avoid retrieval because they do not appreciate its efficiency benefits. PMID:23088195

  18. How to compute isomerization energies of organic molecules with quantum chemical methods.

    PubMed

    Grimme, Stefan; Steinmetz, Marc; Korth, Martin

    2007-03-16

    The reaction energies for 34 typical organic isomerizations including oxygen and nitrogen heteroatoms are investigated with modern quantum chemical methods that have the perspective of also being applicable to large systems. The experimental reaction enthalpies are corrected for vibrational and thermal effects, and the thus derived "experimental" reaction energies are compared to corresponding theoretical data. A series of standard AO basis sets in combination with second-order perturbation theory (MP2, SCS-MP2), conventional density functionals (e.g., PBE, TPSS, B3-LYP, MPW1K, BMK), and new perturbative functionals (B2-PLYP, mPW2-PLYP) are tested. In three cases, obvious errors of the experimental values could be detected, and accurate coupled-cluster [CCSD(T)] reference values have been used instead. It is found that only triple-zeta quality AO basis sets provide results close enough to the basis set limit and that sets like the popular 6-31G(d) should be avoided in accurate work. Augmentation of small basis sets with diffuse functions has a notable effect in B3-LYP calculations that is attributed to intramolecular basis set superposition error and covers basic deficiencies of the functional. The new methods based on perturbation theory (SCS-MP2, X2-PLYP) are found to be clearly superior to many other approaches; that is, they provide mean absolute deviations of less than 1.2 kcal mol-1 and only a few (<10%) outliers. The best performance in the group of conventional functionals is found for the highly parametrized BMK hybrid meta-GGA. Contrary to accepted opinion, hybrid density functionals offer no real advantage over simple GGAs. For reasonably large AO basis sets, results of poor quality are obtained with the popular B3-LYP functional that cannot be recommended for thermochemical applications in organic chemistry. The results of this study are complementary to often used benchmarks based on atomization energies and should guide chemists in their search for

  19. Clean induced feature CD shift of EUV mask

    NASA Astrophysics Data System (ADS)

    Nesládek, Pavel; Schedel, Thorsten; Bender, Markus

    2016-05-01

    considering, that the tools for CD measurement at the EUV mask are identical as for optical mask. There is one aspect influencing the CD shift, which demands attention. The mask composition of the EUV mask is significantly different from the optical mask. More precisely there are 2 materials influencing the estimated CD in case of EUV mask, whereas there is one material only in case of optical masks, in first approximation. For optical masks, the CD changes can be attributed to modification of the absorber/ARC layer, as the quartz substrate can be hardly modified by the wet process. For EUV Masks chemical modification of the Ru capping layer - thinning, oxidization etc. are rather more probable and we need to take into account, how this effects can influence the CD measurement process. CD changes measured can be interpreted as either change in the feature size, or modification of the chemical nature of both absorber/ARC layer stack and the Ru capping layer. In our work we try to separate the effect of absorber and Ru/capping layer on the CD shift observed and propose independent way of estimation both parameters.

  20. Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder

    PubMed Central

    Thurber, Kent R.; Tycko, Robert

    2009-01-01

    Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of 79Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determination of internal sample temperatures. Advantages of this method include high signal-to-noise, proximity of the 79Br NMR frequency to that of 13C, applicability from 20 K to 320 K or higher, and simultaneity with adjustment of the MAS axis direction. We show that spin-lattice relaxation in KBr is driven by a quadrupolar mechanism. We demonstrate a simple approach to including KBr powder in hydrated samples, such as biological membrane samples, hydrated amyloid fibrils, and hydrated microcrystalline proteins, that allows direct assessment of the effects of frictional and radio-frequency heating under experimentally relevant conditions. PMID:18930418

  1. Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder.

    PubMed

    Thurber, Kent R; Tycko, Robert

    2009-01-01

    Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of (79)Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determination of internal sample temperatures. Advantages of this method include high signal-to-noise, proximity of the (79)Br NMR frequency to that of (13)C, applicability from 20 K to 320 K or higher, and simultaneity with adjustment of the MAS axis direction. We show that spin-lattice relaxation in KBr is driven by a quadrupolar mechanism. We demonstrate a simple approach to including KBr powder in hydrated samples, such as biological membrane samples, hydrated amyloid fibrils, and hydrated microcrystalline proteins, that allows direct assessment of the effects of frictional and radio-frequency heating under experimentally relevant conditions.

  2. Inclusion compound of vitamin B6 in β-CD. Physico-chemical and structural investigations

    NASA Astrophysics Data System (ADS)

    Borodi, Gheorghe; Kacso, Irina; Farcaş, Sorin I.; Bratu, Ioan

    2009-08-01

    Structural and physico-chemical characterization of supramolecular assembly of vitamin B6 with β-cyclodextrin (β-CD) prepared by different methods (kneading, co-precipitation and freeze-drying) has been performed by using several spectroscopic techniques (FTIR, 1H NMR, UV-Vis), powder X-ray diffraction and DSC in order to evidence the inclusion compound formation. An analysis of the chemical shifts observed in the 1H-NMR spectra and of the vibrational frequency shifts led to the tentative conclusion that the vitamin B6 probably enters the cyclodextrin torus when forming the β-CD-vitamin B6 inclusion complex.

  3. Dual-echo, chemical shift gradient-echo magnetic resonance imaging to quantify hepatic steatosis: Implications for living liver donation.

    PubMed

    Rinella, Mary E; McCarthy, Richard; Thakrar, Kiran; Finn, John Paul; Rao, Sambasiva M; Koffron, Alan J; Abecassis, Michael; Blei, Andres T

    2003-08-01

    In living liver donation, a fatty liver poses risks for both recipient and donor. Currently, liver biopsy is the standard for assessing the presence and extent of steatosis. The goals of this study were to correlate a steatosis index derived from magnetic resonance imaging (MRI) to the histologic grade on biopsy as well as to determine the topographic distribution of steatosis within the liver. We examined the ability of dual-echo, chemical shift gradient-echo MRI to predict the degree of steatosis on liver biopsy. A total of 22 subjects received both a liver biopsy and detailed MRI evaluation. These individuals included 15 potential living donors and 7 patients with nonalcoholic fatty liver disease. MRI steatosis index was then compared with histologic grade on liver biopsy. The topographic distribution of hepatic steatosis was determined from those subjects in whom MRI detected hepatic steatosis. The steatosis index had a positive correlation with grade of steatosis on liver biopsy (correlation coefficient, 0.84). There was no significant variation in the degree of steatosis among segments. A steatosis index of >0.2 had good positive and negative predictive value for the presence of significant steatosis (>15%) on biopsy. Our quantitative MRI protocol can predict the degree of hepatic steatosis when it is minimal to moderate, and may obviate the need for liver biopsy for the purpose of quantification of steatosis in living donors. Fat saturation added to the MRI protocol may further improve diagnostic accuracy. This technique may be applicable to the larger population with hepatic steatosis.

  4. Profiling modifications for glioblastoma proteome using ultra-tolerant database search: Are the peptide mass shifts biologically relevant or chemically induced?

    PubMed

    Tarasova, Irina A; Chumakov, Peter M; Moshkovskii, Sergei A; Gorshkov, Mikhail V

    2018-05-17

    Peptide mass shifts were profiled using ultra-tolerant database search strategy for shotgun proteomics data sets of human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The main objective of this profiling was revealing the cell response to IFN treatment at the level of protein modifications. To achieve this objective, statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples were analyzed. Detailed analysis of MS/MS spectra allowed further interpretation of the observed mass shifts and differentiation between post-translational and artifact modifications. Malignant cells typically acquire increased sensitivity to viruses due to the deregulated antiviral mechanisms. Therefore, a viral therapy is considered as one of the promising approaches to treat cancer. However, recent studies have demonstrated that malignant cells can preserve intact antiviral mechanisms, e.g. interferon signaling, and develop resistance to virus infection in response to interferon treatment. Post translational modifications, e.g. tyrosine phosphorylation, are the interferon signaling drivers. Thus, comprehensive characterization of modifications is crucially important, yet, most challenging problem in cancer proteomics. Here, we report on the application of the recently introduced ultra-tolerant search strategy for profiling peptide modifications in the human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The specific aim of the study was identification of statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples, as well as determination of whether these shifts represent the biologically relevant modification. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Calcium hydroxide as a processing base in alkali-aided pH-shift protein recovery process.

    PubMed

    Paker, Ilgin; Jaczynski, Jacek; Matak, Kristen E

    2017-02-01

    Protein may be recovered by using pH shifts to solubilize and precipitate protein. Typically, sodium hydroxide is used as the processing base; however, this has been shown to significantly increase sodium in the final recovered protein. Protein was extracted from black bullhead catfish (Ameiurus melas) using a pH-shift method. Protein was solubilized using either sodium hydroxide (NaOH) or calcium hydroxide (Ca(OH) 2 ) and precipitated at pH 5.5 using hydrochloric acid (HCl). Protein solubility was greater when Ca(OH) 2 was used compared to NaOH during this process. Using Ca(OH) 2 as the processing base yielded the greatest lipid recovery (P < 0.05) at 77 g 100 g -1 , whereas the greatest (P < 0.05) protein recovery yield was recorded as 53 g 100 g -1 protein using NaOH. Protein solubilized with Ca(OH) 2 had more (P < 0.05) calcium in the protein fraction, whereas using NaOH increased (P < 0.05) sodium content. Results of our study showed that protein solubility was increased and the recovered protein had significantly more calcium when Ca(OH) 2 was used as the processing base. Results showed both NaOH and Ca(OH) 2 to be an effective processing base for pH-shift protein recovery processes. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  6. The Comparison Study of gas source between two hydrate expeditions in ShenHu area, SCS

    NASA Astrophysics Data System (ADS)

    Cong, X. R.

    2016-12-01

    Two gas hydrate expeditions (GMGS 01&03) were conducted in the Pearl River Mouth Basin, SCS, which were organized by Guangzhou Marine Geological Survey in 2007 and 2015, respectively. Compared with the drilling results of "mixed bio-thermogenic gas and generally dominated by biogenic gas" in 2007, hydrocarbon component measurements revealed a higher content of ethane and propane in 2015 drilling, providing direct evidence that deep thermogenic gas was the source for shallow hydrate formation. According to the geochemical analyses of the results obtained from the industrial boreholes in Baiyun sag, the deep hydrocarbon gas obviously leaked from the reservoir as escape caused by Dongsha movement in the late Miocene, as a result thermogenic gas from Wenchang, Enping and Zhuhai hydrocarbon source rocks migrated to late Miocene shallow strata through faults, diapirs and gas chimney vertically migration. In this paper we report the differences in fluid migration channel types and discuss their effect in fluid vertical migration efficiency in the two Shenhu hydrate drilling areas. For the drilling area in 2007,when the limited deep thermogenic gas experienced long distance migration process from bottom to up along inefficient energy channel, the gas composition might have changed and the carbon isotope fractionation might have happened, which were reflected in the results of higher C1/C2 ratios and lighter carbon isotope in gas hydrate bearing sediments. As a result the gas is with more "biogenic gas" features. It means thermogenic gases in the deep to contributed the formation of shallow gas hydrate indirectly in 2007 Shenhu drill area. On another hand, the gases were transported to the shallow sediment layers efficiently, where gas hydrate formed, through faults and fractures from deep hydrocarbon reservoirs, and as the result they experienced less changes in both components and isotopes in 2015 drilling site.

  7. CVD silicon carbide monofilament reinforced SrO-Al2O3-2SiO2 (SAS) glass-ceramic composites

    NASA Technical Reports Server (NTRS)

    Bansal, Narottam P.

    1995-01-01

    Unidirectional CVD SiC fiber-reinforced SrO.Al2O3.2SiO2 (SAS) glass-ceramic matrix composites have been fabricated by hot pressing at various combinations of temperature, pressure and time. Both carbon-rich surface coated SCS-6 and uncoated SCS-0 fibers were used as reinforcements. Almost fully dense composites have been obtained. Monoclinic celsian, SrAl2Si2O8, was the only crystalline phase observed in the matrix from x-ray diffraction. During three point flexure testing of composites, a test span to thickness ratio of approximately 25 or greater was necessary to avoid sample delamination. Strong and tough SCS-6/SAS composites having a first matrix crack stress of approximately 300 MPa and an ultimate bend strength of approximately 825 MPa were fabricated. No chemical reaction between the SCS-6 fibers and the SAS matrix was observed after high temperature processing. The uncoated SCS-0 fiber-reinforced SAS composites showed only limited improvement in strength over SAS monolithic. The SCS-0/SAS composite having a fiber volume fraction of 0.24 and hot pressed at 1400 deg C exhibited a first matrix cracking stress of approximately 231 +/- 20 MPa and ultimate strength of 265 +/- 17 MPa. From fiber push-out tests, the fiber/matrix interfacial debonding strength (tau(sub debond)) and frictional sliding stress (tau(sub friction)) in the SCS-6/SAS system were evaluated to be approximately 6.7 +/- 2.3 MPa and 4.3 +/- 0.6 MPa, respectively, indicating a weak interface. However, for the SCS-0/SAS composite, much higher values of approximately 17.5 +/- 2.7 MPa for tau(sub debond) and 11.3 +/- 1.6 MPa for tau(sub friction) respectively, were observed; some of the fibers were so strongly bonded to the matrix that they could not be pushed out. Examination of fracture surfaces revealed limited short pull-out length of SCS-0 fibers. The applicability of various micromechanical models for predicting the values of first matrix cracking stress and ultimate strength of these

  8. Ionization cross section, pressure shift and isotope shift measurements of osmium

    NASA Astrophysics Data System (ADS)

    Hirayama, Yoshikazu; Mukai, Momo; Watanabe, Yutaka; Oyaizu, Michihiro; Ahmed, Murad; Kakiguchi, Yutaka; Kimura, Sota; Miyatake, Hiroari; Schury, Peter; Wada, Michiharu; Jeong, Sun-Chan

    2017-11-01

    In-gas-cell laser resonance ionization spectroscopy of neutral osmium atoms was performed with the use of a two-color two-step laser resonance ionization technique. Saturation curves for the ionization scheme were measured, and the ionization cross section was experimentally determined by solving the rate equations for the ground, intermediate and ionization continuum populations. The pressure shift and pressure broadening in the resonance spectra of the excitation transition were measured. The electronic factor {F}247 for the transition {λ }1=247.7583 nm to the intermediate state was deduced from the measured isotope shifts of stable {}{188,189,{190,192}}Os isotopes. The efficient ionization scheme, pressure shift, nuclear isotope shift and {F}247 are expected to be useful for applications of laser ion sources to unstable nuclei and for nuclear spectroscopy based on laser ionization techniques.

  9. Cross-phase modulation spectral shifting: nonlinear phase contrast in a pump-probe microscope

    PubMed Central

    Wilson, Jesse W.; Samineni, Prathyush; Warren, Warren S.; Fischer, Martin C.

    2012-01-01

    Microscopy with nonlinear phase contrast is achieved by a simple modification to a nonlinear pump-probe microscope. The technique measures cross-phase modulation by detecting a pump-induced spectral shift in the probe pulse. Images with nonlinear phase contrast are acquired both in transparent and absorptive media. In paraffin-embedded biopsy sections, cross-phase modulation complements the chemically-specific pump-probe images with structural context. PMID:22567580

  10. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Lauriie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Ribeiro, L.; hide

    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

  11. Linear free energy relationships of the 1H and 13C NMR chemical shifts of 3-methylene-2-substituted-1,4-pentadienes

    NASA Astrophysics Data System (ADS)

    Valentić, Nataša V.; Vitnik, Željko; Kozhushkov, Sergei I.; de Meijere, Armin; Ušćumlić, Gordana S.; Juranić, Ivan O.

    2005-06-01

    Linear free energy relationships (LFER) were applied to the 1H and 13C NMR chemical shifts ( δN, N= 1H and 13C, respectively) in the unsaturated backbone of cross-conjugated trienes 3-methylene-2-substituted-1,4-pentadienes. The NMR data were correlated using five different LFER models, based on the mono, the dual and the triple substituent parameter (MSP, DSP and TSP, respectively) treatment. The simple and extended Hammett equations, and the three postulated unconventional LFER models obtained by adaptation of the later, were used. The geometry data, which are needed in Karplus-type and McConnell-type analysis, were obtained using semi-empirical MNDO-PM3 calculations. In correlating the data the TSP approach was more successful than the MSP and DSP approaches. The fact that the calculated molecular geometries allow accurate prediction of the NMR data confirms the validity of unconventional LFER models used. These results suggest the s- cis conformation of the cross-conjugated triene as the preferred one. Postulated unconventional DSP and TSP equations enable the assessment of electronic substituent effects in the presence of other interfering influences.

  12. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts.

    PubMed

    Doyle, Colleen M; Rumfeldt, Jessica A; Broom, Helen R; Sekhar, Ashok; Kay, Lewis E; Meiering, Elizabeth M

    2016-03-08

    The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.

  13. [Shiftwork and health--experience from a chemical company].

    PubMed

    Oberlinner, C; Lang, S; Nasterlack, M; Yong, M

    2013-03-01

    Shiftwork is an essential part of our society. At the same time scientific evaluations demonstrate possible negative effects of shiftwork on the health status of the employees. Against this background we performed different studies to evaluate these effects within the specific shift system in a large chemical site in Germany. METHODS AND STUDY GROUP: To evaluate the impact of the different working times on job-related stress perception and work-life-balance we performed a cross-sectional study with 1494 blue collar workers (825 shift- and 669 day workers). Employees working in the rotating shift system reported lower frequencies of perceived time pressure (p = 0.008), and lower stress levels (p = 0.01), compared to the day workers. No significant difference was found with regard to work-life-balance and other aspects of job-related stress perception within both groups. Against the general opinion and study-results in the past we did not find a negative effect of our shift-system on self-reported stress. These results are in accordance with results of other cohort-studies on the specific shift system within the company demonstrating no difference in the health status of our shift workers compared to day workers. © Georg Thieme Verlag KG Stuttgart · New York.

  14. Shift work, safety, and aging.

    PubMed

    Folkard, Simon

    2008-04-01

    It has long been recognized that older shift workers may have shorter and more disturbed day sleeps between successive night shifts than their younger colleagues. This has given rise to considerable concern over the safety of aging shift workers because of the increasing age of the work force and increases in retirement age. Because there have been no direct studies of the combined effects of shift work and age on safety, the present paper begins by reviewing the literature relating safety to features of shift systems. It then considers the general effect of age on occupational injury rates before examining existing evidence of the combined effects of shift work and age on performance capabilities. The results of the literature review indicate that when the a priori risk is constant, there is reasonably clear evidence that injury rates are higher at night, and that they increase over successive night shifts more rapidly than over successive day shifts. Further, although occupational injuries are less frequent in older workers, those that do occur tend to be more serious. Finally, there is some suggestive evidence from studies of objectively measured performance capabilities that older workers may be less able to both maintain their performance over the course of a night shift and cope with longer spans of successive night shifts. It is concluded that it seems possible, even though unproven as yet, that older workers may be at greater risk both to injury and accident on the night shift. There is a strong need for future epidemiological studies of the combined effects of shift work and age on injuries and accidents, and that these should attempt to separate the effects of age per se from those of generation.

  15. The accuracy of quantum chemical methods for large noncovalent complexes

    PubMed Central

    Pitoňák, Michal; Řezáč, Jan; Pulay, Peter

    2013-01-01

    We evaluate the performance of the most widely used wavefunction, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set). The methods tested include MP2, MP3, SCS-MP2, SCS(MI)-MP2, MP2.5, MP2.X, MP2C, DFT-D, DFT-D3 (B3-LYP-D3, B-LYP-D3, TPSS-D3, PW6B95-D3, M06-2X-D3) and M06-2X, and semiempirical methods augmented with dispersion and hydrogen bonding corrections: SCC-DFTB-D, PM6-D, PM6-DH2 and PM6-D3H4. The test complexes are the octadecane dimer, the guanine trimer, the circumcoronene…adenine dimer, the coronene dimer, the guanine-cytosine dimer, the circumcoronene…guanine-cytosine dimer, and an amyloid fragment trimer containing phenylalanine residues. The best performing method is MP2.5 with relative root mean square deviation (rRMSD) of 4 %. It can thus be recommended as an alternative to the CCSD(T)/CBS (alternatively QCISD(T)/CBS) benchmark for molecular systems which exceed current computational capacity. The second best non-DFT method is MP2C with rRMSD of 8 %. A method with the most favorable “accuracy/cost” ratio belongs to the DFT family: BLYP-D3, with an rRMSD of 8 %. Semiempirical methods deliver less accurate results (the rRMSD exceeds 25 %). Nevertheless, their absolute errors are close to some much more expensive methods such as M06-2X, MP2 or SCS(MI)-MP2, and thus their price/performance ratio is excellent. PMID:24098094

  16. Improving the distinguishable cluster results: spin-component scaling

    NASA Astrophysics Data System (ADS)

    Kats, Daniel

    2018-06-01

    The spin-component scaling is employed in the energy evaluation to improve the distinguishable cluster approach. SCS-DCSD reaction energies reproduce reference values with a root-mean-squared deviation well below 1 kcal/mol, the interaction energies are three to five times more accurate than DCSD, and molecular systems with a large amount of static electron correlation are still described reasonably well. SCS-DCSD represents a pragmatic approach to achieve chemical accuracy with a simple method without triples, which can also be applied to multi-configurational molecular systems.

  17. Characterization of Damage Progression in SCS-6/timetal 21S (0)4 Under Thermomechanical Fatigue Loadings

    NASA Technical Reports Server (NTRS)

    Castelli, Michael G.

    1994-01-01

    A detailed experimental investigation was performed at a single maximum cyclic stress (sigma max) level to physically characterize the progression of thermomechanical fatigue (lW) damage in continuously reinforced (0 deg) SCS-6/Timetal 21S, a titanium matrix composite. In-phase (IP) and out of-phase (OP) loadings were investigated at sigma max = 1000 MPa with a temperature cycle from 150 to 6500 C. Damage progression, in terms of macroscopic property degradation, was experimentally quantified through an advanced TMF test methodology which incorporates explicit measurements of the isothermal static moduli at the TMF temperature extremes and the coefficient of thermal expansion (CTE) as functions of the TMF cycles. Detailed characterization of the physical damage progression at the microstructural level was performed by interrupting multiple TMF tests at various stages of mechanical property degradation and analyzing the microstructure through extensive destructive metallography. Further, the extent of damage was also quantified through residual static strength measurements. Results indicated that damage initiation occurred very early in cyclic life (N less than 0.1Nf) for both the IP and OP TMF loadings. IP TMF damage was found to be dominated by fiber breakage with a physical damage progression in the microstructure which was difficult to quantify. OP TMF loadings produced matrix cracking exclusively associated with surface initiations. Here, damage progression was easily distinguished in terms of both the number of cracks and their relative inward progressions toward the outer fiber rows with increased cycling. The point at which the leading cracks reached the outer fiber rows (when localized fiber/matrix de-bonding and matrix crack bridging occurred) appeared to be reflected in the macroscopic property degradation curves.

  18. Thermomechanical Fatigue Damage/Failure Mechanisms in SCS-6/Timetal 21S [0/90](Sub S) Composite

    NASA Technical Reports Server (NTRS)

    Castelli, Michael G.

    1994-01-01

    The thermomechanical fatigue (TMF) deformation, damage, and life behaviors of SCS6/Timetal 21S (0/90)s were investigated under zero-tension conditions. In-phase (IP) and out-of-phase (OP) loadings were investigated with a temperature cycle from 150 to 650 deg C. An advanced TMF test technique was used to quantify mechanically damage progression. The technique incorporated explicit measurements of the macroscopic (1) isothermal static moduli at the temperature extremes of the TMF cycle and (2) coefficient of thermal expansion (CTE) as functions of the TMF cycles. The importance of thermal property degradation and its relevance to accurate post-test data analysis and interpretation is briefly addressed. Extensive fractography and metallography were conducted on specimens from failed and interrupted tests to characterize the extent of damage at the microstructure level. Fatigue life results indicated trends analogous to those established for similar unidirectional(0) reinforced titanium matrix composite systems. High stress IP and mid to low stress OP loading conditions were life-limiting in comparison to maximum temperature isothermal conditions. Dominant damage mechanisms changed with cycle type. Damage resulting from IP TMF conditions produced measurable decreases in static moduli but only minimal changes in the CTE. Metallography on interrupted and failed specimens revealed extensive (0) fiber cracking with sparse matrix damage. No surface initiated matrix cracks were present. Comparable OP TMF conditions initiated environment enhanced surface cracking and matrix cracking initiated at (90) fiber/matrix (F/M) interfaces. Notable static moduli and CTE degradations were measured. Fractography and metallography revealed that the transverse cracks originating from the surface and (90) F/M interfaces tended to converge and coalesce at the (0) fibers.

  19. Adaptation to shift work: physiologically based modeling of the effects of lighting and shifts' start time.

    PubMed

    Postnova, Svetlana; Robinson, Peter A; Postnov, Dmitry D

    2013-01-01

    Shift work has become an integral part of our life with almost 20% of the population being involved in different shift schedules in developed countries. However, the atypical work times, especially the night shifts, are associated with reduced quality and quantity of sleep that leads to increase of sleepiness often culminating in accidents. It has been demonstrated that shift workers' sleepiness can be improved by a proper scheduling of light exposure and optimizing shifts timing. Here, an integrated physiologically-based model of sleep-wake cycles is used to predict adaptation to shift work in different light conditions and for different shift start times for a schedule of four consecutive days of work. The integrated model combines a model of the ascending arousal system in the brain that controls the sleep-wake switch and a human circadian pacemaker model. To validate the application of the integrated model and demonstrate its utility, its dynamics are adjusted to achieve a fit to published experimental results showing adaptation of night shift workers (n = 8) in conditions of either bright or regular lighting. Further, the model is used to predict the shift workers' adaptation to the same shift schedule, but for conditions not considered in the experiment. The model demonstrates that the intensity of shift light can be reduced fourfold from that used in the experiment and still produce good adaptation to night work. The model predicts that sleepiness of the workers during night shifts on a protocol with either bright or regular lighting can be significantly improved by starting the shift earlier in the night, e.g.; at 21:00 instead of 00:00. Finally, the study predicts that people of the same chronotype, i.e. with identical sleep times in normal conditions, can have drastically different responses to shift work depending on their intrinsic circadian and homeostatic parameters.

  20. Shift Work, Chronotype, and Melatonin Patterns among Female Hospital Employees on Day and Night Shifts.

    PubMed

    Leung, Michael; Tranmer, Joan; Hung, Eleanor; Korsiak, Jill; Day, Andrew G; Aronson, Kristan J

    2016-05-01

    Shift work-related carcinogenesis is hypothesized to be mediated by melatonin; however, few studies have considered the potential effect modification of this underlying pathway by chronotype or specific aspects of shift work such as the number of consecutive nights in a rotation. In this study, we examined melatonin patterns in relation to shift status, stratified by chronotype and number of consecutive night shifts, and cumulative lifetime exposure to shift work. Melatonin patterns of 261 female personnel (147 fixed-day and 114 on rotations, including nights) at Kingston General Hospital were analyzed using cosinor analysis. Urine samples were collected from all voids over a 48-hour specimen collection period for measurement of 6-sulfatoxymelatonin concentrations using the Buhlmann ELISA Kit. Chronotypes were assessed using mid-sleep time (MSF) derived from the Munich Chronotype Questionnaire (MCTQ). Sociodemographic, health, and occupational information were collected by questionnaire. Rotational shift nurses working nights had a lower mesor and an earlier time of peak melatonin production compared to day-only workers. More pronounced differences in mesor and acrophase were seen among later chronotypes, and shift workers working ≥3 consecutive nights. Among nurses, cumulative shift work was associated with a reduction in mesor. These results suggest that evening-types and/or shift workers working ≥3 consecutive nights are more susceptible to adverse light-at-night effects, whereas long-term shift work may also chronically reduce melatonin levels. Cumulative and current exposure to shift work, including nights, affects level and timing of melatonin production, which may be related to carcinogenesis and cancer risk. Cancer Epidemiol Biomarkers Prev; 25(5); 830-8. ©2016 AACR. ©2016 American Association for Cancer Research.

  1. In-line phase shift tomosynthesis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hammonds, Jeffrey C.; Price, Ronald R.; Pickens, David R.

    2013-08-15

    Purpose: The purpose of this work is to (1) demonstrate laboratory measurements of phase shift images derived from in-line phase-contrast radiographs using the attenuation-partition based algorithm (APBA) of Yan et al.[Opt. Express 18(15), 16074–16089 (2010)], (2) verify that the APBA reconstructed images obey the linearity principle, and (3) reconstruct tomosynthesis phase shift images from a collection of angularly sampled planar phase shift images.Methods: An unmodified, commercially available cabinet x-ray system (Faxitron LX-60) was used in this experiment. This system contains a tungsten anode x-ray tube with a nominal focal spot size of 10 μm. The digital detector uses CsI/CMOS withmore » a pixel size of 50 × 50 μm. The phantoms used consisted of one acrylic plate, two polystyrene plates, and a habanero pepper. Tomosynthesis images were reconstructed from 51 images acquired over a ±25° arc. All phase shift images were reconstructed using the APBA.Results: Image contrast derived from the planar phase shift image of an acrylic plate of uniform thickness exceeded the contrast of the traditional attenuation image by an approximate factor of two. Comparison of the planar phase shift images from a single, uniform thickness polystyrene plate with two polystyrene plates demonstrated an approximate linearity of the estimated phase shift with plate thickness (−1600 rad vs −2970 rad). Tomographic phase shift images of the habanero pepper exhibited acceptable spatial resolution and contrast comparable to the corresponding attenuation image.Conclusions: This work demonstrated the feasibility of laboratory-based phase shift tomosynthesis and suggests that phase shift imaging could potentially provide a new imaging biomarker. Further investigation will be needed to determine if phase shift contrast will be able to provide new tissue contrast information or improved clinical performance.« less

  2. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, Michael; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Sargsyan, A.; Martin, D.; Lui, J.; Macias, B.; Arbeille, P.; hide

    2014-01-01

    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 30% of ISS astronauts experience 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 space flight-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 space flight, 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 space flight, as well as the VIIP-related effects of those shifts, is predicted by the crewmember's pre-flight condition 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. 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 ultrasound

  3. Osmotically shrunken LIPOCEST agents: an innovative class of magnetic resonance imaging contrast media based on chemical exchange saturation transfer.

    PubMed

    Terreno, Enzo; Delli Castelli, Daniela; Violante, Elisabetta; Sanders, Honorius M H F; Sommerdijk, Nico A J M; Aime, Silvio

    2009-01-01

    The peculiar properties of osmotically shrunken liposomes acting as magnetic resonance imaging-chemical exchange saturation transfer (MRI-CEST) contrast agents have been investigated. Attention has been primarily devoted to assessing the contribution arising from encapsulated and incorporated paramagnetic lanthanide(III)-based shift reagents in determining the chemical shift of the intraliposomal water protons, which is a relevant factor for generating the CEST contrast. It is demonstrated that a highly shifted resonance for the encapsulated water can be attained by increasing the percentage of the amphiphilic shift reagent incorporated in the liposome bilayer. It is also demonstrated that the shift contribution arising from the bulk magnetic susceptibility can be optimized through the modulation of the osmotic shrinkage. In terms of sensitivity, it is shown that the saturation transfer efficiency can be significantly improved by increasing the size of the vesicle, thus allowing a high number of exchangeable protons to be saturated. In addition, the role played by the intensity of the saturating radiofrequency field has also been highlighted.

  4. Shifting scintillator neutron detector

    DOEpatents

    Clonts, Lloyd G; Cooper, Ronald G; Crow, Jr., Morris Lowell; Hannah, Bruce W; Hodges, Jason P; Richards, John D; Riedel, Richard A

    2014-03-04

    Provided are sensors and methods for detecting thermal neutrons. Provided is an apparatus having a scintillator for absorbing a neutron, the scintillator having a back side for discharging a scintillation light of a first wavelength in response to the absorbed neutron, an array of wavelength-shifting fibers proximate to the back side of the scintillator for shifting the scintillation light of the first wavelength to light of a second wavelength, the wavelength-shifting fibers being disposed in a two-dimensional pattern and defining a plurality of scattering plane pixels where the wavelength-shifting fibers overlap, a plurality of photomultiplier tubes, in coded optical communication with the wavelength-shifting fibers, for converting the light of the second wavelength to an electronic signal, and a processor for processing the electronic signal to identify one of the plurality of scattering plane pixels as indicative of a position within the scintillator where the neutron was absorbed.

  5. APPROACHES FOR INCORPORATING NON-CHEMICAL STRESSORS INTO CUMULATIVE RISK ASSESSMENTS

    EPA Science Inventory

    Over the past twenty years, the risk assessment paradigm has gradually shifted from an individual chemical approach to a community-based model. Inherent in community-based risk assessment is consideration of the totality of stressors affecting a defined population including both ...

  6. Associations between number of consecutive night shifts and impairment of neurobehavioral performance during a subsequent simulated night shift.

    PubMed

    Magee, Michelle; Sletten, Tracey L; Ferguson, Sally A; Grunstein, Ronald R; Anderson, Clare; Kennaway, David J; Lockley, Steven W; Rajaratnam, Shantha Mw

    2016-05-01

    This study aimed to investigate sleep and circadian phase in the relationships between neurobehavioral performance and the number of consecutive shifts worked. Thirty-four shift workers [20 men, mean age 31.8 (SD 10.9) years] worked 2-7 consecutive night shifts immediately prior to a laboratory-based, simulated night shift. For 7 days prior, participants worked their usual shift sequence, and sleep was assessed with logs and actigraphy. Participants completed a 10-minute auditory psychomotor vigilance task (PVT) at the start (~21:00 hours) and end (~07:00 hours) of the simulated night shift. Mean reaction times (RT), number of lapses and RT distribution was compared between those who worked 2-3 consecutive night shifts versus those who worked 4-7 shifts. Following 4-7 shifts, night shift workers had significantly longer mean RT at the start and end of shift, compared to those who worked 2-3 shifts. The slowest and fastest 10% RT were significantly slower at the start, but not end, of shift among participants who worked 4-7 nights. Those working 4-7 nights also demonstrated a broader RT distribution at the start and end of shift and had significantly slower RT based on cumulative distribution analysis (5 (th), 25 (th), 50 (th), 75 (th)percentiles at the start of shift; 75th percentile at the end of shift). No group differences in sleep parameters were found for 7 days and 24 hours prior to the simulated night shift. A greater number of consecutive night shifts has a negative impact on neurobehavioral performance, likely due to cognitive slowing.

  7. Enantiodifferentiation through frequency-selective pure-shift (1)H nuclear magnetic resonance spectroscopy.

    PubMed

    Castañar, Laura; Pérez-Trujillo, Míriam; Nolis, Pau; Monteagudo, Eva; Virgili, Albert; Parella, Teodor

    2014-04-04

    A frequency-selective 1D (1) H nuclear magnetic resonance (NMR) experiment for the fast and sensitive determination of chemical-shift differences between overlapped resonances is proposed. The resulting fully homodecoupled (1) H NMR resonances appear as resolved 1D singlets without their typical J(HH) coupling constant multiplet structures. The high signal dispersion that is achieved is then exploited in enantiodiscrimination studies by using chiral solvating agents. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 5 CFR 532.505 - Night shift differentials.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... employee regularly assigned to a night shift who is temporarily assigned to a day shift or to a night shift... regularly assigned to a day shift who is temporarily assigned to a night shift shall be paid a night shift... schedule involving work on both day and night shifts shall be paid a night shift differential only for any...

  9. Isothermal Damage and Fatigue Behavior of SCS-6/Timetal 21S [0/90](Sub S) Composite at 650 Deg C

    NASA Technical Reports Server (NTRS)

    Castelli, Michael G.

    1994-01-01

    The isothermal fatigue damage and life behaviors of SCS-6/Timetal 21S (0/90)s were investigated at 650 C. Strain ratcheting and degradation of the composite's static elastic modulus were carefully monitored as functions of cycles to indicate damage progression. Extensive fractographic and metallographic analyses were conducted to determine damage/failure mechanisms. Resulting fatigue lives show considerable reductions in comparison to (0) reinforced titanium matrix composites subjected to comparable conditions. Notable stiffness degradations were found to occur after the first cycle of loading, even at relatively low maximum stress levels, where cyclic lives are greater than 25,000 cycles. This was attributed to the extremely weak fiber/matrix bond which fails under relatively low transverse loads. Stiffness degradations incurred on first cycle loadings and degradations thereafter were found to increase with increasing maximum stress. Environmental effects associated with oxidation of the (90) fiber interfaces clearly played a role in the damage mechanisms as fracture surfaces revealed environment assisted matrix cracking along the (90) fibers. Metallographic analysis indicated that all observable matrix fatigue cracks initiated at the (90) fiber/matrix interfaces. Global de-bonding in the loading direction was found along the (90) fibers. No surface initiated cracks were evident and minimal if any (0) fiber cracking was visible.

  10. Nuclear magnetic resonance, vibrational spectroscopic studies, physico-chemical properties and computational calculations on (nitrophenyl) octahydroquinolindiones by DFT method.

    PubMed

    Pasha, M A; Siddekha, Aisha; Mishra, Soni; Azzam, Sadeq Hamood Saleh; Umapathy, S

    2015-02-05

    In the present study, 2'-nitrophenyloctahydroquinolinedione and its 3'-nitrophenyl isomer were synthesized and characterized by FT-IR, FT-Raman, (1)H NMR and (13)C NMR spectroscopy. The molecular geometry, vibrational frequencies, (1)H and (13)C NMR chemical shift values of the synthesized compounds in the ground state have been calculated by using the density functional theory (DFT) method with the 6-311++G (d,p) basis set and compared with the experimental data. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution using GAR2PED programme. Isotropic chemical shifts for (1)H and (13)C NMR were calculated using gauge-invariant atomic orbital (GIAO) method. The experimental vibrational frequencies, (1)H and (13)C NMR chemical shift values were found to be in good agreement with the theoretical values. On the basis of vibrational analysis, molecular electrostatic potential and the standard thermodynamic functions have been investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Health Effects of Shift Work

    PubMed Central

    LaDou, Joseph

    1982-01-01

    More than 13.5 million American workers, close to 20 percent of the work force, are assigned to evening or night shifts. In some industries such as automobile, petrochemical and textile manufacturing the proportion of shift workers is greater than 50 percent. As the popularity of shift work and other “alternative work schedules” grows, concern is increasing over the disturbance created in the lives of workers and their families by these economically and socially useful innovations. Twenty percent of workers are unable to tolerate shift work. Daily physiologic variations termed circadian rhythms are interactive and require a high degree of phase relationship to produce subjective feelings of wellbeing. Disturbance of these activities, circadian desynchronization, whether from passage over time zones or from shift rotation, results in health effects such as disturbance of the quantity and quality of sleep, disturbance of gastrointestinal and other organ system activities, and aggravation of diseases such as diabetes mellitus, epilepsy and thyrotoxicosis. Worker selection can reduce the number of health problems resulting from shift work. The periodic examination of shift workers is recommended. PMID:6962577

  12. The importance of pollen chemistry in evolutionary host shifts of bees

    PubMed Central

    Vanderplanck, Maryse; Vereecken, Nicolas J.; Grumiau, Laurent; Esposito, Fabiana; Lognay, Georges; Wattiez, Ruddy; Michez, Denis

    2017-01-01

    Although bee-plant associations are generally maintained through speciation processes, host shifts have occurred during evolution. Understanding shifts between both phylogenetically and morphologically unrelated plants (i.e., host-saltation) is especially important since they could have been key processes in the origin and radiation of bees. Probably far from being a random process, such host-saltation might be driven by hidden constraints associated with plant traits. We selected two clades of oligolectic bees (i.e., Colletes succinctus group and Melitta leporina group) foraging on co-flowering but unrelated host-plants to test this hypothesis. We analyzed floral scent, floral color and chemical composition of pollen from host and non-host plants of these two clades. We did not find evidence for host-plant evolution in the Melitta leporina group driven by one of the assayed floral traits. On the contrary, hosts of the C. succinctus group display similar primary nutritive content of pollen (i.e., amino acids and sterols) but not similar floral scent or color, suggesting that shared pollen chemistry probably mediates saltation in this clade. Our study revealed that constraints shaping floral associations are diverse and clearly depend on species life-history traits, but evidence suggests that pollen chemistry may act as a major floral filter and guide evolutionary host-shifts. PMID:28216663

  13. Performance and sleepiness in nurses working 12-h day shifts or night shifts in a community hospital.

    PubMed

    Wilson, Marian; Permito, Regan; English, Ashley; Albritton, Sandra; Coogle, Carlana; Van Dongen, Hans P A

    2017-10-05

    Hospitals are around-the-clock operations and nurses are required to care for patients night and day. The nursing shortage and desire for a more balanced work-to-home life has popularized 12-h shifts for nurses. The present study investigated sleep/wake cycles and fatigue levels in 22 nurses working 12-h shifts, comparing day versus night shifts. Nurses (11day shift and 11 night shift) were recruited from a suburban acute-care medical center. Participants wore a wrist activity monitor and kept a diary to track their sleep/wake cycles for 2 weeks. They also completed a fatigue test battery, which included the Psychomotor Vigilance Test (PVT) and the Karolinska Sleepiness Scale (KSS), at the beginning, middle and end of 4 duty shifts. Daily sleep duration was 7.1h on average. No overall difference in mean daily sleep duration was found between nurses working day shifts versus night shifts. Objective performance on the PVT remained relatively good and stable at the start, middle, and end of duty shifts in day shift workers, but gradually degraded across duty time in night shift workers. Compared to day shift workers, night shift workers also exhibited more performance variability among measurement days and between participants at each testing time point. The same pattern was observed for subjective sleepiness on the KSS. However, congruence between objective and subjective measures of fatigue was poor. Our findings suggest a need for organizations to evaluate practices and policies to mitigate the inevitable fatigue that occurs during long night shifts, in order to improve patient and healthcare worker safety. Examination of alternative shift lengths or sanctioned workplace napping may be strategies to consider. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. A lanthanide complex with dual biosensing properties: CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts) with europium DOTA-tetraglycinate.

    PubMed

    Coman, Daniel; Kiefer, Garry E; Rothman, Douglas L; Sherry, A Dean; Hyder, Fahmeed

    2011-12-01

    Responsive contrast agents (RCAs) composed of lanthanide(III) ion (Ln3R) complexes with a variety of1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (DOTA4S) derivatives have shown great potential as molecular imaging agents for MR. A variety of LnDOTA–tetraamide complexes have been demonstrated as RCAs for molecular imaging using chemical exchange saturation transfer (CEST). The CEST method detects proton exchange between bulk water and any exchangeable sites on the ligand itself or an inner sphere of bound water that is shifted by a paramagnetic Ln3R ion bound in the core of the macrocycle. It has also been shown that molecular imaging is possible when the RCA itself is observed (i.e. not its effect on bulk water) using a method called biosensor imaging of redundant deviation in shifts (BIRDS). The BIRDS method utilizes redundant information stored in the nonexchangeable proton resonances emanating from the paramagnetic RCA for ambient factors such as temperature and/or pH.Thus, CEST and BIRDS rely on exchangeable and nonexchangeable protons, respectively, for biosensing. We posited that it would be feasible to combine these two biosensing features into the same RCA (i.e. dual CEST and BIRDS properties). A complex between europium(III) ion (Eu3R) and DOTA–tetraglycinate [DOTA–(gly)S4] was used to demonstrate that its CEST characteristics are preserved, while its BIRDS properties are also detectable. The in vitro temperature sensitivity of EuDOTA–(gly)S4 was used to show that qualitative MR contrast with CEST can be calibrated using quantitative MR mapping with BIRDS, thereby enabling quantitative molecular imaging at high spatial resolution.

  15. Thigh muscle segmentation of chemical shift encoding-based water-fat magnetic resonance images: The reference database MyoSegmenTUM.

    PubMed

    Schlaeger, Sarah; Freitag, Friedemann; Klupp, Elisabeth; Dieckmeyer, Michael; Weidlich, Dominik; Inhuber, Stephanie; Deschauer, Marcus; Schoser, Benedikt; Bublitz, Sarah; Montagnese, Federica; Zimmer, Claus; Rummeny, Ernst J; Karampinos, Dimitrios C; Kirschke, Jan S; Baum, Thomas

    2018-01-01

    Magnetic resonance imaging (MRI) can non-invasively assess muscle anatomy, exercise effects and pathologies with different underlying causes such as neuromuscular diseases (NMD). Quantitative MRI including fat fraction mapping using chemical shift encoding-based water-fat MRI has emerged for reliable determination of muscle volume and fat composition. The data analysis of water-fat images requires segmentation of the different muscles which has been mainly performed manually in the past and is a very time consuming process, currently limiting the clinical applicability. An automatization of the segmentation process would lead to a more time-efficient analysis. In the present work, the manually segmented thigh magnetic resonance imaging database MyoSegmenTUM is presented. It hosts water-fat MR images of both thighs of 15 healthy subjects and 4 patients with NMD with a voxel size of 3.2x2x4 mm3 with the corresponding segmentation masks for four functional muscle groups: quadriceps femoris, sartorius, gracilis, hamstrings. The database is freely accessible online at https://osf.io/svwa7/?view_only=c2c980c17b3a40fca35d088a3cdd83e2. The database is mainly meant as ground truth which can be used as training and test dataset for automatic muscle segmentation algorithms. The segmentation allows extraction of muscle cross sectional area (CSA) and volume. Proton density fat fraction (PDFF) of the defined muscle groups from the corresponding images and quadriceps muscle strength measurements/neurological muscle strength rating can be used for benchmarking purposes.

  16. Assessing the productivity change of water companies in England and Wales: A dynamic metafrontier approach.

    PubMed

    Molinos-Senante, María; Maziotis, Alexandros; Sala-Garrido, Ramon

    2017-07-15

    The assessment of productivity change and its drivers across water companies and over time is a powerful tool for both regulators and companies when setting water tariffs. Water and sewerage companies (WaSCs) and water only companies (WoCs) provide different services. Hence, their productivity change cannot directly be evaluated jointly. In this paper and for the first time, we provide a pioneering approach to assess and compare the dynamics of productivity change of WaSCs and WoCs. To achieve this, both the traditional Malmquist productivity index and the metafrontier Malmquist productivity index and its components are computed to assess the productivity change for a sample of English and Welsh water companies over the period 2001-2014. The findings from both indices indicate that productivity for both WaSCs and WoCs did not improve during this period, mainly due to the negative shift in the production frontier which offset the positive effect of efficiency change. It is also reported that the performance of the WoCs over time was slightly better than that of the WaSCs. Finally, our study provides some insights into the relationship between productivity change and the regulatory cycle. This information is essential to improve the regulation of water and sewerage services, contributing to the long-term sustainability of the urban water cycle. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2011-07-01

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

  18. Can short-wavelength depleted bright light during single simulated night shifts prevent circadian phase shifts?

    PubMed

    Regente, J; de Zeeuw, J; Bes, F; Nowozin, C; Appelhoff, S; Wahnschaffe, A; Münch, M; Kunz, D

    2017-05-01

    In single night shifts, extending habitual wake episodes leads to sleep deprivation induced decrements of performance during the shift and re-adaptation effects the next day. We investigated whether short-wavelength depleted (=filtered) bright light (FBL) during a simulated night shift would counteract such effects. Twenty-four participants underwent a simulated night shift in dim light (DL) and in FBL. Reaction times, subjective sleepiness and salivary melatonin concentrations were assessed during both nights. Daytime sleep was recorded after both simulated night shifts. During FBL, we found no melatonin suppression compared to DL, but slightly faster reaction times in the second half of the night. Daytime sleep was not statistically different between both lighting conditions (n = 24) and there was no significant phase shift after FBL (n = 11). To conclude, our results showed positive effects from FBL during simulated single night shifts which need to be further tested with larger groups, in more applied studies and compared to standard lighting. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Quantum-chemical insights from deep tensor neural networks

    PubMed Central

    Schütt, Kristof T.; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R.; Tkatchenko, Alexandre

    2017-01-01

    Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol−1) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems. PMID:28067221

  20. Quantum-chemical insights from deep tensor neural networks.

    PubMed

    Schütt, Kristof T; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R; Tkatchenko, Alexandre

    2017-01-09

    Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol -1 ) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems.