Controls on the physical properties of gas-hydrate-bearing sediments because of the interaction between gas hydrate and porous media

USGS Publications Warehouse

Lee, Myung W.; Collett, Timothy S.

2005-01-01

Physical properties of gas-hydrate-bearing sediments depend on the pore-scale interaction between gas hydrate and porous media as well as the amount of gas hydrate present. Well log measurements such as proton nuclear magnetic resonance (NMR) relaxation and electromagnetic propagation tool (EPT) techniques depend primarily on the bulk volume of gas hydrate in the pore space irrespective of the pore-scale interaction. However, elastic velocities or permeability depend on how gas hydrate is distributed in the pore space as well as the amount of gas hydrate. Gas-hydrate saturations estimated from NMR and EPT measurements are free of adjustable parameters; thus, the estimations are unbiased estimates of gas hydrate if the measurement is accurate. However, the amount of gas hydrate estimated from elastic velocities or electrical resistivities depends on many adjustable parameters and models related to the interaction of gas hydrate and porous media, so these estimates are model dependent and biased. NMR, EPT, elastic-wave velocity, electrical resistivity, and permeability measurements acquired in the Mallik 5L-38 well in the Mackenzie Delta, Canada, show that all of the well log evaluation techniques considered provide comparable gas-hydrate saturations in clean (low shale content) sandstone intervals with high gas-hydrate saturations. However, in shaly intervals, estimates from log measurement depending on the pore-scale interaction between gas hydrate and host sediments are higher than those estimates from measurements depending on the bulk volume of gas hydrate.

Hydraulic Conductivity Calibration of Logging NMR in a Granite Aquifer, Laramie Range, Wyoming.

PubMed

Ren, Shuangpo; Parsekian, Andrew D; Zhang, Ye; Carr, Bradley J

2018-05-15

In granite aquifers, fractures can provide both storage volume and conduits for groundwater. Characterization of fracture hydraulic conductivity (K) in such aquifers is important for predicting flow rate and calibrating models. Nuclear magnetic resonance (NMR) well logging is a method to quickly obtain near-borehole hydraulic conductivity (i.e., K NMR ) at high-vertical resolution. On the other hand, FLUTe flexible liner technology can produce a K profile at comparable resolution but requires a fluid driving force between borehole and formation. For three boreholes completed in a fractured granite, we jointly interpreted logging NMR data and FLUTe K estimates to calibrate an empirical equation for translating borehole NMR data to K estimates. For over 90% of the depth intervals investigated from these boreholes, the estimated K NMR are within one order of magnitude of K FLUTe . The empirical parameters obtained from calibrating the NMR data suggest that "intermediate diffusion" and/or "slow diffusion" during the NMR relaxation time may occur in the flowing fractures when hydraulic aperture are sufficiently large. For each borehole, "intermediate diffusion" dominates the relaxation time, therefore assuming "fast diffusion" in the interpretation of NMR data from fractured rock may lead to inaccurate K NMR estimates. We also compare calibrations using inexpensive slug tests that suggest reliable K NMR estimates for fractured rock may be achieved using limited calibration against borehole hydraulic measurements. © 2018, National Ground Water Association.

AEM and NMR: Tools for the Future of Groundwater Management

NASA Astrophysics Data System (ADS)

Abraham, J. D.; Cannia, J. C.; Lawrie, K.

2012-12-01

Within the world, understanding groundwater resources and their management are growing in importance to society as groundwater resources are stressed by drought and continued development. To minimize conflicts, tools and techniques need to be applied to support knowledge-based decisions and management. Airborne electromagnetic (AEM) surveys provide high-quality subsurface data not available from any other source for building the complex hydrogeologic frameworks needed by water-resource managers for effective groundwater management. Traditionally, point data, such as borehole logs, borehole geophysics, surface geophysics, and aquifer tests were interpolated over long distances to create hydrogeologic frameworks. These methods have enjoyed a long history of being the best available technology to inform our understanding of groundwater and how it moves. The AEM techniques proivde pathway for geoscientists to follow to develop more accurate descriptions of the hydrogeological framework. However, the critical and challenging measurements in characterizing aquifers include effective porosity and hydraulic conductivity. These parameters are not reliable derived from AEM. Typically, values for effective porosity and hydraulic conductivity are derived by lithological comparisons with published data; direct measurements of hydraulic conductivity acquired by a few constant head aquifer tests or slug tests; and expensive and time consuming laboratory measurements of cores which can be biased by sampling and the difficulty of making measurements on unconsolidated materials. Aquifer tests are considered to be the best method to gather information on hydraulic conductivity but are rare because of cost and difficult logistics. Also they are unique in design and interpretation from site to site. Nuclear Magnetic Resonance (NMR) can provide a direct measurement of the presence of water in the pore space of aquifer materials. Detection and direct measurement is possible due to the nuclear magnetization of the hydrogen (protons) in the water. These measurements are the basis of the familiar MRI (magnetic resonance imaging) in medical applications. NMR is also widely used in logging applications within the petroleum industry. Effective porosity values were derived directly from the borehole and surface NMR data, and hydraulic conductivity values were calculated using empirical relationships calibrated and verified with few laboratory permeameter and aquifer tests. NMR provides measurements of the effective porosity and hydraulic conductivity at a resolution not possible using traditional methods. Unlike aquifer tests, NMR logs are not unique in design and are applied in similar fashion from borehole to borehole providing a standard way of measuring hydraulic properties. When the hydraulic properties from the NMR are integrated with hydrogeological framework interpretations of AEM data large areas can be characterized. This allows a much more robust method for conceptualizing groundwater models then simply using previously published data for assigning effective porosity and hydraulic conductivity. Examples from the North Platte River Basin in Nebraska and the Murray Darling Basin of Australia illustrate that borehole and surface NMR allows superior, rapid measurements of the complexities of aquifers within when integrated with AEM.

NMR Parameters Determination through ACE Committee Machine with Genetic Implanted Fuzzy Logic and Genetic Implanted Neural Network

NASA Astrophysics Data System (ADS)

Asoodeh, Mojtaba; Bagheripour, Parisa; Gholami, Amin

2015-06-01

Free fluid porosity and rock permeability, undoubtedly the most critical parameters of hydrocarbon reservoir, could be obtained by processing of nuclear magnetic resonance (NMR) log. Despite conventional well logs (CWLs), NMR logging is very expensive and time-consuming. Therefore, idea of synthesizing NMR log from CWLs would be of a great appeal among reservoir engineers. For this purpose, three optimization strategies are followed. Firstly, artificial neural network (ANN) is optimized by virtue of hybrid genetic algorithm-pattern search (GA-PS) technique, then fuzzy logic (FL) is optimized by means of GA-PS, and eventually an alternative condition expectation (ACE) model is constructed using the concept of committee machine to combine outputs of optimized and non-optimized FL and ANN models. Results indicated that optimization of traditional ANN and FL model using GA-PS technique significantly enhances their performances. Furthermore, the ACE committee of aforementioned models produces more accurate and reliable results compared with a singular model performing alone.

Mechanisms of action of (meth)acrylates in hemolytic activity, in vivo toxicity and dipalmitoylphosphatidylcholine (DPPC) liposomes determined using NMR spectroscopy.

PubMed

Fujisawa, Seiichiro; Kadoma, Yoshinori

2012-01-01

We investigated the quantitative structure-activity relationships between hemolytic activity (log 1/H(50)) or in vivo mouse intraperitoneal (ip) LD(50) using reported data for α,β-unsaturated carbonyl compounds such as (meth)acrylate monomers and their (13)C-NMR β-carbon chemical shift (δ). The log 1/H(50) value for methacrylates was linearly correlated with the δC(β) value. That for (meth)acrylates was linearly correlated with log P, an index of lipophilicity. The ipLD(50) for (meth)acrylates was linearly correlated with δC(β) but not with log P. For (meth)acrylates, the δC(β) value, which is dependent on the π-electron density on the β-carbon, was linearly correlated with PM3-based theoretical parameters (chemical hardness, η; electronegativity, χ; electrophilicity, ω), whereas log P was linearly correlated with heat of formation (HF). Also, the interaction between (meth)acrylates and DPPC liposomes in cell membrane molecular models was investigated using (1)H-NMR spectroscopy and differential scanning calorimetry (DSC). The log 1/H(50) value was related to the difference in chemical shift (ΔδHa) (Ha: H (trans) attached to the β-carbon) between the free monomer and the DPPC liposome-bound monomer. Monomer-induced DSC phase transition properties were related to HF for monomers. NMR chemical shifts may represent a valuable parameter for investigating the biological mechanisms of action of (meth)acrylates.

Mechanisms of Action of (Meth)acrylates in Hemolytic Activity, in Vivo Toxicity and Dipalmitoylphosphatidylcholine (DPPC) Liposomes Determined Using NMR Spectroscopy

PubMed Central

Fujisawa, Seiichiro; Kadoma, Yoshinori

2012-01-01

We investigated the quantitative structure-activity relationships between hemolytic activity (log 1/H50) or in vivo mouse intraperitoneal (ip) LD50 using reported data for α,β-unsaturated carbonyl compounds such as (meth)acrylate monomers and their 13C-NMR β-carbon chemical shift (δ). The log 1/H50 value for methacrylates was linearly correlated with the δCβ value. That for (meth)acrylates was linearly correlated with log P, an index of lipophilicity. The ipLD50 for (meth)acrylates was linearly correlated with δCβ but not with log P. For (meth)acrylates, the δCβ value, which is dependent on the π-electron density on the β-carbon, was linearly correlated with PM3-based theoretical parameters (chemical hardness, η; electronegativity, χ; electrophilicity, ω), whereas log P was linearly correlated with heat of formation (HF). Also, the interaction between (meth)acrylates and DPPC liposomes in cell membrane molecular models was investigated using 1H-NMR spectroscopy and differential scanning calorimetry (DSC). The log 1/H50 value was related to the difference in chemical shift (ΔδHa) (Ha: H (trans) attached to the β-carbon) between the free monomer and the DPPC liposome-bound monomer. Monomer-induced DSC phase transition properties were related to HF for monomers. NMR chemical shifts may represent a valuable parameter for investigating the biological mechanisms of action of (meth)acrylates. PMID:22312284

Real-time oil-saturation monitoring in rock cores with low-field NMR.

PubMed

Mitchell, J; Howe, A M; Clarke, A

2015-07-01

Nuclear magnetic resonance (NMR) provides a powerful suite of tools for studying oil in reservoir core plugs at the laboratory scale. Low-field magnets are preferred for well-log calibration and to minimize magnetic-susceptibility-induced internal gradients in the porous medium. We demonstrate that careful data processing, combined with prior knowledge of the sample properties, enables real-time acquisition and interpretation of saturation state (relative amount of oil and water in the pores of a rock). Robust discrimination of oil and brine is achieved with diffusion weighting. We use this real-time analysis to monitor the forced displacement of oil from porous materials (sintered glass beads and sandstones) and to generate capillary desaturation curves. The real-time output enables in situ modification of the flood protocol and accurate control of the saturation state prior to the acquisition of standard NMR core analysis data, such as diffusion-relaxation correlations. Although applications to oil recovery and core analysis are demonstrated, the implementation highlights the general practicality of low-field NMR as an inline sensor for real-time industrial process control. Copyright © 2015 Elsevier Inc. All rights reserved.

Correlation of the Capacity Factor in Vesicular Electrokinetic Chromatography with the Octanol:Water Partition Coefficient for Charged and Neutral Analytes

PubMed Central

Razak, J. L.; Cutak, B. J.; Larive, C. K.; Lunte, C. E.

2008-01-01

Purpose The aim of this study was to develop a method based upon electrokinetic chromatography (EKC) using oppositely charged surfactant vesicles as a buffer modifier to estimate hydrophobicity (log P) for a range of neutral and charged compounds. Methods Vesicles were formed from cetyltrimethylammonium bromide (CTAB) and sodium n-octyl sulfate (SOS). The size and polydispersity of the vesicles were characterized by electron microscopy, dynamic light scattering, and pulsed-field gradient NMR (PFG-NMR). PFG-NMR was also used to determine if ion-pairing between cationic analytes and free SOS monomer occurred. The CTAB/SOS vesicles were used as a buffer modifier in capillary electrophoresis (CE). The capacity factor (log k′) was calculated by determining the mobility of the analytes both in the presence and absence of vesicles. Log k′ was determined for 29 neutral and charged analytes. Results There was a linear relationship between the log of capacity factor (log k′) and octanol/water partition coefficient (log P) for both neutral and basic species at pH 6.0, 7.3, and 10.2. This indicated that interaction between the cation and vesicle was dominated by hydrophobic forces. At pH 4.3, the log k′ values for the least hydrophobic basic analytes were higher than expected, indicating that electrostatic attraction as well as hydrophobic forces contributed to the overall interaction between the cation and vesicle. Anionic compounds could not be evaluated using this system. Conclusion Vesicular electrokinetic chromatography (VEKC) using surfactant vesicles as buffer modifiers is a promising method for the estimation of hydrophobicity. PMID:11336344

Comparative study of inversion methods of three-dimensional NMR and sensitivity to fluids

NASA Astrophysics Data System (ADS)

Tan, Maojin; Wang, Peng; Mao, Keyu

2014-04-01

Three-dimensional nuclear magnetic resonance (3D NMR) logging can simultaneously measure transverse relaxation time (T2), longitudinal relaxation time (T1), and diffusion coefficient (D). These parameters can be used to distinguish fluids in the porous reservoirs. For 3D NMR logging, the relaxation mechanism and mathematical model, Fredholm equation, are introduced, and the inversion methods including Singular Value Decomposition (SVD), Butler-Reeds-Dawson (BRD), and Global Inversion (GI) methods are studied in detail, respectively. During one simulation test, multi-echo CPMG sequence activation is designed firstly, echo trains of the ideal fluid models are synthesized, then an inversion algorithm is carried on these synthetic echo trains, and finally T2-T1-D map is built. Futhermore, SVD, BRD, and GI methods are respectively applied into a same fluid model, and the computing speed and inversion accuracy are compared and analyzed. When the optimal inversion method and matrix dimention are applied, the inversion results are in good aggreement with the supposed fluid model, which indicates that the inversion method of 3D NMR is applieable for fluid typing of oil and gas reservoirs. Additionally, the forward modeling and inversion tests are made in oil-water and gas-water models, respectively, the sensitivity to the fluids in different magnetic field gradients is also examined in detail. The effect of magnetic gradient on fluid typing in 3D NMR logging is stuied and the optimal manetic gradient is choosen.

Studies of a peatified angiosperm log cross section from Indonesia by nuclear magnetic resonance spectroscopy and analytical pyrolysis

USGS Publications Warehouse

Bates, A.L.; Hatcher, P.G.; Lerch, H. E.; Cecil, C.B.; Neuzil, S.G.; ,

1991-01-01

Samples from a 10 cm cross-sectional radius of a peatified angiosperm log from Sumatra, Indonesia, were examined by 13C nuclear magnetic resonance and pyrolysis-gas chromatography in order to understand chemical changes due to the peatification process. NMR results show degradation by selective loss of carbohydrates in all parts of the log section compared with fresh wood; however, the degree of degradation is less near the center of the log section. The degree of ring substitution of aromatic lignin monomeric units, as measured by dipolar dephasing NMR methods, appears to be less at the center of the log section than at the periphery. The methoxyl carbon content of lignin in the log is lower than in unaltered angiospermous lignin but does not appear to change as a function of either radial position or the degree of aromatic ring substitution. Pyrolysis-gas chromatography indicates higher yields of catechols in the outer areas relative to the heartwood. Other than the variations in catechol contents and in the yields of carbohydrate-derived pyrolysis products (e.g. levoglucosan, angelicalactones), the pyrolysis results do not show significant changes related to radial position, indicating that the lignin is not significantly altered across the log section. ?? 1991.

Field experiment provides ground truth for surface nuclear magnetic resonance measurement

USGS Publications Warehouse

Knight, R.; Grunewald, E.; Irons, T.; Dlubac, K.; Song, Y.; Bachman, H.N.; Grau, B.; Walsh, D.; Abraham, J.D.; Cannia, J.

2012-01-01

The need for sustainable management of fresh water resources is one of the great challenges of the 21st century. Since most of the planet's liquid fresh water exists as groundwater, it is essential to develop non-invasive geophysical techniques to characterize groundwater aquifers. A field experiment was conducted in the High Plains Aquifer, central United States, to explore the mechanisms governing the non-invasive Surface NMR (SNMR) technology. We acquired both SNMR data and logging NMR data at a field site, along with lithology information from drill cuttings. This allowed us to directly compare the NMR relaxation parameter measured during logging,T2, to the relaxation parameter T2* measured using the SNMR method. The latter can be affected by inhomogeneity in the magnetic field, thus obscuring the link between the NMR relaxation parameter and the hydraulic conductivity of the geologic material. When the logging T2data were transformed to pseudo-T2* data, by accounting for inhomogeneity in the magnetic field and instrument dead time, we found good agreement with T2* obtained from the SNMR measurement. These results, combined with the additional information about lithology at the site, allowed us to delineate the physical mechanisms governing the SNMR measurement. Such understanding is a critical step in developing SNMR as a reliable geophysical method for the assessment of groundwater resources.

Detecting Microbially Induced Calcite Precipitation in a Model Well-Bore Using Downhole Low-Field NMR

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

Kirkland, Catherine M.; Zanetti, Sam; Grunewald, Elliot

Microbially induced calcite precipitation (MICP) has been widely researched recently due to its relevance for subsurface engineering applications including sealing leakage pathways and permeability modification. These applications of MICP are inherently difficult to monitor nondestructively in time and space. Nuclear magnetic resonance (NMR) can characterize the pore size distributions, porosity, and permeability of subsurface formations. This investigation used a low-field NMR well-logging probe to monitor MICP in a sand-filled bioreactor, measuring NMR signal amplitude and T 2 relaxation over an 8 day experimental period. Following inoculation with the ureolytic bacteria, Sporosarcina pasteurii, and pulsed injections of urea and calcium substrate,more » the NMR measured water content in the reactor decreased to 76% of its initial value. T 2 relaxation distributions bifurcated from a single mode centered about approximately 650 ms into a fast decaying population ( T 2 less than 10 ms) and a larger population with T 2 greater than 1000 ms. The combination of changes in pore volume and surface minerology accounts for the changes in the T 2 distributions. Destructive sampling confirmed final porosity was approximately 88% of the original value. Here, these results indicate the low-field NMR well-logging probe is sensitive to the physical and chemical changes caused by MICP in a laboratory bioreactor.« less

Detecting Microbially Induced Calcite Precipitation in a Model Well-Bore Using Downhole Low-Field NMR

DOE PAGES

Kirkland, Catherine M.; Zanetti, Sam; Grunewald, Elliot; ...

2016-12-20

Microbially induced calcite precipitation (MICP) has been widely researched recently due to its relevance for subsurface engineering applications including sealing leakage pathways and permeability modification. These applications of MICP are inherently difficult to monitor nondestructively in time and space. Nuclear magnetic resonance (NMR) can characterize the pore size distributions, porosity, and permeability of subsurface formations. This investigation used a low-field NMR well-logging probe to monitor MICP in a sand-filled bioreactor, measuring NMR signal amplitude and T 2 relaxation over an 8 day experimental period. Following inoculation with the ureolytic bacteria, Sporosarcina pasteurii, and pulsed injections of urea and calcium substrate,more » the NMR measured water content in the reactor decreased to 76% of its initial value. T 2 relaxation distributions bifurcated from a single mode centered about approximately 650 ms into a fast decaying population ( T 2 less than 10 ms) and a larger population with T 2 greater than 1000 ms. The combination of changes in pore volume and surface minerology accounts for the changes in the T 2 distributions. Destructive sampling confirmed final porosity was approximately 88% of the original value. Here, these results indicate the low-field NMR well-logging probe is sensitive to the physical and chemical changes caused by MICP in a laboratory bioreactor.« less

Interaction of Cesium Ions with Calix[4]arene-bis(t-octylbenzo-18-crown-6): NMR and Theoretical Study

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

Kriz, Jaroslav; Dybal, Jiri; Vanura, Petr

2011-01-01

Using 1H, 13C, and 133Cs NMR spectra, it is shown that calix[4]arene-bis (t-octylbenzo-18-crown-6) (L) forms complexes with one (L 3 Cs ) and two (L 3 2Cs ) Cs ions offered by cesium bis(1,2-dicarbollide) cobaltate (CsDCC) in nitrobenzene-d5. The ions interact with all six oxygen atoms in the crown-ether ring and the electrons of the calixarene aromatic moieties. According to extraction technique, the stability constant of the first complex is log nb(L 3 Cs ) = 8.8 ( 0.1. According to 133Cs NMR spectra, the value of the equilibrium constant of the second complex is log Knb (2)(L 3 2Csmore » ) = 6.3(0.2, i.e., its stabilization constant is log nb(L 3 2Cs ) = 15.1 ( 0.3. Self-diffusion measurements by 1H pulsed-field gradient (PFG) NMRcombined with density functional theory (DFT) calculations suggest that one DCC ion is tightly associated with L 3 Cs , decreasing its positive charge and consequently stabilizing the second complex, L 3 2Cs . Using a saturation-transfer 133Cs NMR technique, the correlation times ex of chemical exchange between L 3 Cs and L 3 2Cs as well as between L 3 2Cs and free Cs ions were determined as 33.6 and 29.2 ms, respectively.« less

A new method of evaluating tight gas sands pore structure from nuclear magnetic resonance (NMR) logs

NASA Astrophysics Data System (ADS)

Xiao, Liang; Mao, Zhi-qiang; Xie, Xiu-hong

2016-04-01

Tight gas sands always display such characteristics of ultra-low porosity, permeability, high irreducible water, low resistivity contrast, complicated pore structure and strong heterogeneity, these make that the conventional methods are invalid. Many effective gas bearing formations are considered as dry zones or water saturated layers, and cannot be identified and exploited. To improve tight gas sands evaluation, the best method is quantitative characterizing rock pore structure. The mercury injection capillary pressure (MICP) curves are advantageous in predicting formation pore structure. However, the MICP experimental measurements are limited due to the environment and economy factors, this leads formation pore structure cannot be consecutively evaluated. Nuclear magnetic resonance (NMR) logs are considered to be promising in evaluating rock pore structure. Generally, to consecutively quantitatively evaluate tight gas sands pore structure, the best method is constructing pseudo Pc curves from NMR logs. In this paper, based on the analysis of lab experimental results for 20 core samples, which were drilled from tight gas sandstone reservoirs of Sichuan basin, and simultaneously applied for lab MICP and NMR measurements, the relationships of piecewise power function between nuclear magnetic resonance (NMR) transverse relaxation T2 time and pore-throat radius Rc are established. A novel method, which is used to transform NMR reverse cumulative curve as pseudo capillary pressure (Pc) curve is proposed, and the corresponding model is established based on formation classification. By using this model, formation pseudo Pc curves can be consecutively synthesized. The pore throat radius distribution, and pore structure evaluation parameters, such as the average pore throat radius (Rm), the threshold pressure (Pd), the maximum pore throat radius (Rmax) and so on, can also be precisely extracted. After this method is extended into field applications, several tight gas sandstone reservoirs are processed, and the predicted results are compared with core derived results. Good consistency between evaluated results with core derived results illustrates the dependability of the proposed method. Comparing with the previous methods, this presented model is much more theoretical, and the applicability is much improved. Combining with the evaluated results, our target tight gas sands are well evaluated, and many potential gas-bearing layers are effectively identified.

Nuclear magnetic resonance relaxation and diffusion measurements as a proxy for soil properties

NASA Astrophysics Data System (ADS)

Duschl, Markus; Pohlmeier, Andreas; Galvosas, Petrik; Vereecken, Harry

2013-04-01

Nuclear Magnetic Resonance (NMR) relaxation and NMR diffusion measurements are two of a series of fast and non-invasive NMR applications widely used e.g. as well logging tools in petroleum exploration [1]. For experiments with water, NMR relaxation measures the relaxation behaviour of former excited water molecules, and NMR diffusion evaluates the self-diffusion of water. Applied in porous media, both relaxation and diffusion measurements depend on intrinsic properties of the media like pore size distribution, connectivity and tortuosity of the pores, and water saturation [2, 3]. Thus, NMR can be used to characterise the pore space of porous media not only in consolidated sediments but also in soil. The physical principle behind is the relaxation of water molecules in an external magnetic field after excitation. In porous media water molecules in a surface layer of the pores relax faster than the molecules in bulk water because of interactions with the pore wall. Thus, the relaxation in smaller pores is generally faster than in bigger pores resulting in a relaxation time distribution for porous media with a range of pore sizes like soil [4]. In NMR diffusion experiments, there is an additional encoding of water molecules by application of a magnetic field gradient. Subsequent storage of the magnetization and decoding enables the determination of the mean square displacement and therefore of the self-diffusion of the water molecules [5]. Employing various relaxation and diffusion experiments, we get a measure of the surface to volume ratio of the pores and the tortuosity of the media. In this work, we show the characterisation of a set of sand and soil samples covering a wide range of textural classes by NMR methods. Relaxation times were monitored by the Carr-Purcell-Meiboom-Gill sequence and analysed using inverse Laplace transformation. Apparent self-diffusion constants were detected by a 13-intervall pulse sequence and variation of the storage time. We correlated the results with various soil properties like texture, water retention parameters, and hydraulic conductivity. This way we show that we can predict soil properties by NMR measurements and that we are able use results of NMR measurements as a proxy without the need of direct measurements. [1] Song, Y.-Q., Vadose Zone Journal, 9 (2010) [2] Stingaciu, L. R., et al., Water Resources Research, 46 (2010) [3] Vogt, C., et al., Journal of Applied Geophysics, 50 (2002) [4] Barrie, P. J., Annual Reports on NMR Spectroscopy, 41 (2000) [5] Stallmach, F., Galvosas, P., Annual Reports on NMR Spectroscopy, 61 (2007)

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

PubMed

Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian A; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian L; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

2018-01-02

NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

Thermophysical properties derived from lab measurements and downhole logging at New Jersey Shallow Shelf (IODP Expedition 313)

NASA Astrophysics Data System (ADS)

Fehr, A.; Pechnig, R.; Inwood, J.; Lofi, J.; Bosch, F. P.; Clauser, C.

2012-04-01

The IODP drilling expedition 313 New Jersey Shallow Shelf was proposed for obtaining deep sub-seafloor samples and downhole logging measurements in the crucial inner shelf region. The inner to central shelf off-shore New Jersey is an ideal location for studying the history of sea-level changes and its relationship to sequence stratigraphy and onshore/offshore groundwater flows. The region features rapid depositional rates, tectonic stability, and well-preserved, cosmopolitan age control fossils suitable for characterizing the sediments of this margin throughout the time interval of interest. Past sea-level rise and fall is documented in sedimentary layers deposited during Earth's history. In addition, the inner shelf is characterised by relatively fresh pore water intervals alternating vertically with saltier intervals (Mountain et al., 2010). Therefore, three boreholes were drilled in the so-called New Jersey/Mid-Atlantic transect during IODP Expedition 313 New Jersey Shallow Shelf. Numerous questions have arisen concerning the age and origin of the brackish waters recovered offshore at depth. Here we present an analysis of thermophysical properties to be used as input parameters in constructing numerical models for future groundwater flow simulations. Our study is based mainly on Nuclear Magnetic Resonance (NMR) measurements for inferring porosity and permeability, and thermal conductivity. We performed NMR measurements on samples from boreholes M0027A, M0028A and M0029A and thermal conductivity measurements on the whole round cores prior to the Onshore Party. These results are compared with data from alternative laboratory measurements and with petrophysical properties inferred from downhole logging data. We deduced petrophysical properties from downhole logging data and compared them with results obtained with laboratory measurements. In water saturated samples, the number of spins in the fluid is proportional to sample porosity. NMR porosities were calculated from the zero amplitudes of the transverse relaxation measurements by normalizing the CPMG (Carr, Purcell, Meiboom, Gill) amplitudes of the measured samples to the amplitudes measured on a pure water cylinder which is equivalent to a porosity of 100 %. The NMR porosities fit well with porosities determined by Multi Sensor Core Logger (MSCL) and porosity measured on discrete samples using a helium gas pycnometer. Using log interpretation procedures, the volume fraction of different rock types and their porosity can be derived. From the volume fraction of each rock type and its porosity, continuous profiles of thermal conductivity can be derived by using a suitable mixing law, e.g. such as the geometric mean. In combination with thermal conductivity measurements on cores, these continuous thermal conductivity profiles can be calibrated, validated and finally used to provide reliable input parameter for numerical models. The porosity values from NMR seem to correlate well with porosities deduced from other measurements. In order to compare NMR permeabilities, we need permeability determined by an alternative method. The thermal conductivity derived from logs correlates with the measurements performed on cores. In a next step, a numerical model will be set up and the measured thermophysical properties will be implemented in order to study transport processes in passive continental margins. This numerical model will be based on existing geological models deduced from seismic data and drillings.

Application of MRIL-WD (Magnetic Resonance Imaging Logging While Drilling) for irreducible water saturation, total reservoir, free-fluid, bound-fluid porosity measurements and its value for the petrophysical analysis of RT/RM data from the Shah Deniz well

NASA Astrophysics Data System (ADS)

Amirov, Elnur

2016-04-01

Sperry-Sun (Sperry Drilling Services) is the leader in MWD/LWD reliability, has developed the industry's first LWD NMR/MRIL-WD (nuclear magnetic resonance) tool. The MRIL-WD (magnetic resonance imaging logging-while-drilling) service directly measures the T1 component of hydrogen in subsurface rock units while drilling to obtain total reservoir porosity and to dissect the observed total porosity into its respective components of free fluid and bound fluid porosity. These T1 data are used to secure accurate total, free-fluid, capillary-bound water, and clay-bound water porosity of the reservoir sections which can be drilled in the several Runs. Over the last decade, results from Magnetic Resonance Imaging logs (NMR) have added significant value to petrophysical analysis and understanding by providing total, free-fluid and bound-fluid porosities, combined with fluid typing capabilities. With MRIL-WD very valuable Real-Time or Recorded Memory data/information is now available during or shortly after the drilling operation (formation properties measurement can be taken right after a drill bit penetration), while trip in and trip out as well. A key point in utilizing MRIL in an LWD environment is motion-tolerant measurements. Recent MRIL-WD logging runs from the Shah Deniz wells located in the Khazarian-Caspian Sea of the Azerbaijan Republic helped to delineate and assess hydrocarbon bearing zones. Acquired results demonstrate how MRIL data can be acquired while-drilling and provide reliable/high quality measurements. Magnetic Resonance Imaging logs at some developments wells have become a cornerstone in formation evaluation and petrophysical understanding. By providing total, free-fluid, and bound-fluid porosities together with fluid typing, MRIL results have significantly added to the assessment of reservoirs. In order to reduce NPT (Non-Productive Time) and save the rig operations time, there is always the desire to obtain logging results as soon as possible, preferably while the drilling of the brand new wells (logging-while-drilling, LWD). The MRIL-WD Tool can accomplish any tasks reliably and in a timely manner thus saving drilling time and reducing the overall risk for the well. Control of water production and identification of pay zones with high irreducible water saturation are also very important for formation evaluation and petrophysical analysis in oil fields located in the Azerbaijan Republic and also other fields around the world. Sometimes above-mentioned problems can cause delay in completion decisions which will create additional expenses for field management. In many wells, breakthroughs in reservoir characterization have been achieved in directly determining hydrocarbon volumes, net permeability thickness, and hydrocarbon type, thus circumventing the problems associated with obtaining wireline data and the considerable amount of rig time required (so MRIL-WD can considerably reduce the NPT). Some reservoir zones with relatively low water saturation, which calculated from the other conventional logs, can produce with relatively high percentage of water cut, primarily because much of the water is movable. However, other zones with high calculated water saturation produce water free hydrocarbons. The difficulty in predicting water production can be related with the producing from the complex lithology, which can contain low-permeability, medium- to fine-grained shaly sands. Where grains are small, the formations have high surface to volume ratios that result in high irreducible water saturation and due to this we can see low resistivity values. As a result the use of resistivity logs as pay indicator, sometimes can cause low resistivity pay zones might be overlooked and consequently net field pay could be underestimated. In the last few years, nuclear magnetic resonance logs have shown great promise in solving problems of formation evaluation that could not be directly resolved with conventional logs. The capability of MRIL-WD can help many engineers to differentiate between the immovable and movable water in oil reservoirs in many fields. Sometimes MRIL-WD have also been capable of providing better formation permeability than conventional logs, a feature which can save time and expense in well-completion decisions. The RT & RM bound fluid and total porosity measurements can provide a tremendous new insight into the formation evaluation of shaly sands and low resistivity pays. Unlike traditional porosity devices, which are affected by rock matrix changes, the MRIL-WD tool can be used in complex or mixed lithology sequences and provide measurements of porosity that are lithology independent.

In-situ gas hydrate hydrate saturation estimated from various well logs at the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

USGS Publications Warehouse

Lee, M.W.; Collett, T.S.

2011-01-01

In 2006, the U.S. Geological Survey (USGS) completed detailed analysis and interpretation of available 2-D and 3-D seismic data and proposed a viable method for identifying sub-permafrost gas hydrate prospects within the gas hydrate stability zone in the Milne Point area of northern Alaska. To validate the predictions of the USGS and to acquire critical reservoir data needed to develop a long-term production testing program, a well was drilled at the Mount Elbert prospect in February, 2007. Numerous well log data and cores were acquired to estimate in-situ gas hydrate saturations and reservoir properties.Gas hydrate saturations were estimated from various well logs such as nuclear magnetic resonance (NMR), P- and S-wave velocity, and electrical resistivity logs along with pore-water salinity. Gas hydrate saturations from the NMR log agree well with those estimated from P- and S-wave velocity data. Because of the low salinity of the connate water and the low formation temperature, the resistivity of connate water is comparable to that of shale. Therefore, the effect of clay should be accounted for to accurately estimate gas hydrate saturations from the resistivity data. Two highly gas hydrate-saturated intervals are identified - an upper ???43 ft zone with an average gas hydrate saturation of 54% and a lower ???53 ft zone with an average gas hydrate saturation of 50%; both zones reach a maximum of about 75% saturation. ?? 2009.

Multidimensional NMR approaches towards highly resolved, sensitive and high-throughput quantitative metabolomics.

PubMed

Marchand, Jérémy; Martineau, Estelle; Guitton, Yann; Dervilly-Pinel, Gaud; Giraudeau, Patrick

2017-02-01

Multi-dimensional NMR is an appealing approach for dealing with the challenging complexity of biological samples in metabolomics. This article describes how spectroscopists have recently challenged their imagination in order to make 2D NMR a powerful tool for quantitative metabolomics, based on innovative pulse sequences combined with meticulous analytical chemistry approaches. Clever time-saving strategies have also been explored to make 2D NMR a high-throughput tool for metabolomics, relying on alternative data acquisition schemes such as ultrafast NMR. Currently, much work is aimed at drastically boosting the NMR sensitivity thanks to hyperpolarisation techniques, which have been used in combination with fast acquisition methods and could greatly expand the application potential of NMR metabolomics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reactive Transport Modeling and Geophysical Monitoring of Bioclogging at Reservoir Scale

NASA Astrophysics Data System (ADS)

Surasani, V.; Commer, M.; Ajo Franklin, J. B.; Li, L.; Hubbard, S. S.

2012-12-01

In Microbial-Enhanced-Hydrocarbon-Recovery (MEHR), preferential bioclogging targets the growth of the biofilms (def. immobilized biopolymers with active cells embodied in it) in highly permeable thief zones to enhance sweep efficiency in oil reservoirs. During MEHR, understanding and controlling bioclogging is hindered by the lack of advanced modeling and monitoring tools; these deficiencies contribute to suboptimal performance. Our focus in this study was on developing a systematic approach to understand and monitor bioclogging at the reservoir scale using a combination of reactive transport modeling and geophysical imaging tools (EM & seismic). In this study, we created a realistic reservoir model from a heterogeneous gas reservoir in the Southern Sacramento basin, California; the model well (Citizen Green #1) was characterized using sonic, electrical, nuclear, and NMR logs for hydrologic and geophysical properties. From the simplified 2D log data model, a strip of size 150m x75m with several high permeability streaks is identified for bioclogging simulation experiments. From the NMR log data it is observed that a good linear correlation exist between logarithmic permeability (0.55- 3.34 log (mD)) versus porosity (0.041-0.28). L. mesenteroides was chosen as the model bacteria. In the presence of sucrose, it enzymatically catalyzes the production of dextran, a useful bioclogging agent. Using microbial kinetics from our laboratory experiment and reservoir heterogeneity, a reactive transport model (RTM) is established for two kinds of bioclogging treatments based on whether microbes are present in situ or are supplied externally. In both cases, sucrose media (1.5 M) is injected at the rate of 1 liter/s for 20 days into the center of high permeable strip to stimulate microbes. Simulations show that the high dextran production was deep into the formation from the injection well. This phenomenon can be explained precisely with bacterial kinetics and injection rate. In the in situ treatment, dextran contributes to a maximum porosity reduction of 9.2%, while in the exogenous microbes treatment, the dextran contributes to a maximum of 10.9% porosity reduction. After RTM, the potential geophysical signature of the treatment was evaluated using previously developed experimental rock physics models and realistic forward modeling approaches. Seismic experiments during dextran production performed by Kwan & Ajo-Franklin (2011) were combined with full waveform viscoelastic modeling to yield a predicted attenuation response from the dextran distributions modeled using RTM. The response suggests that crosswell attenuation tomography may be a viable approach for in situ monitoring of the bioclogging process. Modeling the EM response involved the induced polarization (IP) method, where the simulated resistance amplitude and phase changes can be attributed to porosity reduction. Our studies suggest that the IP signals provide a valuable additional indicator. Both geophysical data methods in a joint imaging approach potentially increase the resolution of each geophysical attribute change. Likewise, reactive transport modeling and geophysical monitoring can provide a powerful tool for predicting different bioclogging scenarios in subsurface. The combination may enhance our capabilities of controlling and monitoring the MEHR bioclogging process at reservoir scale.

An overview of tools for the validation of protein NMR structures.

PubMed

Vuister, Geerten W; Fogh, Rasmus H; Hendrickx, Pieter M S; Doreleijers, Jurgen F; Gutmanas, Aleksandras

2014-04-01

Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11% of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate proper analysis of the experimental models, a number of program suites are available. We discuss nine of these tools in this review: PROCHECK-NMR, PSVS, GLM-RMSD, CING, Molprobity, Vivaldi, ResProx, NMR constraints analyzer and QMEAN. We evaluate these programs for their ability to assess the structural quality, restraints and their violations, chemical shifts, peaks and the handling of multi-model NMR ensembles. We document both the input required by the programs and output they generate. To discuss their relative merits we have applied the tools to two representative examples from the PDB: a small, globular monomeric protein (Staphylococcal nuclease from S. aureus, PDB entry 2kq3) and a small, symmetric homodimeric protein (a region of human myosin-X, PDB entry 2lw9).

Characterization of aspartame-cyclodextrin complexation.

PubMed

Sohajda, Tamás; Béni, Szabolcs; Varga, Erzsébet; Iványi, Róbert; Rácz, Akos; Szente, Lajos; Noszál, Béla

2009-12-05

The inclusion complex formation of aspartame (guest) and various cyclodextrins (host) were examined using 1H NMR titration and capillary electrophoresis. Initially the protonation constants of aspartame were determined by NMR-pH titration with in situ pH measurement to yield log K1=7.83 and log K2=2.96. Based on these values the stability of the complexes formed by aspartame and 21 different cyclodextrins (CDs) were studied at pH 2.5, pH 5.2 and pH 9.0 values where aspartame exists predominantly in monocationic, zwitterionic and monoanionic form, respectively. The host cyclodextrin derivatives differed in various sidechains, degree of substitution, charge and purity so that the effect of these properties could be examined systematically. Concerning size, the seven-membered beta-cyclodextrin and its derivatives have been found to be the most suitable host molecules for complexation. Highest stability was observed for the acetylated derivative with a degree of substitution of 7. The purity of the CD enhanced the complexation while the degree of substitution did not provide obvious consequences. Finally, geometric aspects of the inclusion complex were assessed by 2D ROESY NMR and molecular modelling which proved that the guest's aromatic ring enters the wider end of the host cavity.

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.

Numerical simulation of multi-dimensional NMR response in tight sandstone

NASA Astrophysics Data System (ADS)

Guo, Jiangfeng; Xie, Ranhong; Zou, Youlong; Ding, Yejiao

2016-06-01

Conventional logging methods have limitations in the evaluation of tight sandstone reservoirs. The multi-dimensional nuclear magnetic resonance (NMR) logging method has the advantage that it can simultaneously measure transverse relaxation time (T 2), longitudinal relaxation time (T 1) and diffusion coefficient (D). In this paper, we simulate NMR measurements of tight sandstone with different wettability and saturations by the random walk method and obtain the magnetization decays of Carr-Purcell-Meiboom-Gill pulse sequences with different wait times (TW) and echo spacings (TE) under a magnetic field gradient, resulting in D-T 2-T 1 maps by the multiple echo trains joint inversion method. We also study the effects of wettability, saturation, signal-to-noise ratio (SNR) of data and restricted diffusion on the D-T 2-T 1 maps in tight sandstone. The results show that with decreasing wetting fluid saturation, the surface relaxation rate of the wetting fluid gradually increases and the restricted diffusion phenomenon becomes more and more obvious, which leads to the wetting fluid signal moving along the direction of short relaxation and the direction of the diffusion coefficient decreasing in D-T 2-T 1 maps. Meanwhile, the non-wetting fluid position in D-T 2-T 1 maps does not change with saturation variation. With decreasing SNR, the ability to identify water and oil signals based on NMR maps gradually decreases. The wetting fluid D-T 1 and D-T 2 correlations in NMR diffusion-relaxation maps of tight sandstone are obtained through expanding the wetting fluid restricted diffusion models, and are further applied to recognize the wetting fluid in simulated D-T 2 maps and D-T 1 maps.

Methods and apparatus to produce stick-slip motion of logging tool attached to a wireline drawn upward by a continuously rotating wireline drum

DOEpatents

Vail, III, William Banning; Momii, Steven Thomas

1998-01-01

Methods and apparatus are described to produce stick-slip motion of a logging tool within a cased well attached to a wireline that is drawn upward by a continuously rotating wireline drum. The stick-slip motion results in the periodic upward movement of the tool in the cased well described in terms of a dwell time during which time the tool is stationary, the move time during which time the tool moves, and the stroke that is upward distance that the tool translates during the "slip" portion of the stick-slip motion. This method of measurement is used to log the well at different vertical positions of the tool. Therefore, any typical "station-to-station logging tool" may be modified to be a "continuous logging tool", where "continuous" means that the wireline drum continually rotates while the tool undergoes stick-slip motion downhole and measurements are performed during the dwell times when the tool is momentarily stationary. The stick-slip methods of operation and the related apparatus are particularly described in terms of making measurements of formation resistivity from within a cased well during the dwell times when the tool is momentarily stationary during the periodic stick-slip motion of the logging tool.

Methods and apparatus to produce stick-slip motion of logging tool attached to a wireline drawn upward by a continuously rotating wireline drum

DOEpatents

Vail, W.B. III; Momii, S.T.

1998-02-10

Methods and apparatus are described to produce stick-slip motion of a logging tool within a cased well attached to a wireline that is drawn upward by a continuously rotating wireline drum. The stick-slip motion results in the periodic upward movement of the tool in the cased well described in terms of a dwell time during which time the tool is stationary, the move time during which time the tool moves, and the stroke that is upward distance that the tool translates during the ``slip`` portion of the stick-slip motion. This method of measurement is used to log the well at different vertical positions of the tool. Therefore, any typical ``station-to-station logging tool`` may be modified to be a ``continuous logging tool,`` where ``continuous`` means that the wireline drum continually rotates while the tool undergoes stick-slip motion downhole and measurements are performed during the dwell times when the tool is momentarily stationary. The stick-slip methods of operation and the related apparatus are particularly described in terms of making measurements of formation resistivity from within a cased well during the dwell times when the tool is momentarily stationary during the periodic stick-slip motion of the logging tool. 12 figs.

Gallium(III) chelates of mixed phosphonate-carboxylate triazamacrocyclic ligands relevant to nuclear medicine: Structural, stability and in vivo studies.

PubMed

Prata, Maria I M; André, João P; Kovács, Zoltán; Takács, Anett I; Tircsó, Gyula; Tóth, Imre; Geraldes, Carlos F G C

2017-12-01

Three triaza macrocyclic ligands, H 6 NOTP (1,4,7-triazacyclononane-N,N',N″-trimethylene phosphonic acid), H 4 NO2AP (1,4,7-triazacyclononane-N-methylenephosphonic acid-N',N″-dimethylenecarboxylic acid), and H 5 NOA2P (1,4,7-triazacyclononane-N,N'-bis(methylenephosphonic acid)-N″-methylene carboxylic acid), and their gallium(III) chelates were studied in view of their potential interest as scintigraphic and PET (Positron Emission Tomography) imaging agents. A 1 H, 31 P and 71 Ga multinuclear NMR study gave an insight on the structure, internal dynamics and stability of the chelates in aqueous solution. In particular, the analysis of 71 Ga NMR spectra gave information on the symmetry of the Ga 3+ coordination sphere and the stability of the chelates towards hydrolysis. The 31 P NMR spectra afforded information on the protonation of the non-coordinated oxygen atoms from the pendant phosphonate groups and on the number of species in solution. The 1 H NMR spectra allowed the analysis of the structure and the number of species in solution. 31 P and 1 H NMR titrations combined with potentiometry afforded the measurement of the protonation constants (log K Hi ) and the microscopic protonation scheme of the triaza macrocyclic ligands. The remarkably high thermodynamic stability constant (log K GaL =34.44 (0.04) and stepwise protonation constants of Ga(NOA2P) 2- were determined by potentiometry and 69 Ga and 31 P NMR titrations. Biodistribution and gamma imaging studies have been performed on Wistar rats using the radiolabeled 67 Ga(NO2AP) - and 67 Ga(NOA2P) 2- chelates, having both demonstrated to have renal excretion. The correlation of the molecular properties of the chelates with their pharmacokinetic properties has been analysed. Copyright © 2017 Elsevier Inc. All rights reserved.

Fragment-Based Drug Discovery Using NMR Spectroscopy

PubMed Central

Harner, Mary J.; Frank, Andreas O.; Fesik, Stephen W.

2013-01-01

Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool for fragment-based drug discovery over the last two decades. While NMR has been traditionally used to elucidate the three-dimensional structures and dynamics of biomacromolecules and their interactions, it can also be a very valuable tool for the reliable identification of small molecules that bind to proteins and for hit-to-lead optimization. Here, we describe the use of NMR spectroscopy as a method for fragment-based drug discovery and how to most effectively utilize this approach for discovering novel therapeutics based on our experience. PMID:23686385

What's new in well logging and formation evaluation

USGS Publications Warehouse

Prensky, S.

2011-01-01

A number of significant new developments is emerging in well logging and formation evaluation. Some of the new developments include an ultrasonic wireline imager, an electromagnetic free-point indicator, wired and fiber-optic coiled tubing systems, and extreme-temperature logging-while-drilling (LWD) tools. The continued consolidation of logging and petrophysical service providers in 2010 means that these innovations are increasingly being provided by a few large companies. Weatherford International has launched a slimhole cross-dipole tool as part of the company's line of compact logging tools. The 26-ft-long Compact Cross-Dipole Sonic (CXD) tool can be run as part of a quad-combo compact logging string. Halliburton has introduced a version of its circumferential acoustic scanning tool (CAST) that runs on monoconductor cable (CAST-M) to provide high-resolution images in open hole and in cased hole for casing and cement evaluation.

Logging while fishing: An alternate method to cut and thread fishing

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

Tollefsen, E.; Crary, S.; Flores, B.

1996-12-31

New technology has been introduced to allow completion of the wireline logging program after the tool string has become lodged in the wellbore. Charges associated with extracting a stuck tool are substantial. These charges result from the nonproductive time during the fishing trip, an associated wiper trip, and re-logging the well. The ability to continue the logging program while retrieving the logging string from the wellbore is needed. Logging While Fishing (LWF) is a hybrid of existing technologies combined with a new sub capable of severing a cable remotely. This new method is comprised of cut and thread fishing, drillpipemore » conveyed logging, and bridled tool techniques. Utilizing these techniques it is possible to complete wireline logging operations while removing a stuck tool from the wellbore. Completing logging operations using this hybrid method will save operating companies time and money. Other benefits, depending on the situation, include reduced fishing time and an increased level of safety. This application has been demonstrated on jobs in the Gulf of Mexico, North Sea, Venezuela, and Southeast Asia.« less

Logging-while-coring method and apparatus

DOEpatents

Goldberg, David S.; Myers, Gregory J.

2007-11-13

A method and apparatus for downhole coring while receiving logging-while-drilling tool data. The apparatus includes core collar and a retrievable core barrel. The retrievable core barrel receives core from a borehole which is sent to the surface for analysis via wireline and latching tool The core collar includes logging-while-drilling tools for the simultaneous measurement of formation properties during the core excavation process. Examples of logging-while-drilling tools include nuclear sensors, resistivity sensors, gamma ray sensors, and bit resistivity sensors. The disclosed method allows for precise core-log depth calibration and core orientation within a single borehole, and without at pipe trip, providing both time saving and unique scientific advantages.

Logging-while-coring method and apparatus

DOEpatents

Goldberg, David S.; Myers, Gregory J.

2007-01-30

A method and apparatus for downhole coring while receiving logging-while-drilling tool data. The apparatus includes core collar and a retrievable core barrel. The retrievable core barrel receives core from a borehole which is sent to the surface for analysis via wireline and latching tool The core collar includes logging-while-drilling tools for the simultaneous measurement of formation properties during the core excavation process. Examples of logging-while-drilling tools include nuclear sensors, resistivity sensors, gamma ray sensors, and bit resistivity sensors. The disclosed method allows for precise core-log depth calibration and core orientation within a single borehole, and without at pipe trip, providing both time saving and unique scientific advantages.

75 FR 75995 - Request for Comments on Helium-3 Use in the Oil and Natural Gas Well Logging Industry

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-07

... manufacture neutron detectors used by the well logging industry or wireline or Logging-While-Drilling tools incorporating neutron detectors, and whether companies purchase or lease logging tools that contain neutron detectors. DOE also seeks information on the volumes of Helium-3 anticipated by the oil and gas well logging...

Teaching NMR spectra analysis with nmr.cheminfo.org.

PubMed

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

2018-06-01

Teaching spectra analysis and structure elucidation requires students to get trained on real problems. This involves solving exercises of increasing complexity and when necessary using computational tools. Although desktop software packages exist for this purpose, nmr.cheminfo.org platform offers students an online alternative. It provides a set of exercises and tools to help solving them. Only a small number of exercises are currently available, but contributors are invited to submit new ones and suggest new types of problems. Copyright © 2018 John Wiley & Sons, Ltd.

SPINS: standardized protein NMR storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra.

PubMed

Baran, Michael C; Moseley, Hunter N B; Sahota, Gurmukh; Montelione, Gaetano T

2002-10-01

Modern protein NMR spectroscopy laboratories have a rapidly growing need for an easily queried local archival system of raw experimental NMR datasets. SPINS (Standardized ProteIn Nmr Storage) is an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and dissemination of results to the public domain by automatic preparation of the header files required for submission of data to the BioMagResBank (BMRB). The current version of SPINS coordinates the process from data collection to BMRB deposition of raw NMR data by standardizing and integrating the storage and retrieval of these data in a local laboratory file system. Additional facilities include a data mining query tool, graphical database administration tools, and a NMRStar v2. 1.1 file generator. SPINS also includes a user-friendly internet-based graphical user interface, which is optionally integrated with Varian VNMR NMR data collection software. This paper provides an overview of the data model underlying the SPINS database system, a description of its implementation in Oracle, and an outline of future plans for the SPINS project.

Assigning uncertainties in the inversion of NMR relaxation data.

PubMed

Parker, Robert L; Song, Yi-Qaio

2005-06-01

Recovering the relaxation-time density function (or distribution) from NMR decay records requires inverting a Laplace transform based on noisy data, an ill-posed inverse problem. An important objective in the face of the consequent ambiguity in the solutions is to establish what reliable information is contained in the measurements. To this end we describe how upper and lower bounds on linear functionals of the density function, and ratios of linear functionals, can be calculated using optimization theory. Those bounded quantities cover most of those commonly used in the geophysical NMR, such as porosity, T(2) log-mean, and bound fluid volume fraction, and include averages over any finite interval of the density function itself. In the theory presented statistical considerations enter to account for the presence of significant noise in the signal, but not in a prior characterization of density models. Our characterization of the uncertainties is conservative and informative; it will have wide application in geophysical NMR and elsewhere.

The GNAT: A new tool for processing NMR data.

PubMed

Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam A; Morris, Gareth A; Nilsson, Mathias

2018-06-01

The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T 1 /T 2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available. © 2018 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.

Dissemination of original NMR data enhances reproducibility and integrity in chemical research.

PubMed

Bisson, Jonathan; Simmler, Charlotte; Chen, Shao-Nong; Friesen, J Brent; Lankin, David C; McAlpine, James B; Pauli, Guido F

2016-08-25

The notion of data transparency is gaining a strong awareness among the scientific community. The availability of raw data is actually regarded as a fundamental way to advance science by promoting both integrity and reproducibility of research outcomes. Particularly, in the field of natural product and chemical research, NMR spectroscopy is a fundamental tool for structural elucidation and quantification (qNMR). As such, the accessibility of original NMR data, i.e., Free Induction Decays (FIDs), fosters transparency in chemical research and optimizes both peer review and reproducibility of reports by offering the fundamental tools to perform efficient structural verification. Although original NMR data are known to contain a wealth of information, they are rarely accessible along with published data. This viewpoint discusses the relevance of the availability of original NMR data as part of good research practices not only to promote structural correctness, but also to enhance traceability and reproducibility of both chemical and biological results.

Correlating Petrophysical Well Logs Using Fractal-based Analysis to Identify Changes in the Signal Complexity Across Neutron, Density, Dipole Sonic, and Gamma Ray Tool Types

NASA Astrophysics Data System (ADS)

Matthews, L.; Gurrola, H.

2015-12-01

Typical petrophysical well log correlation is accomplished by manual pattern recognition leading to subjective correlations. The change in character in a well log is dependent upon the change in the response of the tool to lithology. The petrophysical interpreter looks for a change in one log type that would correspond to the way a different tool responds to the same lithology. To develop an objective way to pick changes in well log characteristics, we adapt a method of first arrival picking used in seismic data to analyze changes in the character of well logs. We chose to use the fractal method developed by Boschetti et al[1] (1996). This method worked better than we expected and we found similar changes in the fractal dimension across very different tool types (sonic vs density vs gamma ray). We reason the fractal response of the log is not dependent on the physics of the tool response but rather the change in the complexity of the log data. When a formation changes physical character in time or space the recorded magnitude in tool data changes complexity at the same time even if the original tool response is very different. The relative complexity of the data regardless of the tool used is dependent upon the complexity of the medium relative to tool measurement. The relative complexity of the recorded magnitude data changes as a tool transitions from one character type to another. The character we are measuring is the roughness or complexity of the petrophysical curve. Our method provides a way to directly compare different log types based on a quantitative change in signal complexity. For example, using changes in data complexity allow us to correlate gamma ray suites with sonic logs within a well and then across to an adjacent well with similar signatures. Our method creates reliable and automatic correlations to be made in data sets beyond the reasonable cognitive limits of geoscientists in both speed and consistent pattern recognition. [1] Fabio Boschetti, Mike D. Dentith, and Ron D. List, (1996). A fractal-based algorithm for detecting first arrivals on seismic traces. Geophysics, Vol.61, No.4, P. 1095-1102.

[Microspeciation of amphoteric molecules of unusual acid-base properties].

PubMed

Kóczián, Kristóf

2007-01-01

The phisico-chemical properties of bio- and drug molecules greatly influence their interactions in the body and strongly effect the mechanism of drug action. Among these properties, macroscopic and site-specific protonation constants are of crucial importance. Latter one is the tool to calculate the relative concentration of the various microspecies in the compartments of the body at different pH values, and also, it is the versatile parameter to improve the pharmacokinetic properties of a new molecule in a particular family of drugs. In the present thesis work, the microspeciation of three molecules of great pharmaceutical importance and unusual acid-base properties, were carried out. The microconstants of tenoxicam, the non-steroidal anti-inflammatory drug, were described, introducing a novel deductive method using Hammett constants. For this purpose, a total of 8 tenoxicam and piroxicam derivatives were synthesised. To the best of our knowledge, the log k(N)O microconstant of tenoxicam obtained thus is the lowest enolate basicity value, which, however, can be well explained by the effects of the intramolecular environment. The developed evaluation procedure is suitable for microconstant determination of compounds in other molecule families. Besides, prodrug-type compounds and analogues similar to the structures of selective COX-2 isoenzyme inhibitors were synthesised. The other two molecules studied, the 6-aminopenicillanic acid and 7-cephalosporanic acid, the core molecules of the two most important beta-lactam antibiotic-types were derivatised and investigated by 1D and 2D NMR techniques. The NMR-pH titration on the parent compounds and their ester derivatives, combined with in situ pH-measurements allowed the microspeciation of these easily decomposing molecules. One of the protonation constant of 7-ACA (log kN(O) = 4.12), to the best of our knowledge, is the least non-aromatic basic amino-site among the natural compounds.

Environmental corrections of a dual-induction logging while drilling tool in vertical wells

NASA Astrophysics Data System (ADS)

Kang, Zhengming; Ke, Shizhen; Jiang, Ming; Yin, Chengfang; Li, Anzong; Li, Junjian

2018-04-01

With the development of Logging While Drilling (LWD) technology, dual-induction LWD logging is not only widely applied in deviated wells and horizontal wells, but it is used commonly in vertical wells. Accordingly, it is necessary to simulate the response of LWD tools in vertical wells for logging interpretation. In this paper, the investigation characteristics, the effects of the tool structure, skin effect and drilling environment of a dual-induction LWD tool are simulated by the three-dimensional (3D) finite element method (FEM). In order to closely simulate the actual situation, real structure of the tool is taking into account. The results demonstrate that the influence of the background value of the tool structure can be eliminated. The values of deducting the background of a tool structure and analytical solution have a quantitative agreement in homogeneous formations. The effect of measurement frequency could be effectively eliminated by chart of skin effect correction. In addition, the measurement environment, borehole size, mud resistivity, shoulder bed, layer thickness and invasion, have an effect on the true resistivity. To eliminate these effects, borehole correction charts, shoulder bed correction charts and tornado charts are computed based on real tool structure. Based on correction charts, well logging data can be corrected automatically by a suitable interpolation method, which is convenient and fast. Verified with actual logging data in vertical wells, this method could obtain the true resistivity of formation.

EASY: a simple tool for simultaneously removing background, deadtime and acoustic ringing in quantitative NMR spectroscopy--part I: basic principle and applications.

PubMed

Jaeger, Christian; Hemmann, Felix

2014-01-01

Elimination of Artifacts in NMR SpectroscopY (EASY) is a simple but very effective tool to remove simultaneously any real NMR probe background signal, any spectral distortions due to deadtime ringdown effects and -specifically- severe acoustic ringing artifacts in NMR spectra of low-gamma nuclei. EASY enables and maintains quantitative NMR (qNMR) as only a single pulse (preferably 90°) is used for data acquisition. After the acquisition of the first scan (it contains the wanted NMR signal and the background/deadtime/ringing artifacts) the same experiment is repeated immediately afterwards before the T1 waiting delay. This second scan contains only the background/deadtime/ringing parts. Hence, the simple difference of both yields clean NMR line shapes free of artefacts. In this Part I various examples for complete (1)H, (11)B, (13)C, (19)F probe background removal due to construction parts of the NMR probes are presented. Furthermore, (25)Mg EASY of Mg(OH)2 is presented and this example shows how extremely strong acoustic ringing can be suppressed (more than a factor of 200) such that phase and baseline correction for spectra acquired with a single pulse is no longer a problem. EASY is also a step towards deadtime-free data acquisition as these effects are also canceled completely. EASY can be combined with any other NMR experiment, including 2D NMR, if baseline distortions are a big problem. © 2013 Published by Elsevier Inc.

NMR measurement of bitumen at different temperatures.

PubMed

Yang, Zheng; Hirasaki, George J

2008-06-01

Heavy oil (bitumen) is characterized by its high viscosity and density, which is a major obstacle to both well logging and recovery. Due to the lost information of T2 relaxation time shorter than echo spacing (TE) and interference of water signal, estimation of heavy oil properties from NMR T2 measurements is usually problematic. In this work, a new method has been developed to overcome the echo spacing restriction of NMR spectrometer during the application to heavy oil (bitumen). A FID measurement supplemented the start of CPMG. Constrained by its initial magnetization (M0) estimated from the FID and assuming log normal distribution for bitumen, the corrected T2 relaxation time of bitumen sample can be obtained from the interpretation of CPMG data. This new method successfully overcomes the TE restriction of the NMR spectrometer and is nearly independent on the TE applied in the measurement. This method was applied to the measurement at elevated temperatures (8-90 degrees C). Due to the significant signal-loss within the dead time of FID, the directly extrapolated M0 of bitumen at relatively lower temperatures (<60 degrees C) was found to be underestimated. However, resulting from the remarkably lowered viscosity, the extrapolated M0 of bitumen at over 60 degrees C can be reasonably assumed to be the real value. In this manner, based on the extrapolation at higher temperatures (> or = 60 degrees C), the M0 value of bitumen at lower temperatures (<60 degrees C) can be corrected by Curie's Law. Consequently, some important petrophysical properties of bitumen, such as hydrogen index (HI), fluid content and viscosity were evaluated by using corrected T2.

A nanoliter volume nuclear magnetic resonance (NMR) system using tunneling magneto-resistive (TMR) sensors to recognize biomolecules

NASA Astrophysics Data System (ADS)

Gomez, Pablo

The need to incorporate advanced engineering tools in biology, biochemistry and medicine is in great demand. Many of the existing instruments and tools are usually expensive and require special facilities. With the advent of nanotechnology in the past decade, new approaches to develop devices and tools have been generated by academia and industry. One such technology, NMR spectroscopy, has been used by biochemists for more than 2 decades to study the molecular structure of chemical compounds. However, NMR spectrometers are very expensive and require special laboratory rooms for their proper operation. High magnetic fields with strengths in the order of several Tesla make these instruments unaffordable to most research groups. This doctoral research proposes a new technology to develop NMR spectrometers that can operate at field strengths of less than 0.5 Tesla using an inexpensive permanent magnet and spin dependent nanoscale magnetic devices. This portable NMR system is intended to analyze samples as small as a few nanoliters. The main problem to resolve when downscaling the variables is to obtain an NMR signal with high Signal-To-Noise-Ratio (SNR). A special Tunneling Magneto-Resistive (TMR) sensor design was developed to achieve this goal. The minimum specifications for each component of the proposed NMR system were established. A complete NMR system was designed based on these minimum requirements. The goat was always to find cost effective realistic components. The novel design of the NMR system uses technologies such as Direct Digital Synthesis (DDS), Digital Signal Processing (DSP) and a special Backpropagation Neural Network that finds the best match of the NMR spectrum. The system was designed, calculated and simulated with excellent results. In addition, a general method to design TMR Sensors was developed. The technique was automated and a computer program was written to help the designer perform this task interactively.

Tools and data acquisition of borehole geophysical logging for the Florida Power and Light Company Turkey Point Power Plant in support of a groundwater, surface-water, and ecological monitoring plan, Miami-Dade County, Florida

USGS Publications Warehouse

Wacker, Michael A.

2010-01-01

Borehole geophysical logs were obtained from selected exploratory coreholes in the vicinity of the Florida Power and Light Company Turkey Point Power Plant. The geophysical logging tools used and logging sequences performed during this project are summarized herein to include borehole logging methods, descriptions of the properties measured, types of data obtained, and calibration information.

Single-scan 2D NMR: An Emerging Tool in Analytical Spectroscopy

PubMed Central

Giraudeau, Patrick; Frydman, Lucio

2016-01-01

Two-dimensional Nuclear Magnetic Resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing an increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago a so-called “ultrafast” (UF) approach was proposed, capable to deliver arbitrary 2D NMR spectra involving any kind of homo- or hetero-nuclear correlations, in a single scan. During the intervening years the performance of this sub-second 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool witnessing an expanded scope of applications. The present reviews summarizes the principles and the main developments which have contributed to the success of this approach, and focuses on applications which have been recently demonstrated in various areas of analytical chemistry –from the real time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications. PMID:25014342

FoodPro: A Web-Based Tool for Evaluating Covariance and Correlation NMR Spectra Associated with Food Processes

PubMed Central

Chikayama, Eisuke; Yamashina, Ryo; Komatsu, Keiko; Tsuboi, Yuuri; Sakata, Kenji; Kikuchi, Jun; Sekiyama, Yasuyo

2016-01-01

Foods from agriculture and fishery products are processed using various technologies. Molecular mixture analysis during food processing has the potential to help us understand the molecular mechanisms involved, thus enabling better cooking of the analyzed foods. To date, there has been no web-based tool focusing on accumulating Nuclear Magnetic Resonance (NMR) spectra from various types of food processing. Therefore, we have developed a novel web-based tool, FoodPro, that includes a food NMR spectrum database and computes covariance and correlation spectra to tasting and hardness. As a result, FoodPro has accumulated 236 aqueous (extracted in D2O) and 131 hydrophobic (extracted in CDCl3) experimental bench-top 60-MHz NMR spectra, 1753 tastings scored by volunteers, and 139 hardness measurements recorded by a penetrometer, all placed into a core database. The database content was roughly classified into fish and vegetable groups from the viewpoint of different spectrum patterns. FoodPro can query a user food NMR spectrum, search similar NMR spectra with a specified similarity threshold, and then compute estimated tasting and hardness, covariance, and correlation spectra to tasting and hardness. Querying fish spectra exemplified specific covariance spectra to tasting and hardness, giving positive covariance for tasting at 1.31 ppm for lactate and 3.47 ppm for glucose and a positive covariance for hardness at 3.26 ppm for trimethylamine N-oxide. PMID:27775560

FoodPro: A Web-Based Tool for Evaluating Covariance and Correlation NMR Spectra Associated with Food Processes.

PubMed

Chikayama, Eisuke; Yamashina, Ryo; Komatsu, Keiko; Tsuboi, Yuuri; Sakata, Kenji; Kikuchi, Jun; Sekiyama, Yasuyo

2016-10-19

Foods from agriculture and fishery products are processed using various technologies. Molecular mixture analysis during food processing has the potential to help us understand the molecular mechanisms involved, thus enabling better cooking of the analyzed foods. To date, there has been no web-based tool focusing on accumulating Nuclear Magnetic Resonance (NMR) spectra from various types of food processing. Therefore, we have developed a novel web-based tool, FoodPro, that includes a food NMR spectrum database and computes covariance and correlation spectra to tasting and hardness. As a result, FoodPro has accumulated 236 aqueous (extracted in D₂O) and 131 hydrophobic (extracted in CDCl₃) experimental bench-top 60-MHz NMR spectra, 1753 tastings scored by volunteers, and 139 hardness measurements recorded by a penetrometer, all placed into a core database. The database content was roughly classified into fish and vegetable groups from the viewpoint of different spectrum patterns. FoodPro can query a user food NMR spectrum, search similar NMR spectra with a specified similarity threshold, and then compute estimated tasting and hardness, covariance, and correlation spectra to tasting and hardness. Querying fish spectra exemplified specific covariance spectra to tasting and hardness, giving positive covariance for tasting at 1.31 ppm for lactate and 3.47 ppm for glucose and a positive covariance for hardness at 3.26 ppm for trimethylamine N -oxide.

New roles of LWD and wireline logging in scientific ocean drilling

NASA Astrophysics Data System (ADS)

Sanada, Y.; Kido, Y. N.; Moe, K.; Aoike, K.

2014-12-01

D/V Chikyu implemented by CDEX/JAMSTEC joined IODP from 2007. Various LWD (Logging While Drilling) and wireline logging have been carried out in many expeditions and for various purposes. Significant features of logging in Chikyu expeditions are many use of LWD than wireline logging, and riser dirlling. riser selected specific tools for each scientific target, and 3) carried out various borehole experiments. LWD has been more popular than wireline logging in Chikyu expeditions, because its advantages match theirs science targets. The advantages are followings. 1) LWD has more opportunities for measurement in unstable borehole, such as in the series of Nankai trough drilling expeditions. 2) LWD realtime data allows us to make realtime interpretation and operational decision. Realtime interpretation was required to set obsevartory at the properposition. 3) LWD before coring allows us to make a strategy of spot coring.We can design coring intervals for our interest and core length to improve core recovery.Riser drilling brings us merits for logging. One is hole stability (good hole condition) and the other is the use of large diameter tools. Controled drilling mud in riser drilling system prevent mud invasion to formation and mitigates collapse of borehole wall. They reduce the risk of tool stack and improve data quality. Large diameter of riser pipe enhances variation of tool seizes. A couple of new tools were used for new measurement and improvement of the data quality. For example, SonicScanner (trademark of Schulumberger) successfully measured compressional and share velocity in very low velocities at the soft sediment, where it has been difficult to measure them with conventional DSI tool (Exp319). The stress and pore pressure in the borehole were measured with the wireline logging tool, (Schlumberger MDT). The single probe tool enable to measure temporal formation fluid pressure. The double packer tool enable to fracture test by sealing and pumping in the borehole. These in-situ measurement and stress experiment data are very important to understand physical properties and mechanism of fault zone (Exp319).Those new technologies and tools also expand the envelope of scientific ocean drilling.

A novel method for quantitative geosteering using azimuthal gamma-ray logging.

PubMed

Yuan, Chao; Zhou, Cancan; Zhang, Feng; Hu, Song; Li, Chaoliu

2015-02-01

A novel method for quantitative geosteering by using azimuthal gamma-ray logging is proposed. Real-time up and bottom gamma-ray logs when a logging tool travels through a boundary surface with different relative dip angles are simulated with the Monte Carlo method. Study results show that response points of up and bottom gamma-ray logs when the logging tool moves towards a highly radioactive formation can be used to predict the relative dip angle, and then the distance from the drilling bit to the boundary surface is calculated. Copyright © 2014 Elsevier Ltd. All rights reserved.

Chelation of heavy group 2 (radio)metals by p-tert-butylcalix[4]arene-1,3-crown-6 and logK determination via NMR

NASA Astrophysics Data System (ADS)

Bauer, David; Gott, Matthew; Steinbach, Jörg; Mamat, Constantin

2018-06-01

A crown-bridged calix[4]arene scaffold was investigated as lead compound for the ligation of heavy alkaline earth metals such as strontium and barium, which appear to be useful for radiopharmaceutical applications in diagnosis as well as in radiotherapy. In particular barium, due to its chemical similarities, could serve as a surrogate for radium, a metal of high radiopharmaceutical interest. The ability of p-tert-butylcalix[4]arene-1,3-crown-6 (1) in particular to chelate cations, such as group 1 and 2 metal ions or ammonium ions is well known. Also, the manifold possibilities of structural modification on the upper- and lower-rim as well as on the crown itself produce properties that may lead to a highly selective and effective chelating agent. In this work, titration experiments of the perchlorate salts of Ba2+, Sr2+ and Pb2+ with ligand 1 were performed to determine their stability constants (logK = 4.7, 4.3, and 3.3, respectively) by 1H NMR measurements in acetonitrile-d3.

Detecting well casing leaks in Bangladesh using a salt spiking method

USGS Publications Warehouse

Stahl, M.O.; Ong, J.B.; Harvey, C.F.; Johnson, C.D.; Badruzzaman, A.B.M.; Tarek, M.H.; VanGeen, A.; Anderson, J.A.; Lane, J.W.

2014-01-01

We apply fluid-replacement logging in arsenic-contaminated regions of Bangladesh using a low-cost, down-well fluid conductivity logging tool to detect leaks in the cased section of wells. The fluid-conductivity tool is designed for the developing world: it is lightweight and easily transportable, operable by one person, and can be built for minimal cost. The fluid-replacement test identifies leaking casing by comparison of fluid conductivity logs collected before and after spiking the wellbore with a sodium chloride tracer. Here, we present results of fluid-replacement logging tests from both leaking and non-leaking casing from wells in Araihazar and Munshiganj, Bangladesh, and demonstrate that the low-cost tool produces measurements comparable to those obtained with a standard geophysical logging tool. Finally, we suggest well testing procedures and approaches for preventing casing leaks in Bangladesh and other developing countries.

Detecting well casing leaks in Bangladesh using a salt spiking method.

PubMed

Stahl, M O; Ong, J B; Harvey, C F; Johnson, C D; Badruzzaman, A B M; Tarek, M H; van Geen, A; Anderson, J A; Lane, J W

2014-09-01

We apply fluid-replacement logging in arsenic-contaminated regions of Bangladesh using a low-cost, down-well fluid conductivity logging tool to detect leaks in the cased section of wells. The fluid-conductivity tool is designed for the developing world: it is lightweight and easily transportable, operable by one person, and can be built for minimal cost. The fluid-replacement test identifies leaking casing by comparison of fluid conductivity logs collected before and after spiking the wellbore with a sodium chloride tracer. Here, we present results of fluid-replacement logging tests from both leaking and non-leaking casing from wells in Araihazar and Munshiganj, Bangladesh, and demonstrate that the low-cost tool produces measurements comparable to those obtained with a standard geophysical logging tool. Finally, we suggest well testing procedures and approaches for preventing casing leaks in Bangladesh and other developing countries. © 2014, National Ground Water Association.

Magic Angle Spinning NMR Metabolomics

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

Zhi Hu, Jian

Nuclear Magnetic Resonance (NMR) spectroscopy is a non-destructive, quantitative, reproducible, untargeted and unbiased method that requires no or minimal sample preparation, and is one of the leading analytical tools for metabonomics research [1-3]. The easy quantification and the no need of prior knowledge about compounds present in a sample associated with NMR are advantageous over other techniques [1,4]. 1H NMR is especially attractive because protons are present in virtually all metabolites and its NMR sensitivity is high, enabling the simultaneous identification and monitoring of a wide range of low molecular weight metabolites.

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

Mukul M. Sharma; Steven L. Bryant; Carlos Torres-Verdin

The petrophysical properties of rocks, particularly their relative permeability and wettability, strongly influence the efficiency and the time-scale of all hydrocarbon recovery processes. However, the quantitative relationships needed to account for the influence of wettability and pore structure on multi-phase flow are not yet available, largely due to the complexity of the phenomena controlling wettability and the difficulty of characterizing rock properties at the relevant length scales. This project brings together several advanced technologies to characterize pore structure and wettability. Grain-scale models are developed that help to better interpret the electric and dielectric response of rocks. These studies allow themore » computation of realistic configurations of two immiscible fluids as a function of wettability and geologic characteristics. These fluid configurations form a basis for predicting and explaining macroscopic behavior, including the relationship between relative permeability, wettability and laboratory and wireline log measurements of NMR and dielectric response. Dielectric and NMR measurements have been made show that the response of the rocks depends on the wetting and flow properties of the rock. The theoretical models can be used for a better interpretation and inversion of standard well logs to obtain accurate and reliable estimates of fluid saturation and of their producibility. The ultimate benefit of this combined theoretical/empirical approach for reservoir characterization is that rather than reproducing the behavior of any particular sample or set of samples, it can explain and predict trends in behavior that can be applied at a range of length scales, including correlation with wireline logs, seismic, and geologic units and strata. This approach can substantially enhance wireline log interpretation for reservoir characterization and provide better descriptions, at several scales, of crucial reservoir flow properties that govern oil recovery.« less

Unconventional Tight Reservoirs Characterization with Nuclear Magnetic Resonance

NASA Astrophysics Data System (ADS)

Santiago, C. J. S.; Solatpour, R.; Kantzas, A.

2017-12-01

The increase in tight reservoir exploitation projects causes producing many papers each year on new, modern, and modified methods and techniques on estimating characteristics of these reservoirs. The most ambiguous of all basic reservoir property estimations deals with permeability. One of the logging methods that is advertised to predict permeability but is always met by skepticism is Nuclear Magnetic Resonance (NMR). The ability of NMR to differentiate between bound and movable fluids and providing porosity increased the capability of NMR as a permeability prediction technique. This leads to a multitude of publications and the motivation of a review paper on this subject by Babadagli et al. (2002). The first part of this presentation is dedicated to an extensive review of the existing correlation models for NMR based estimates of tight reservoir permeability to update this topic. On the second part, the collected literature information is used to analyze new experimental data. The data are collected from tight reservoirs from Canada, the Middle East, and China. A case study is created to apply NMR measurement in the prediction of reservoir characterization parameters such as porosity, permeability, cut-offs, irreducible saturations etc. Moreover, permeability correlations are utilized to predict permeability. NMR experiments were conducted on water saturated cores. NMR T2 relaxation times were measured. NMR porosity, the geometric mean relaxation time (T2gm), Irreducible Bulk Volume (BVI), and Movable Bulk Volume (BVM) were calculated. The correlation coefficients were computed based on multiple regression analysis. Results are cross plots of NMR permeability versus the independently measured Klinkenberg corrected permeability. More complicated equations are discussed. Error analysis of models is presented and compared. This presentation is beneficial in understanding existing tight reservoir permeability models. The results can be used as a guide for choosing the best permeability estimation model for tight reservoirs data.

Determination of partition coefficients using 1 H NMR spectroscopy and time domain complete reduction to amplitude-frequency table (CRAFT) analysis.

PubMed

Soulsby, David; Chica, Jeryl A M

2017-08-01

We have developed a simple, direct and novel method for the determination of partition coefficients and partitioning behavior using 1 H NMR spectroscopy combined with time domain complete reduction to amplitude-frequency tables (CRAFT). After partitioning into water and 1-octanol using standard methods, aliquots from each layer are directly analyzed using either proton or selective excitation NMR experiments. Signal amplitudes for each compound from each layer are then extracted directly from the time domain data in an automated fashion and analyzed using the CRAFT software. From these amplitudes, log P and log D 7.4 values can be calculated directly. Phase, baseline and internal standard issues, which can be problematic when Fourier transformed data are used, are unimportant when using time domain data. Furthermore, analytes can contain impurities because only a single resonance is examined and need not be UV active. Using this approach, we examined a variety of pharmaceutically relevant compounds and determined partition coefficients that are in excellent agreement with literature values. To demonstrate the utility of this approach, we also examined salicylic acid in more detail demonstrating an aggregation effect as a function of sample loading and partition coefficient behavior as a function of pH value. This method provides a valuable addition to the medicinal chemist toolbox for determining these important constants. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Authentication of animal origin of heparin and low molecular weight heparin including ovine, porcine and bovine species using 1D NMR spectroscopy and chemometric tools.

PubMed

Monakhova, Yulia B; Diehl, Bernd W K; Fareed, Jawed

2018-02-05

High resolution (600MHz) nuclear magnetic resonance (NMR) spectroscopy is used to distinguish heparin and low-molecular weight heparins (LMWHs) produced from porcine, bovine and ovine mucosal tissues as well as their blends. For multivariate analysis several statistical methods such as principal component analysis (PCA), factor discriminant analysis (FDA), partial least squares - discriminant analysis (PLS-DA), linear discriminant analysis (LDA) were utilized for the modeling of NMR data of more than 100 authentic samples. Heparin and LMWH samples from the independent test set (n=15) were 100% correctly classified according to its animal origin. Moreover, by using 1 H NMR coupled with chemometrics and several batches of bovine heparins from two producers were differentiated. Thus, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of animal origin and process based manufacturing difference in heparin products. Copyright © 2017 Elsevier B.V. All rights reserved.

Why Is It so? The [superscript 1]H-NMR CH[subscript 2] Splitting in Substituted Propanes

ERIC Educational Resources Information Center

Lim, Kieran F.; Dereani, Marino

2010-01-01

Nuclear magnetic resonance (NMR) spectroscopy is an important tool in the structural analysis of both organic and inorganic molecules. Proton NMR spectra can yield information about the chemical or bonding environment surrounding various protons, the number of protons in those environments, and the number of neighbouring protons around each…

Monitoring chemical reactions by low-field benchtop NMR at 45 MHz: pros and cons.

PubMed

Silva Elipe, Maria Victoria; Milburn, Robert R

2016-06-01

Monitoring chemical reactions is the key to controlling chemical processes where NMR can provide support. High-field NMR gives detailed structural information on chemical compounds and reactions; however, it is expensive and complex to operate. Conversely, low-field NMR instruments are simple and relatively inexpensive alternatives. While low-field NMR does not provide the detailed information as the high-field instruments as a result of their smaller chemical shift dispersion and the complex secondary coupling, it remains of practical value as a process analytical technology (PAT) tool and is complimentary to other established methods, such as ReactIR and Raman spectroscopy. We have tested a picoSpin-45 (currently under ThermoFisher Scientific) benchtop NMR instrument to monitor three types of reactions by 1D (1) H NMR: a Fischer esterification, a Suzuki cross-coupling, and the formation of an oxime. The Fischer esterification is a relatively simple reaction run at high concentration and served as proof of concept. The Suzuki coupling is an example of a more complex, commonly used reaction involving overlapping signals. Finally, the oxime formation involved a reaction in two phases that cannot be monitored by other PAT tools. Here, we discuss the pros and cons of monitoring these reactions at a low-field of 45 MHz by 1D (1) H NMR. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

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.

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.

PubMed

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M; Montelione, Gaetano T

2013-08-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.

PDBStat: A Universal Restraint Converter and Restraint Analysis Software Package for Protein NMR

PubMed Central

Tejero, Roberto; Snyder, David; Mao, Binchen; Aramini, James M.; Montelione, Gaetano T

2013-01-01

The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data. PMID:23897031

Anatomising proton NMR spectra with pure shift 2D J-spectroscopy: A cautionary tale

NASA Astrophysics Data System (ADS)

Kiraly, Peter; Foroozandeh, Mohammadali; Nilsson, Mathias; Morris, Gareth A.

2017-09-01

Analysis of proton NMR spectra has been a key tool in structure determination for over 60 years. A classic tool is 2D J-spectroscopy, but common problems are the difficulty of obtaining the absorption mode lineshapes needed for accurate results, and the need for a 45° shear of the final 2D spectrum. A novel 2D NMR method is reported here that allows straightforward determination of homonuclear couplings, using a modified version of the PSYCHE method to suppress couplings in the direct dimension. The method illustrates the need for care when combining pure shift data acquisition with multiple pulse methods.

The impact of a personal digital assistant (PDA) case log in a medical student clerkship.

PubMed

Ho, Kendall; Lauscher, Helen Novak; Broudo, Marc; Jarvis-Selinger, Sandra; Fraser, Joan; Hewes, Deborah; Scott, Ian

2009-10-01

Medical education literature emphasizes that reflection and self-audit are pivotal steps in learning and that personal digital assistants (PDAs) have potential as decision support tools. The purpose was to examine the efficacy of PDA-based resources and patient-encounter logging systems among 3rd-year medical clerks during pediatrics rotations. Students in rotations were assigned to control (using paper-based logs and references) or intervention groups (using PDA-based logs and resources). Students completed pre- and postrotation Paediatrics Competency Surveys, participated in focus groups, and were compared on year-end examination grades. Use of PDA logs far outweighed that of paper logs (1,020 PDA logs and 87 paper logs). PDA logs were ranked significantly higher in enhancing learning and reflection than paper logs (t = 2.52, p < .01). PDA logs also facilitated specific learning experiences. PDA-based patient-encounter logs appear to be effective case documentation and reflection tools. The difference in number of logs between control and intervention groups demonstrates the utility of the PDA for "point-of-care" patient logging.

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.

PubMed

Nowling, Ronald J; Vyas, Jay; Weatherby, Gerard; Fenwick, Matthew W; Ellis, Heidi J C; Gryk, Michael R

2011-05-01

NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension.

Genesis analysis of high-gamma ray sandstone reservoir and its log evaluation techniques: a case study from the Junggar basin, northwest China.

PubMed

Wang, Liang; Mao, Zhiqiang; Sun, Zhongchun; Luo, Xingping; Song, Yong; Liu, Zhen

2013-01-01

In the Junggar basin, northwest China, many high gamma-ray (GR) sandstone reservoirs are found and routinely interpreted as mudstone non-reservoirs, with negative implications for the exploration and exploitation of oil and gas. Then, the high GR sandstone reservoirs' recognition principles, genesis, and log evaluation techniques are systematically studied. Studies show that the sandstone reservoirs with apparent shale content greater than 50% and GR value higher than 110API can be regarded as high GR sandstone reservoir. The high GR sandstone reservoir is mainly and directly caused by abnormally high uranium enrichment, but not the tuff, feldspar or clay mineral. Affected by formation's high water sensitivity and poor borehole quality, the conventional logs can not recognize reservoir and evaluate the physical property of reservoirs. Then, the nuclear magnetic resonance (NMR) logs is proposed and proved to be useful in reservoir recognition and physical property evaluation.

Genesis Analysis of High-Gamma Ray Sandstone Reservoir and Its Log Evaluation Techniques: A Case Study from the Junggar Basin, Northwest China

PubMed Central

Wang, Liang; Mao, Zhiqiang; Sun, Zhongchun; Luo, Xingping; Song, Yong; Liu, Zhen

2013-01-01

In the Junggar basin, northwest China, many high gamma-ray (GR) sandstone reservoirs are found and routinely interpreted as mudstone non-reservoirs, with negative implications for the exploration and exploitation of oil and gas. Then, the high GR sandstone reservoirs' recognition principles, genesis, and log evaluation techniques are systematically studied. Studies show that the sandstone reservoirs with apparent shale content greater than 50% and GR value higher than 110API can be regarded as high GR sandstone reservoir. The high GR sandstone reservoir is mainly and directly caused by abnormally high uranium enrichment, but not the tuff, feldspar or clay mineral. Affected by formation's high water sensitivity and poor borehole quality, the conventional logs can not recognize reservoir and evaluate the physical property of reservoirs. Then, the nuclear magnetic resonance (NMR) logs is proposed and proved to be useful in reservoir recognition and physical property evaluation. PMID:24078797

Field test results--a new logging tool for formation density and lithology measurements

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

Borai, A.M.; Muhsin, M.A.

1983-03-01

The formation porosity can be determined from borehole density measurements if the density of the rock is known. Generally, this is determined from the lithology. The Litho-Density Tool, LDT, provides an improved measurement of the formation density and a new measurement of lithology. Field tests of LDT proved that the tool could be run alone in a wide range of formations to provide porosity values comparable to those obtained by running a density log combined with a neutron log.

[superscript 31]P NMR of the Pyruvate Kinase Reaction: An Undergraduate Experiment in Enzyme Kinetics

ERIC Educational Resources Information Center

Werner, R. Marshall; Johnson, Austin

2017-01-01

Understanding how to perform an enzyme assay is a critical learning skill in the undergraduate biochemistry curriculum. Students in biochemistry typically have been exposed to the use of NMR spectroscopy as a tool to determine chemical structure, but rarely are they exposed to the utility of NMR to evaluate enzyme kinetics. Furthermore, coverage…

Hydrolysis Studies and Quantitative Determination of Aluminum Ions Using [superscript 27]Al NMR: An Undergraduate Analytical Chemistry Experiment

ERIC Educational Resources Information Center

Curtin, Maria A.; Ingalls, Laura R.; Campbell, Andrew; James-Pederson, Magdalena

2008-01-01

This article describes a novel experiment focused on metal ion hydrolysis and the equilibria related to metal ions in aqueous systems. Using [superscript 27]Al NMR, the students become familiar with NMR spectroscopy as a quantitative analytical tool for the determination of aluminum by preparing a standard calibration curve using standard aluminum…

Determination of Molecular Self-Diffusion Coefficients Using Pulsed-Field-Gradient NMR: An Experiment for Undergraduate Physical Chemistry Laboratory

ERIC Educational Resources Information Center

Harmon, Jennifer; Coffman, Cierra; Villarrial, Spring; Chabolla, Steven; Heisel, Kurt A.; Krishnan, Viswanathan V.

2012-01-01

NMR spectroscopy has become one of the primary tools that chemists utilize to characterize a range of chemical species in the solution phase, from small organic molecules to medium-sized proteins. A discussion of NMR spectroscopy is an essential component of physical and biophysical chemistry lecture courses, and a number of instructional…

Two-Dimensional NMR Evidence for Cleavage of Lignin and Xylan Substituents in Wheat Straw Through Hydrothermal Pretreatment and Enzymatic Hydrolysis

Treesearch

Daniel J. Yelle; Prasad Kaparaju; Christopher G. Hunt; Kolby Hirth; Hoon Kim; John Ralph; Claus Felby

2012-01-01

Solution-state two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy of plant cell walls is a powerful tool for characterizing changes in cell wall chemistry during the hydrothermal pretreatment process of wheat straw for second-generation bioethanol production. One-bond 13C-1H NMR correlation spectroscopy, via...

A study on directional resistivity logging-while-drilling based on self-adaptive hp-FEM

NASA Astrophysics Data System (ADS)

Liu, Dejun; Li, Hui; Zhang, Yingying; Zhu, Gengxue; Ai, Qinghui

2014-12-01

Numerical simulation of resistivity logging-while-drilling (LWD) tool response provides guidance for designing novel logging instruments and interpreting real-time logging data. In this paper, based on self-adaptive hp-finite element method (hp-FEM) algorithm, we analyze LWD tool response against model parameters and briefly illustrate geosteering capabilities of directional resistivity LWD. Numerical simulation results indicate that the change of source spacing is of obvious influence on the investigation depth and detecting precision of resistivity LWD tool; the change of frequency can improve the resolution of low-resistivity formation and high-resistivity formation. The simulation results also indicate that the self-adaptive hp-FEM algorithm has good convergence speed and calculation accuracy to guide the geologic steering drilling and it is suitable to simulate the response of resistivity LWD tools.

A fast forward algorithm for real-time geosteering of azimuthal gamma-ray logging.

PubMed

Qin, Zhen; Pan, Heping; Wang, Zhonghao; Wang, Bintao; Huang, Ke; Liu, Shaohua; Li, Gang; Amara Konaté, Ahmed; Fang, Sinan

2017-05-01

Geosteering is an effective method to increase the reservoir drilling rate in horizontal wells. Based on the features of an azimuthal gamma-ray logging tool and strata spatial location, a fast forward calculation method of azimuthal gamma-ray logging is deduced by using the natural gamma ray distribution equation in formation. The response characteristics of azimuthal gamma-ray logging while drilling in the layered formation models with different thickness and position are simulated and summarized by using the method. The result indicates that the method calculates quickly, and when the tool nears a boundary, the method can be used to identify the boundary and determine the distance from the logging tool to the boundary in time. Additionally, the formation parameters of the algorithm in the field can be determined after a simple method is proposed based on the information of an offset well. Therefore, the forward method can be used for geosteering in the field. A field example validates that the forward method can be used to determine the distance from the azimuthal gamma-ray logging tool to the boundary for geosteering in real-time. Copyright © 2017 Elsevier Ltd. All rights reserved.

SpaceOps 2012 Plus 2: Social Tools to Simplify ISS Flight Control Communications and Log Keeping

NASA Technical Reports Server (NTRS)

Cowart, Hugh S.; Scott, David W.

2014-01-01

A paper written for the SpaceOps 2012 Conference (Simplify ISS Flight Control Communications and Log Keeping via Social Tools and Techniques) identified three innovative concepts for real time flight control communications tools based on social mechanisms: a) Console Log Tool (CoLT) - A log keeping application at Marshall Space Flight Center's (MSFC) Payload Operations Integration Center (POIC) that provides "anywhere" access, comment and notifications features similar to those found in Social Networking Systems (SNS), b) Cross-Log Communication via Social Techniques - A concept from Johnsson Space Center's (JSC) Mission Control Center Houston (MCC-H) that would use microblogging's @tag and #tag protocols to make information/requests visible and/or discoverable in logs owned by @Destination addressees, and c) Communications Dashboard (CommDash) - A MSFC concept for a Facebook-like interface to visually integrate and manage basic console log content, text chat streams analogous to voice loops, text chat streams dedicated to particular conversations, generic and position-specific status displays/streams, and a graphically based hailing display. CoLT was deployed operationally at nearly the same time as SpaceOps 2012, the Cross- Log Communications idea is currently waiting for a champion to carry it forward, and CommDash was approved as a NASA Iinformation Technoloby (IT) Labs project. This paper discusses lessons learned from two years of actual CoLT operations, updates CommDash prototype development status, and discusses potential for using Cross-Log Communications in both MCC-H and/or POIC environments, and considers other ways for synergizing console applcations.

SBIR Phase II Final Report: Low cost Autonomous NMR and Multi-sensor Soil Monitoring Instrument

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

Walsh, David O.

In this 32-month SBIR Phase 2 program, Vista Clara designed, assembled and successfully tested four new NMR instruments for soil moisture measurement and monitoring: An enhanced performance man-portable Dart NMR logging probe and control unit for rapid, mobile measurement in core holes and 2” PVC access wells; A prototype 4-level Dart NMR monitoring probe and prototype multi-sensor soil monitoring control unit for long-term unattended monitoring of soil moisture and other measurements in-situ; A non-invasive 1m x 1m Discus NMR soil moisture sensor with surface based magnet/coil array for rapid measurement of soil moisture in the top 50 cm of themore » subsurface; A non-invasive, ultra-lightweight Earth’s field surface NMR instrument for non-invasive measurement and mapping of soil moisture in the top 3 meters of the subsurface. The Phase 2 research and development achieved most, but not all of our technical objectives. The single-coil Dart in-situ sensor and control unit were fully developed, demonstrated and successfully commercialized within the Phase 2 period of performance. The multi-level version of the Dart probe was designed, assembled and demonstrated in Phase 2, but its final assembly and testing were delayed until close to the end of the Phase 2 performance period, which limited our opportunities for demonstration in field settings. Likewise, the multi-sensor version of the Dart control unit was designed and assembled, but not in time for it to be deployed for any long-term monitoring demonstrations. The prototype ultra-lightweight surface NMR instrument was developed and demonstrated, and this result will be carried forward into the development of a new flexible surface NMR instrument and commercial product in 2018.« less

Analysis of the interface variability in NMR structure ensembles of protein-protein complexes.

PubMed

Calvanese, Luisa; D'Auria, Gabriella; Vangone, Anna; Falcigno, Lucia; Oliva, Romina

2016-06-01

NMR structures consist in ensembles of conformers, all satisfying the experimental restraints, which exhibit a certain degree of structural variability. We analyzed here the interface in NMR ensembles of protein-protein heterodimeric complexes and found it to span a wide range of different conservations. The different exhibited conservations do not simply correlate with the size of the systems/interfaces, and are most probably the result of an interplay between different factors, including the quality of experimental data and the intrinsic complex flexibility. In any case, this information is not to be missed when NMR structures of protein-protein complexes are analyzed; especially considering that, as we also show here, the first NMR conformer is usually not the one which best reflects the overall interface. To quantify the interface conservation and to analyze it, we used an approach originally conceived for the analysis and ranking of ensembles of docking models, which has now been extended to directly deal with NMR ensembles. We propose this approach, based on the conservation of the inter-residue contacts at the interface, both for the analysis of the interface in whole ensembles of NMR complexes and for the possible selection of a single conformer as the best representative of the overall interface. In order to make the analyses automatic and fast, we made the protocol available as a web tool at: https://www.molnac.unisa.it/BioTools/consrank/consrank-nmr.html. Copyright © 2016 Elsevier Inc. All rights reserved.

Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 2, Non-catalyzed reactions with the wood cell wall

Treesearch

Daniel J. Yelle; John Ralph; Charles R. Frihart

2011-01-01

Solution-state NMR provides a powerful tool to observe the presence or absence of covalent bonds between wood and adhesives. Finely ground wood can be dissolved in an NMR compatible solvent system containing dimethylsulfoxide-d6 and N-methylimidazole-d6, in which the wood polymers remain largely intact. High-resolution...

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.

PubMed

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

2016-07-01

The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization. Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/ mohamed@kuicr.kyoto-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Fragment based drug discovery: practical implementation based on ¹⁹F NMR spectroscopy.

PubMed

Jordan, John B; Poppe, Leszek; Xia, Xiaoyang; Cheng, Alan C; Sun, Yax; Michelsen, Klaus; Eastwood, Heather; Schnier, Paul D; Nixey, Thomas; Zhong, Wenge

2012-01-26

Fragment based drug discovery (FBDD) is a widely used tool for discovering novel therapeutics. NMR is a powerful means for implementing FBDD, and several approaches have been proposed utilizing (1)H-(15)N heteronuclear single quantum coherence (HSQC) as well as one-dimensional (1)H and (19)F NMR to screen compound mixtures against a target of interest. While proton-based NMR methods of fragment screening (FBS) have been well documented and are widely used, the use of (19)F detection in FBS has been only recently introduced (Vulpetti et al. J. Am. Chem. Soc.2009, 131 (36), 12949-12959) with the aim of targeting "fluorophilic" sites in proteins. Here, we demonstrate a more general use of (19)F NMR-based fragment screening in several areas: as a key tool for rapid and sensitive detection of fragment hits, as a method for the rapid development of structure-activity relationship (SAR) on the hit-to-lead path using in-house libraries and/or commercially available compounds, and as a quick and efficient means of assessing target druggability.

A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.

PubMed

Nagatoishi, Satoru; Yamaguchi, Sou; Katoh, Etsuko; Kajita, Keita; Yokotagawa, Takane; Kanai, Satoru; Furuya, Toshio; Tsumoto, Kouhei

2018-05-01

19 F NMR has recently emerged as an efficient, sensitive tool for analyzing protein binding to small molecules, and surface plasmon resonance (SPR) is also a popular tool for this purpose. Herein a combination of 19 F NMR and SPR was used to find novel binders to the ATP-binding pocket of MAP kinase extracellular regulated kinase 2 (ERK2) by fragment screening with an original fluorinated-fragment library. The 19 F NMR screening yielded a high primary hit rate of binders to the ERK2 ATP-binding pocket compared with the rate for the SPR screening. Hit compounds were evaluated and categorized according to their ability to bind to different binding sites in the ATP-binding pocket. The binding manner was characterized by using isothermal titration calorimetry and docking simulation. Combining 19 F NMR with other biophysical methods allows the identification of multiple types of hit compounds, thereby increasing opportunities for drug design using preferred fragments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

DOE PAGES

Perras, Frederic A.

2015-12-15

Here, nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities.

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

Perspectives on NMR in drug discovery: a technique comes of age

PubMed Central

Pellecchia, Maurizio; Bertini, Ivano; Cowburn, David; Dalvit, Claudio; Giralt, Ernest; Jahnke, Wolfgang; James, Thomas L.; Homans, Steve W.; Kessler, Horst; Luchinat, Claudio; Meyer, Bernd; Oschkinat, Hartmut; Peng, Jeff; Schwalbe, Harald; Siegal, Gregg

2009-01-01

In the past decade, the potential of harnessing the ability of nuclear magnetic resonance (NMR) spectroscopy to monitor intermolecular interactions as a tool for drug discovery has been increasingly appreciated in academia and industry. In this Perspective, we highlight some of the major applications of NMR in drug discovery, focusing on hit and lead generation, and provide a critical analysis of its current and potential utility. PMID:19172689

Stone tool production and utilization by bonobo-chimpanzees (Pan paniscus).

PubMed

Roffman, Itai; Savage-Rumbaugh, Sue; Rubert-Pugh, Elizabeth; Ronen, Avraham; Nevo, Eviatar

2012-09-04

Using direct percussion, language-competent bonobo-chimpanzees Kanzi and Pan-Banisha produced a significantly wider variety of flint tool types than hitherto reported, and used them task-specifically to break wooden logs or to dig underground for food retrieval. For log breaking, small flakes were rotated drill-like or used as scrapers, whereas thick cortical flakes were used as axes or wedges, leaving consistent wear patterns along the glued slits, the weakest areas of the log. For digging underground, a variety of modified stone tools, as well as unmodified flint nodules, were used as shovels. Such tool production and utilization competencies reported here in Pan indicate that present-day Pan exhibits Homo-like technological competencies.

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

McCord, Jason

WLS gathers all known relevant contextual data along with standard event log information, processes it into an easily consumable format for analysis by 3rd party tools, and forwards the logs to any compatible log server.

Development of high resolution NMR spectroscopy as a structural tool

NASA Astrophysics Data System (ADS)

Feeney, James

1992-06-01

The discovery of the nuclear magnetic resonance (NMR) phenomenon and its development and exploitation as a scientific tool provide an excellent basis for a case-study for examining the factors which control the evolution of scientific techniques. Since the detection of the NMR phenomenon and the subsequent rapid discovery of all the important NMR spectral parameters in the late 1940s, the method has emerged as one of the most powerful techniques for determining structures of molecules in solution and for analysis of complex mixtures. The method has made a dramatic impact on the development of structural chemistry over the last 30 years and is now one of the key techniques in this area. Support for NMR instrumentation attracts a dominant slice of public funding in most scientifically developed countries. The technique is an excellent example of how instrumentation and technology have revolutionised structural chemistry and it is worth exploring how it has been developed so successfully. Clearly its wide range of application and the relatively direct connection between the NMR data and molecular structure has created a major market for the instrumentation. This has provided several competing manufacturers with the incentive to develop better and better instruments. Understanding the complexity of the basics of NMR spectroscopy has been an ongoing challenge attracting the attention of physicists. The well-organised specialist NMR literature and regular scientific meetings have ensured rapid exploitation of any theoretical advances that have a practical relevance. In parallel, the commercial development of the technology has allowed the fruits of such theoretical advances to be enjoyed by the wider scientific community.

MULTIVARIATE CURVE RESOLUTION OF NMR SPECTROSCOPY METABONOMIC DATA

EPA Science Inventory

Sandia National Laboratories is working with the EPA to evaluate and develop mathematical tools for analysis of the collected NMR spectroscopy data. Initially, we have focused on the use of Multivariate Curve Resolution (MCR) also known as molecular factor analysis (MFA), a tech...

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.

PubMed

Hendrickx, Pieter M S; Gutmanas, Aleksandras; Kleywegt, Gerard J

2013-04-01

We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. Copyright © 2013 Wiley Periodicals, Inc.

Visualization and processing of computed solid-state NMR parameters: MagresView and MagresPython.

PubMed

Sturniolo, Simone; Green, Timothy F G; Hanson, Robert M; Zilka, Miri; Refson, Keith; Hodgkinson, Paul; Brown, Steven P; Yates, Jonathan R

2016-09-01

We introduce two open source tools to aid the processing and visualisation of ab-initio computed solid-state NMR parameters. The Magres file format for computed NMR parameters (as implemented in CASTEP v8.0 and QuantumEspresso v5.0.0) is implemented. MagresView is built upon the widely used Jmol crystal viewer, and provides an intuitive environment to display computed NMR parameters. It can provide simple pictorial representation of one- and two-dimensional NMR spectra as well as output a selected spin-system for exact simulations with dedicated spin-dynamics software. MagresPython provides a simple scripting environment to manipulate large numbers of computed NMR parameters to search for structural correlations. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Mobile NMR: Measuring Pixels, Images, and Spectra

NASA Astrophysics Data System (ADS)

Bluemich, Bernhard

2007-03-01

The vision of bringing nuclear magnetic resonance out of the lab to the doctor's office, the chemical reactor, or the manufacturing site is becoming reality with the development of mobile NMR. Pioneered for well logging in the oil industry, the concept has been explored for materials testing in a more systematic way since the introduction of the NMR-MOUSE. This is a small, one-sided access NMR sensor which acquires the information of one pixel from a particular spot of a large object. As the sensor explores the stray-fields of a permanent magnet and an rf coil, the magnetic fields are inhomogeneous and the sensitive volume is limited to the region, where both fields are orthogonal and the Larmor frequency lies within the excitation bandwidth. By shaping the magnet and the coil geometries, the shape of the sensitive volume can be tailored to a thin slice or a larger volume a certain distance away from the sensor surface. In the first case, there is a strong field gradient in the depth direction, and in the second case, a homogeneous sweet spot of the field profile is desired. The first case is suitable for measuring high-resolution depth profiles, while the second case is suitable for chemical shift resolved spectroscopy and volume imaging. The basic concepts of open and closed mobile NMR sensors will be discussed along with applications from testing polymer products, cultural heritage, medical tissue, and rock cores.

Genetic transformation of rare Verbascum eriophorum Godr. plants and metabolic alterations revealed by NMR-based metabolomics.

PubMed

Marchev, Andrey; Yordanova, Zhenya; Alipieva, Kalina; Zahmanov, Georgi; Rusinova-Videva, Snezhana; Kapchina-Toteva, Veneta; Simova, Svetlana; Popova, Milena; Georgiev, Milen I

2016-09-01

To develop a protocol to transform Verbascum eriophorum and to study the metabolic differences between mother plants and hairy root culture by applying NMR and processing the datasets with chemometric tools. Verbascum eriophorum is a rare species with restricted distribution, which is poorly studied. Agrobacterium rhizogenes-mediated genetic transformation of V. eriophorum and hairy root culture induction are reported for the first time. To determine metabolic alterations, V. eriophorum mother plants and relevant hairy root culture were subjected to comprehensive metabolomic analyses, using NMR (1D and 2D). Metabolomics data, processed using chemometric tools (and principal component analysis in particular) allowed exploration of V. eriophorum metabolome and have enabled identification of verbascoside (by means of 2D-TOCSY NMR) as the most abundant compound in hairy root culture. Metabolomics data contribute to the elucidation of metabolic alterations after T-DNA transfer to the host V. eriophorum genome and the development of hairy root culture for sustainable bioproduction of high value verbascoside.

Petrophysical evaluation of subterranean formations

DOEpatents

Klein, James D; Schoderbek, David A; Mailloux, Jason M

2013-05-28

Methods and systems are provided for evaluating petrophysical properties of subterranean formations and comprehensively evaluating hydrate presence through a combination of computer-implemented log modeling and analysis. Certain embodiments include the steps of running a number of logging tools in a wellbore to obtain a variety of wellbore data and logs, and evaluating and modeling the log data to ascertain various petrophysical properties. Examples of suitable logging techniques that may be used in combination with the present invention include, but are not limited to, sonic logs, electrical resistivity logs, gamma ray logs, neutron porosity logs, density logs, NRM logs, or any combination or subset thereof.

Solution conformation of carbohydrates: a view by using NMR assisted by modeling.

PubMed

Díaz, Dolores; Canales-Mayordomo, Angeles; Cañada, F Javier; Jiménez-Barbero, Jesús

2015-01-01

Structural elucidation of complex carbohydrates in solution is not a trivial task. From the NMR view point, the limited chemical shift dispersion of sugar NMR spectra demands the combination of a variety of NMR techniques as well as the employment of molecular modeling methods. Herein, a general protocol for assignment of resonances and determination of inter-proton distances within the saccharides by homonuclear and heteronuclear experiments (i.e., (1)H and (13)C) is described. In addition, several computational tools and procedures for getting a final ensemble of geometries that represent the structure in solution are presented.

Certified Reference Material for Use in 1H, 31P, and 19F Quantitative NMR, Ensuring Traceability to the International System of Units.

PubMed

Rigger, Romana; Rück, Alexander; Hellriegel, Christine; Sauermoser, Robert; Morf, Fabienne; Breitruck, KathrinBreitruck; Obkircher, Markus

2017-09-01

In recent years, quantitative NMR (qNMR) spectroscopy has become one of the most important tools for content determination of organic substances and quantitative evaluation of impurities. Using Certified Reference Materials (CRMs) as internal or external standards, the extensively used qNMR method can be applied for purity determination, including unbroken traceability to the International System of Units (SI). The implementation of qNMR toward new application fields, e.g., metabolomics, environmental analysis, and physiological pathway studies, brings along more complex molecules and systems, thus making use of 1H qNMR challenging. A smart workaround is possible by the use of other NMR active nuclei, namely 31P and 19F. This article presents the development of three classes of qNMR CRMs based on different NMR active nuclei (1H, 31P, and 19F), and the corresponding approaches to establish traceability to the SI through primary CRMs from the National Institute of Standards and Technology and the National Metrology Institute of Japan. These TraceCERT® qNMR CRMs are produced under ISO/IEC 17025 and ISO Guide 34 using high-performance qNMR.

Basalt-flow imaging using a high-resolution directional borehole radar

USGS Publications Warehouse

Moulton, C.W.; Wright, D.L.; Hutton, S.R.; Smith, D.V.G.; Abraham, J.D.

2002-01-01

A new high-resolution directional borehole radar-logging tool (DBOR tool) was used to log three wells at the Idaho National Engineering and Environmental Laboratory (INEEL). The radar system uses identical directional cavity-backed monopole transmitting and receiving antennas that can be mechanically rotated while the tool is stationary or moving slowly in a borehole. Faster reconnaissance logging with no antenna rotation was also done to find zones of interest. The microprocessor-controlled motor/encoder in the tool can rotate the antennas azimuthally, to a commanded angle, accurate to a within few degrees. The three logged wells in the unsaturated zone at the INEEL had been cored with good core recovery through most zones. After coring, PVC casing was installed in the wells. The unsaturated zone consists of layered basalt flows that are interbedded with thin layers of coarse-to-fine grained sediments. Several zones were found that show distinctive signatures consistent with fractures in the basalt. These zones may correspond to suspected preferential flow paths. The DBOR data were compared to core, and other borehole log information to help provide better understanding of hydraulic flow and transport in preferential flow paths in the unsaturated zone basalts at the INEEL.

Solution NMR Spectroscopy in Target-Based Drug Discovery.

PubMed

Li, Yan; Kang, Congbao

2017-08-23

Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.

Validation of a low field Rheo-NMR instrument and application to shear-induced migration of suspended non-colloidal particles in Couette flow

NASA Astrophysics Data System (ADS)

Colbourne, A. A.; Blythe, T. W.; Barua, R.; Lovett, S.; Mitchell, J.; Sederman, A. J.; Gladden, L. F.

2018-01-01

Nuclear magnetic resonance rheology (Rheo-NMR) is a valuable tool for studying the transport of suspended non-colloidal particles, important in many commercial processes. The Rheo-NMR imaging technique directly and quantitatively measures fluid displacement as a function of radial position. However, the high field magnets typically used in these experiments are unsuitable for the industrial environment and significantly hinder the measurement of shear stress. We introduce a low field Rheo-NMR instrument (1 H resonance frequency of 10.7MHz), which is portable and suitable as a process monitoring tool. This system is applied to the measurement of steady-state velocity profiles of a Newtonian carrier fluid suspending neutrally-buoyant non-colloidal particles at a range of concentrations. The large particle size (diameter > 200 μm) in the system studied requires a wide-gap Couette geometry and the local rheology was expected to be controlled by shear-induced particle migration. The low-field results are validated against high field Rheo-NMR measurements of consistent samples at matched shear rates. Additionally, it is demonstrated that existing models for particle migration fail to adequately describe the solid volume fractions measured in these systems, highlighting the need for improvement. The low field implementation of Rheo-NMR is complementary to shear stress rheology, such that the two techniques could be combined in a single instrument.

Characterization of complexes of nucleoside-5'-phosphorothioate analogues with zinc ions.

PubMed

Sayer, Alon Haim; Itzhakov, Yehudit; Stern, Noa; Nadel, Yael; Fischer, Bilha

2013-10-07

On the basis of the high affinity of Zn(2+) to sulfur and imidazole, we targeted nucleotides such as GDP-β-S, ADP-β-S, and AP3(β-S)A, as potential biocompatible Zn(2+)-chelators. The thiophosphate moiety enhanced the stability of the Zn(2+)-nucleotide complex by about 0.7 log units. ATP-α,β-CH2-γ-S formed the most stable Zn(2+)-complex studied here, log K 6.50, being ~0.8 and ~1.1 log units more stable than ATP-γ-S-Zn(2+) and ATP-Zn(2+) complexes, and was the major species, 84%, under physiological pH. Guanine nucleotides Zn(2+) complexes were more stable by 0.3-0.4 log units than the corresponding adenine nucleotide complexes. Likewise, AP3(β-S)A-zinc complex was ~0.5 log units more stable than AP3A complex. (1)H- and (31)P NMR monitored Zn(2+) titration showed that Zn(2+) coordinates with the purine nucleotide N7-nitrogen atom, the terminal phosphate, and the adjacent phosphate. In conclusion, replacement of a terminal phosphate by a thiophosphate group resulted in decrease of the acidity of the phosphate moiety by approximately one log unit, and increase of stability of Zn(2+)-complexes of the latter analogues by up to 0.7 log units. A terminal phosphorothioate contributed more to the stability of nucleotide-Zn(2+) complexes than a bridging phosphorothioate.

NUMERICAL STUDY OF ELECTROMAGNETIC WAVES GENERATED BY A PROTOTYPE DIELECTRIC LOGGING TOOL

EPA Science Inventory

To understand the electromagnetic waves generated by a prototype dielectric logging tool, a
numerical study was conducted using both the finite-difference, time-domain method and a frequency- wavenumber method. When the propagation velocity in the borehole was greater than th...

MONITOIRNG OF A CONTROLLED DNAPL SPILL USING A PROTOTYPE DIELECTRIC LOGGING TOOL

EPA Science Inventory

The U. S. Geological Survey (USGS) utilized their prototype dielectric logging tool to monitor a controlled Dense Non-Aqueous Phase Liquid (DNAPL) spill into a large tank located at the University of California Richmond Field Station (RFS) containing multiple sand and clayey sand...

LC-MS and 1H NMR as an improved dereplication tool to identify antifungal diterpenoids from Sagittaria latifolia

USDA-ARS?s Scientific Manuscript database

A dereplication strategy using a combination of liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy (1H NMR) to facilitate compound identification towards antifungal natural product discovery is presented. This analytical approach takes advantage of th...

High-Resolution Solid-State NMR Spectroscopy: Characterization of Polymorphism in Cimetidine, a Pharmaceutical Compound

ERIC Educational Resources Information Center

Pacilio, Julia E.; Tokarski, John T.; Quiñones, Rosalynn; Iuliucci, Robbie J.

2014-01-01

High-resolution solid-state NMR (SSNMR) spectroscopy has many advantages as a tool to characterize solid-phase material that finds applications in polymer chemistry, nanotechnology, materials science, biomolecular structure determination, and others, including the pharmaceutical industry. The technology associated with achieving high resolution…

Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids

DOE PAGES

Bolt, H. L.; Williams, C. E. J.; Brooks, R. V.; ...

2017-01-13

Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as determined by RP-HPLC retention time) may not always provide an effective predictive tool for rational design. Herein, we report the first ever application of partitioning experiments to determine the log D values for a series of peptoids. By comparing log D and average hydrophobicities we highlight the potential advantage of employing themore » former as a predictive tool in the rational design of biologically active peptoids.« less

Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids

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

Bolt, H. L.; Williams, C. E. J.; Brooks, R. V.

Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as determined by RP-HPLC retention time) may not always provide an effective predictive tool for rational design. Herein, we report the first ever application of partitioning experiments to determine the log D values for a series of peptoids. By comparing log D and average hydrophobicities we highlight the potential advantage of employing themore » former as a predictive tool in the rational design of biologically active peptoids.« less

Keystroke Analysis: Reflections on Procedures and Measures

ERIC Educational Resources Information Center

Baaijen, Veerle M.; Galbraith, David; de Glopper, Kees

2012-01-01

Although keystroke logging promises to provide a valuable tool for writing research, it can often be difficult to relate logs to underlying processes. This article describes the procedures and measures that the authors developed to analyze a sample of 80 keystroke logs, with a view to achieving a better alignment between keystroke-logging measures…

Interpreting wireline measurements in coal beds

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

Johnston, D.J.

1991-06-01

When logging coal seams with wireline tools, the interpretation method needed to evaluate the coals is different from that used for conventional oil and gas reservoirs. Wireline logs identify coals easily. For an evaluation, the contribution of each coal component on the raw measurements must be considered. This paper will discuss how each log measurement is affected by each component. The components of a coal will be identified as the mineral matter, macerals, moisture content, rank, gas content, and cleat porosity. The measurements illustrated are from the resistivity, litho-density, neutron, sonic, dielectric, and geochemical tools. Once the coal component effectsmore » have been determined, an interpretation of the logs can be made. This paper will illustrate how to use these corrected logs in a coal evaluation.« less

Investigation of Rhodopsin Dynamics in its Signaling State by Solid-State Deuterium NMR Spectroscopy

PubMed Central

Struts, Andrey V.; Chawla, Udeep; Perera, Suchithranga M.D.C.; Brown, Michael F.

2017-01-01

Site-directed deuterium NMR spectroscopy is a valuable tool to study the structural dynamics of biomolecules in cases where solution NMR is inapplicable. Solid-state 2H NMR spectral studies of aligned membrane samples of rhodopsin with selectively labeled retinal provide information on structural changes of the chromophore in different protein states. In addition, solid-state 2H NMR relaxation time measurements allow one to study the dynamics of the ligand during the transition from the inactive to the active state. Here we describe the methodological aspects of solid-state 2H NMR spectroscopy for functional studies of rhodopsin, with an emphasis on the dynamics of the retinal cofactor. We provide complete protocols for the preparation of NMR samples of rhodopsin with 11-cis-retinal selectively deuterated at the methyl groups in aligned membranes. In addition, we review optimized conditions for trapping the rhodopsin photointermediates; and lastly we address the challenging problem of trapping the signaling state of rhodopsin in aligned membrane films. PMID:25697522

Feasibility of using the linac real-time log data for VMAT treatment verification

NASA Astrophysics Data System (ADS)

Midi, N. S.; Zin, Hafiz M.

2017-05-01

This study investigates the feasibility of using the real-time log data from a linac to verify Volumetric Modulated Arc Therapy (VMAT) treatment. The treatment log data for an Elekta Synergy linac can be recorded at a sampling rate of 4 Hz using the service graphing tool on the linac control computer. A treatment plan that simulates a VMAT treatment was delivered from the linac and all the dynamic treatment parameters including monitor unit (MU), Multileaf Collimator (MLC) position, jaw position, gantry angle and collimator angle were recorded in real-time using the service graphing tool. The recorded raw data were extracted and analysed using algorithms written in Matlab (MathWorks, Natick, MA). The actual treatment parameters logged using the service graphing tool was compared to the prescription and the deviations were analysed. The MLC position errors travelling at the speed range from -3.25 to 5.92 cm/s were between -1.7 mm to 2.5 mm, well within the 3.5 mm tolerance value (AAPM TG-142). The discrepancies of other delivery parameters were also within the tolerance. The real-time linac parameters logged using the service graphing tool can be used as a supplementary data for patient specific VMAT pre-treatment quality assurance.

Numerical simulations of induction and MWD logging tools and data inversion method with X-window interface on a UNIX workstation

NASA Astrophysics Data System (ADS)

Tian, Xiang-Dong

The purpose of this research is to simulate induction and measuring-while-drilling (MWD) logs. In simulation of logs, there are two tasks. The first task, the forward modeling procedure, is to compute the logs from known formation. The second task, the inversion procedure, is to determine the unknown properties of the formation from the measured field logs. In general, the inversion procedure requires the solution of a forward model. In this study, a stable numerical method to simulate induction and MWD logs is presented. The proposed algorithm is based on a horizontal eigenmode expansion method. Vertical propagation of modes is modeled by a three-layer module. The multilayer cases are treated as a cascade of these modules. The mode tracing algorithm possesses stable characteristics that are superior to other methods. This method is applied to simulate the logs in the formations with both vertical and horizontal layers, and also used to study the groove effects of the MWD tool. The results are very good. Two-dimensional inversion of induction logs is an nonlinear problem. Nonlinear functions of the apparent conductivity are expanded into a Taylor series. After truncating the high order terms in this Taylor series, the nonlinear functions are linearized. An iterative procedure is then devised to solve the inversion problem. In each iteration, the Jacobian matrix is calculated, and a small variation computed using the least-squares method is used to modify the background medium. Finally, the inverted medium is obtained. The horizontal eigenstate method is used to solve the forward problem. It is found that a good inverted formation can be obtained by using measurements. In order to help the user simulate the induction logs conveniently, a Wellog Simulator, based on the X-window system, is developed. The application software (FORTRAN codes) embedded in the Simulator is designed to simulate the responses of the induction tools in the layered formation with dipping beds. The graphic user-interface part of the Wellog Simulator is implemented with C and Motif. Through the user interface, the user can prepare the simulation data, select the tools, simulate the logs and plot the results.

Detection of gas hydrate with downhole logs and assessment of gas hydrate concentrations (saturations) and gas volumes on the Blake Ridge with electrical resistivity log data

USGS Publications Warehouse

Collett, T.S.; Ladd, J.

2000-01-01

Let 164 of the Ocean Drilling Program was designed to investigate the occurrence of gas hydrate in the sedimentary section beneath the Blake Ridge on the southeastern continental margin of North America. Site 994, and 997 were drilled on the Blake Ridge to refine our understanding of the in situ characteristics of natural gas hydrate. Because gas hydrate is unstable at surface pressure and temperature conditions, a major emphasis was placed on the downhole logging program to determine the in situ physical properties of the gas hydrate-bearing sediments. Downhole logging tool strings deployed on Leg 164 included the Schlumberger quad-combination tool (NGT, LSS/SDT, DIT, CNT-G, HLDT), the Formation MicroScanner (FMS), and the Geochemical Combination Tool (GST). Electrical resistivity (DIT) and acoustic transit-time (LSS/SDT) downhole logs from Sites 994, 995, and 997 indicate the presence of gas hydrate in the depth interval between 185 and 450 mbsf on the Blake Ridge. Electrical resistivity log calculations suggest that the gas hydrate-bearing sedimentary section on the Blake Ridge may contain between 2 and 11 percent bulk volume (vol%) gas hydrate. We have determined that the log-inferred gas hydrates and underlying free-gas accumulations on the Blake Ridge may contain as much as 57 trillion m3 of gas.

Exploration and Evaluation of Nanometer Low-power Multi-core VLSI Computer Architectures

DTIC Science & Technology

2015-03-01

ICC, the Milkway database was created using the command: milkyway –galaxy –nogui –tcl –log memory.log one.tcl As stated previously, it is...EDA tools. Typically, Synopsys® tools use Milkway databases, whereas, Cadence Design System® use Layout Exchange Format (LEF) formats. To help

High-resolution solution-state NMR of unfractionated plant cell walls

Treesearch

John Ralph; Fachuang Lu; Hoon Kim; Dino Ress; Daniel J. Yelle; Kenneth E. Hammel; Sally A. Ralph; Bernadette Nanayakkara; Armin Wagner; Takuya Akiyama; Paul F. Schatz; Shawn D. Mansfield; Noritsugu Terashima; Wout Boerjan; Bjorn Sundberg; Mattias Hedenstrom

2009-01-01

Detailed structural studies on the plant cell wall have traditionally been difficult. NMR is one of the preeminent structural tools, but obtaining high-resolution solution-state spectra has typically required fractionation and isolation of components of interest. With recent methods for dissolution of, admittedly, finely divided plant cell wall material, the wall can...

New mechanistic insights regarding Pd/Cu catalysts for the Sonogashira reaction: HRMAS NMR studies of silica-immobilized systems.

PubMed

Posset, Tobias; Blümel, Janet

2006-07-05

The title technique, high-resolution magic angle spinning NMR of suspensions, constitutes a powerful new tool for investigating the structures and mobilities of immobilized species and, thus, for optimizing heterobimetallic catalyst systems, such as the Sonogashira coupling of terminal alkynes and aryl halides.

ALOG user's manual: A Guide to using the spreadsheet-based artificial log generator

Treesearch

Matthew F. Winn; Philip A. Araman; Randolph H. Wynne

2012-01-01

Computer programs that simulate log sawing can be valuable training tools for sawyers, as well as a means oftesting different sawing patterns. Most available simulation programs rely on diagrammed-log databases, which canbe very costly and time consuming to develop. Artificial Log Generator (ALOG) is a user-friendly Microsoft® Excel®...

Genotype evaluation of cowpea seeds (Vigna unguiculata) using 1H qNMR combined with exploratory tools and solid-state NMR.

PubMed

Alves Filho, Elenilson G; Silva, Lorena M A; Teofilo, Elizita M; Larsen, Flemming H; de Brito, Edy S

2017-01-01

The ultimate aim of this study was to apply a non-targeted chemometric analysis (principal component analysis and hierarchical clustering analysis using the heat map approach) of NMR data to investigate the variability of organic compounds in nine genotype cowpea seeds, without any complex pre-treatment. In general, both exploratory tools show that Tvu 233, CE-584, and Setentão genotypes presented higher amount mainly of raffinose and Tvu 382 presented the highest content of choline and least content of raffinose. The evaluation of the aromatic region showed the Setentão genotype with highest content of niacin/vitamin B3 whereas Tvu 382 with lowest amount. To investigate rigid and mobile components in the seeds cotyledon, 13 C CP and SP/MAS solid-state NMR experiments were performed. The cotyledon of the cowpea comprised a rigid part consisting of starch as well as a soft portion made of starch, fatty acids, and protein. The variable contact time experiment suggests the presence of lipid-amylose complexes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Qualitative and Quantitative Control of Carbonated Cola Beverages Using 1H NMR Spectroscopy

PubMed Central

2012-01-01

1H Nuclear magnetic resonance (NMR) spectroscopy (400 MHz) was used in the context of food surveillance to develop a reliable analytical tool to differentiate brands of cola beverages and to quantify selected constituents of the soft drinks. The preparation of the samples required only degassing and addition of 0.1% of TSP in D2O for locking and referencing followed by adjustment of pH to 4.5. The NMR spectra obtained can be considered as “fingerprints” and were analyzed by principal component analysis (PCA). Clusters from colas of the same brand were observed, and significant differences between premium and discount brands were found. The quantification of caffeine, acesulfame-K, aspartame, cyclamate, benzoate, hydroxymethylfurfural (HMF), sulfite ammonia caramel (E 150D), and vanillin was simultaneously possible using external calibration curves and applying TSP as internal standard. Limits of detection for caffeine, aspartame, acesulfame-K, and benzoate were 1.7, 3.5, 0.8, and 1.0 mg/L, respectively. Hence, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of soft drinks and quantification of selected constituents. PMID:22356160

Qualitative and quantitative control of carbonated cola beverages using ¹H NMR spectroscopy.

PubMed

Maes, Pauline; Monakhova, Yulia B; Kuballa, Thomas; Reusch, Helmut; Lachenmeier, Dirk W

2012-03-21

¹H Nuclear magnetic resonance (NMR) spectroscopy (400 MHz) was used in the context of food surveillance to develop a reliable analytical tool to differentiate brands of cola beverages and to quantify selected constituents of the soft drinks. The preparation of the samples required only degassing and addition of 0.1% of TSP in D₂O for locking and referencing followed by adjustment of pH to 4.5. The NMR spectra obtained can be considered as "fingerprints" and were analyzed by principal component analysis (PCA). Clusters from colas of the same brand were observed, and significant differences between premium and discount brands were found. The quantification of caffeine, acesulfame-K, aspartame, cyclamate, benzoate, hydroxymethylfurfural (HMF), sulfite ammonia caramel (E 150D), and vanillin was simultaneously possible using external calibration curves and applying TSP as internal standard. Limits of detection for caffeine, aspartame, acesulfame-K, and benzoate were 1.7, 3.5, 0.8, and 1.0 mg/L, respectively. Hence, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of soft drinks and quantification of selected constituents.

Efficient design of multituned transmission line NMR probes: the electrical engineering approach.

PubMed

Frydel, J A; Krzystyniak, M; Pienkowski, D; Pietrzak, M; de Sousa Amadeu, N; Ratajczyk, T; Idzik, K; Gutmann, T; Tietze, D; Voigt, S; Fenn, A; Limbach, H H; Buntkowsky, G

2011-01-01

Transmission line-based multi-channel solid state NMR probes have many advantages regarding the cost of construction, number of RF-channels, and achievable RF-power levels. Nevertheless, these probes are only rarely employed in solid state-NMR-labs, mainly owing to the difficult experimental determination of the necessary RF-parameters. Here, the efficient design of multi-channel solid state MAS-NMR probes employing transmission line theory and modern techniques of electrical engineering is presented. As technical realization a five-channel ((1)H, (31)P, (13)C, (2)H and (15)N) probe for operation at 7 Tesla is described. This very cost efficient design goal is a multi port single coil transmission line probe based on the design developed by Schaefer and McKay. The electrical performance of the probe is determined by measuring of Scattering matrix parameters (S-parameters) in particular input/output ports. These parameters are compared to the calculated parameters of the design employing the S-matrix formalism. It is shown that the S-matrix formalism provides an excellent tool for examination of transmission line probes and thus the tool for a rational design of these probes. On the other hand, the resulting design provides excellent electrical performance. From a point of view of Nuclear Magnetic Resonance (NMR), calibration spectra of particular ports (channels) are of great importance. The estimation of the π/2 pulses length for all five NMR channels is presented. Copyright © 2011 Elsevier Inc. All rights reserved.

Water Log.

ERIC Educational Resources Information Center

Science Activities, 1995

1995-01-01

Presents a Project WET water education activity. Students use a Water Log (journal or portfolio) to write or illustrate their observations, feelings, and actions related to water. The log serves as an assessment tool to monitor changes over time in knowledge of and attitudes toward the water. (LZ)

High-Sensitivity Nuclear Magnetic Resonance at Giga-Pascal Pressures: A New Tool for Probing Electronic and Chemical Properties of Condensed Matter under Extreme Conditions

PubMed Central

Meier, Thomas; Haase, Jürgen

2014-01-01

Nuclear Magnetic Resonance (NMR) is one of the most important techniques for the study of condensed matter systems, their chemical structure, and their electronic properties. The application of high pressure enables one to synthesize new materials, but the response of known materials to high pressure is a very useful tool for studying their electronic structure and developing theories. For example, high-pressure synthesis might be at the origin of life; and understanding the behavior of small molecules under extreme pressure will tell us more about fundamental processes in our universe. It is no wonder that there has always been great interest in having NMR available at high pressures. Unfortunately, the desired pressures are often well into the Giga-Pascal (GPa) range and require special anvil cell devices where only very small, secluded volumes are available. This has restricted the use of NMR almost entirely in the past, and only recently, a new approach to high-sensitivity GPa NMR, which has a resonating micro-coil inside the sample chamber, was put forward. This approach enables us to achieve high sensitivity with experiments that bring the power of NMR to Giga-Pascal pressure condensed matter research. First applications, the detection of a topological electronic transition in ordinary aluminum metal and the closing of the pseudo-gap in high-temperature superconductivity, show the power of such an approach. Meanwhile, the range of achievable pressures was increased tremendously with a new generation of anvil cells (up to 10.1 GPa), that fit standard-bore NMR magnets. This approach might become a new, important tool for the investigation of many condensed matter systems, in chemistry, geochemistry, and in physics, since we can now watch structural changes with the eyes of a very versatile probe. PMID:25350694

High-sensitivity nuclear magnetic resonance at Giga-Pascal pressures: a new tool for probing electronic and chemical properties of condensed matter under extreme conditions.

PubMed

Meier, Thomas; Haase, Jürgen

2014-10-10

Nuclear Magnetic Resonance (NMR) is one of the most important techniques for the study of condensed matter systems, their chemical structure, and their electronic properties. The application of high pressure enables one to synthesize new materials, but the response of known materials to high pressure is a very useful tool for studying their electronic structure and developing theories. For example, high-pressure synthesis might be at the origin of life; and understanding the behavior of small molecules under extreme pressure will tell us more about fundamental processes in our universe. It is no wonder that there has always been great interest in having NMR available at high pressures. Unfortunately, the desired pressures are often well into the Giga-Pascal (GPa) range and require special anvil cell devices where only very small, secluded volumes are available. This has restricted the use of NMR almost entirely in the past, and only recently, a new approach to high-sensitivity GPa NMR, which has a resonating micro-coil inside the sample chamber, was put forward. This approach enables us to achieve high sensitivity with experiments that bring the power of NMR to Giga-Pascal pressure condensed matter research. First applications, the detection of a topological electronic transition in ordinary aluminum metal and the closing of the pseudo-gap in high-temperature superconductivity, show the power of such an approach. Meanwhile, the range of achievable pressures was increased tremendously with a new generation of anvil cells (up to 10.1 GPa), that fit standard-bore NMR magnets. This approach might become a new, important tool for the investigation of many condensed matter systems, in chemistry, geochemistry, and in physics, since we can now watch structural changes with the eyes of a very versatile probe.

Lithology and mineralogy recognition from geochemical logging tool data using multivariate statistical analysis.

PubMed

Konaté, Ahmed Amara; Ma, Huolin; Pan, Heping; Qin, Zhen; Ahmed, Hafizullah Abba; Dembele, N'dji Dit Jacques

2017-10-01

The availability of a deep well that penetrates deep into the Ultra High Pressure (UHP) metamorphic rocks is unusual and consequently offers a unique chance to study the metamorphic rocks. One such borehole is located in the southern part of Donghai County in the Sulu UHP metamorphic belt of Eastern China, from the Chinese Continental Scientific Drilling Main hole. This study reports the results obtained from the analysis of oxide log data. A geochemical logging tool provides in situ, gamma ray spectroscopy measurements of major and trace elements in the borehole. Dry weight percent oxide concentration logs obtained for this study were SiO 2 , K 2 O, TiO 2 , H 2 O, CO 2 , Na 2 O, Fe 2 O 3 , FeO, CaO, MnO, MgO, P 2 O 5 and Al 2 O 3 . Cross plot and Principal Component Analysis methods were applied for lithology characterization and mineralogy description respectively. Cross plot analysis allows lithological variations to be characterized. Principal Component Analysis shows that the oxide logs can be summarized by two components related to the feldspar and hydrous minerals. This study has shown that geochemical logging tool data is accurate and adequate to be tremendously useful in UHP metamorphic rocks analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods

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

Bingol, Kerem; Brüschweiler, Rafael

Metabolomics continues to make rapid progress through the development of new and better methods and their applications to gain insight into the metabolism of a wide range of different biological systems from a systems biology perspective. Customization of NMR databases and search tools allows the faster and more accurate identification of known metabolites, whereas the identification of unknowns, without a need for extensive purification, requires new strategies to integrate NMR with mass spectrometry, cheminformatics, and computational methods. For some applications, the use of covalent and non-covalent attachments in the form of labeled tags or nanoparticles can significantly reduce the complexitymore » of these tasks.« less

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

Koeller, E.; Dobmann, G.; Kuhn, W.

Initial results are presented on the application of NMR techniques to prepregs in order to characterize the crosslink state under exposure to room and elevated (50 C) temperature. The experiments were conducted with a MSL-400 Bruker NMR spectrometer and microimaging system which works at 400 MHz. Aside from the sensitive measurement of the cross-link density there is also the potential to separate the influence of moisture content as a further parameter contributing to the aging process. It is shown that these experimental results correlate with results of destructive tests and document the potential of NMR as a NDT tool. Anmore » NMR-image of the moisture distribution in a glassfiber reinforced expoxy resin sample is shown. 17 refs.« less

87Sr solid-state NMR as a structurally sensitive tool for the investigation of materials: antiosteoporotic pharmaceuticals and bioactive glasses.

PubMed

Bonhomme, Christian; Gervais, Christel; Folliet, Nicolas; Pourpoint, Frédérique; Diogo, Cristina Coelho; Lao, Jonathan; Jallot, Edouard; Lacroix, Joséphine; Nedelec, Jean-Marie; Iuga, Dinu; Hanna, John V; Smith, Mark E; Xiang, Ye; Du, Jincheng; Laurencin, Danielle

2012-08-01

Strontium is an element of fundamental importance in biomedical science. Indeed, it has been demonstrated that Sr(2+) ions can promote bone growth and inhibit bone resorption. Thus, the oral administration of Sr-containing medications has been used clinically to prevent osteoporosis, and Sr-containing biomaterials have been developed for implant and tissue engineering applications. The bioavailability of strontium metal cations in the body and their kinetics of release from materials will depend on their local environment. It is thus crucial to be able to characterize, in detail, strontium environments in disordered phases such as bioactive glasses, to understand their structure and rationalize their properties. In this paper, we demonstrate that (87)Sr NMR spectroscopy can serve as a valuable tool of investigation. First, the implementation of high-sensitivity (87)Sr solid-state NMR experiments is presented using (87)Sr-labeled strontium malonate (with DFS (double field sweep), QCPMG (quadrupolar Carr-Purcell-Meiboom-Gill), and WURST (wideband, uniform rate, and smooth truncation) excitation). Then, it is shown that GIPAW DFT (gauge including projector augmented wave density functional theory) calculations can accurately compute (87)Sr NMR parameters. Last and most importantly, (87)Sr NMR is used for the study of a (Ca,Sr)-silicate bioactive glass of limited Sr content (only ~9 wt %). The spectrum is interpreted using structural models of the glass, which are generated through molecular dynamics (MD) simulations and relaxed by DFT, before performing GIPAW calculations of (87)Sr NMR parameters. Finally, changes in the (87)Sr NMR spectrum after immersion of the glass in simulated body fluid (SBF) are reported and discussed.

ALOG: A spreadsheet-based program for generating artificial logs

Treesearch

Matthew F. Winn; Randolph H. Wynne; Philip A. Araman

2004-01-01

Log sawing simulation computer programs can be valuable tools for training sawyers as well as for testing different sawing patterns. Most available simulation programs rely on databases from which to draw logs and can be very costly and time-consuming to develop. ALOG (Artificial LOg Generator) is a Microsoft Excel®-based computer program that was developed to...

Pre-selection and assessment of green organic solvents by clustering chemometric tools.

PubMed

Tobiszewski, Marek; Nedyalkova, Miroslava; Madurga, Sergio; Pena-Pereira, Francisco; Namieśnik, Jacek; Simeonov, Vasil

2018-01-01

The study presents the result of the application of chemometric tools for selection of physicochemical parameters of solvents for predicting missing variables - bioconcentration factors, water-octanol and octanol-air partitioning constants. EPI Suite software was successfully applied to predict missing values for solvents commonly considered as "green". Values for logBCF, logK OW and logK OA were modelled for 43 rather nonpolar solvents and 69 polar ones. Application of multivariate statistics was also proved to be useful in the assessment of the obtained modelling results. The presented approach can be one of the first steps and support tools in the assessment of chemicals in terms of their greenness. Copyright © 2017 Elsevier Inc. All rights reserved.

Nuclear magnetic resonance and high-performance liquid chromatography techniques for the characterization of bioactive compounds from Humulus lupulus L. (hop).

PubMed

Bertelli, Davide; Brighenti, Virginia; Marchetti, Lucia; Reik, Anna; Pellati, Federica

2018-06-01

Humulus lupulus L. (hop) represents one of the most cultivated crops, it being a key ingredient in the brewing process. Many health-related properties have been described for hop extracts, making this plant gain more interest in the field of pharmaceutical and nutraceutical research. Among the analytical tools available for the phytochemical characterization of plant extracts, quantitative nuclear magnetic resonance (qNMR) represents a new and powerful technique. In this ambit, the present study was aimed at the development of a new, simple, and efficient qNMR method for the metabolite fingerprinting of bioactive compounds in hop cones, taking advantage of the novel ERETIC 2 tool. To the best of our knowledge, this is the first attempt to apply this method to complex matrices of natural origin, such as hop extracts. The qNMR method set up in this study was applied to the quantification of both prenylflavonoids and bitter acids in eight hop cultivars. The performance of this analytical method was compared with that of HPLC-UV/DAD, which represents the most frequently used technique in the field of natural product analysis. The quantitative data obtained for hop samples by means of the two aforementioned techniques highlighted that the amount of bioactive compounds was slightly higher when qNMR was applied, although the order of magnitude of the values was the same. The accuracy of qNMR was comparable to that of the chromatographic method, thus proving to be a reliable tool for the analysis of these secondary metabolites in hop extracts. Graphical abstract Graphical abstract related to the extraction and analytical methods applied in this work for the analysis of bioactive compounds in Humulus lupulus L. (hop) cones.

Nuclear magnetic resonance magnet actively cooled by pulse tube refrigerator

NASA Astrophysics Data System (ADS)

Kirichek, Oleg; Carr, Philip; Johnson, Chris; Atrey, Milind

2005-05-01

High field NMR spectrometers have been an essential tool for biomolecular scientists for many years. They have been instrumental in the pursuit of understanding of the structure, function and dynamics of proteins and other biological molecules. In addition, NMR is increasingly used for small molecule applications such as metabonomics, providing capabilities that aid drug discovery, as well as general organic and inorganic chemistry [M. Pellecchia et al., Nature Reviews Drug Discovery 1, 211 (2002)]. However, access to these systems is restricted due to the requirement to periodically refill them with liquid cryogens. This is both logistically demanding and expensive. A new system combining NMR spectrometry and Pulse Tube Refrigeration (PTR) has been developed and successfully tested. This approach eliminates the dependence on liquid cryogens, reduces spectrometer downtime, and also significantly reduces the size of the system. In the near future this new type of analytical tool may become ubiquitous in biomedical and chemical laboratories.

Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins.

PubMed

Ellis, Heidi J C; Nowling, Ronald J; Vyas, Jay; Martyn, Timothy O; Gryk, Michael R

2011-04-11

The CONNecticut Joint University Research (CONNJUR) team is a group of biochemical and software engineering researchers at multiple institutions. The vision of the team is to develop a comprehensive application that integrates a variety of existing analysis tools with workflow and data management to support the process of protein structure determination using Nuclear Magnetic Resonance (NMR). The use of multiple disparate tools and lack of data management, currently the norm in NMR data processing, provides strong motivation for such an integrated environment. This manuscript briefly describes the domain of NMR as used for protein structure determination and explains the formation of the CONNJUR team and its operation in developing the CONNJUR application. The manuscript also describes the evolution of the CONNJUR application through four prototypes and describes the challenges faced while developing the CONNJUR application and how those challenges were met.

Solid-State NMR Spectroscopy of Metal–Organic Framework Compounds (MOFs)

PubMed Central

Hoffmann, Herbert C.; Debowski, Marta; Müller, Philipp; Paasch, Silvia; Senkovska, Irena; Kaskel, Stefan; Brunner, Eike

2012-01-01

Nuclear Magnetic Resonance (NMR) spectroscopy is a well-established method for the investigation of various types of porous materials. During the past decade, metal–organic frameworks have attracted increasing research interest. Solid-state NMR spectroscopy has rapidly evolved into an important tool for the study of the structure, dynamics and flexibility of these materials, as well as for the characterization of host–guest interactions with adsorbed species such as xenon, carbon dioxide, water, and many others. The present review introduces and highlights recent developments in this rapidly growing field.

Determination of NMR chemical shifts for cholesterol crystals from first-principles

NASA Astrophysics Data System (ADS)

Kucukbenli, Emine; de Gironcoli, Stefano

2011-03-01

Solid State Nuclear Magnetic Resonance (NMR) is a powerful tool in crystallography when combined with theoretical predictions. So far, empirical calculations of spectra have been employed for an unambiguous identification. However, many complex systems are outside the scope of these methods. Our implementation of ultrasoft and projector augmented wave pseudopotentials within ab initio gauge including projector augmented plane wave (GIPAW) method in Quantum Espresso simulation package allows affordable calculations of NMR spectra for systems of thousands of electrons. We report here the first ab initio determination of NMR spectra for several crystal structures of cholesterol. Cholesterol crystals, the main component of human gallstones, are of interest to medical research as their structural properties can shed light on the pathologies of gallbladder. With our application we show that ab initio calculations can be employed to aid NMR crystallography.

A solution-state NMR approach to elucidating pMDI-wood bonding mechanisms in loblolly pine

Treesearch

Daniel Joseph Yelle

2009-01-01

Solution-state NMR spectroscopy is a powerful tool for unambiguously determining the existence or absence of covalent chemical bonds between wood components and adhesives. Finely ground wood cell wall material dissolves in a solvent system containing DMSO-d6 and NMI-d6, keeping wood component polymers intact and in a near-...

10 CFR 39.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... neutron generator tube to produce neutrons for use in well logging applications. Uranium sinker bar means a weight containing depleted uranium used to pull a logging tool toward the bottom of a well. Well... drilled holes for the purpose of oil, gas, mineral, groundwater, or geological exploration. Well logging...

10 CFR 39.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... neutron generator tube to produce neutrons for use in well logging applications. Uranium sinker bar means a weight containing depleted uranium used to pull a logging tool toward the bottom of a well. Well... drilled holes for the purpose of oil, gas, mineral, groundwater, or geological exploration. Well logging...

10 CFR 39.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... neutron generator tube to produce neutrons for use in well logging applications. Uranium sinker bar means a weight containing depleted uranium used to pull a logging tool toward the bottom of a well. Well... drilled holes for the purpose of oil, gas, mineral, groundwater, or geological exploration. Well logging...

10 CFR 39.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... neutron generator tube to produce neutrons for use in well logging applications. Uranium sinker bar means a weight containing depleted uranium used to pull a logging tool toward the bottom of a well. Well... drilled holes for the purpose of oil, gas, mineral, groundwater, or geological exploration. Well logging...

10 CFR 39.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... neutron generator tube to produce neutrons for use in well logging applications. Uranium sinker bar means a weight containing depleted uranium used to pull a logging tool toward the bottom of a well. Well... drilled holes for the purpose of oil, gas, mineral, groundwater, or geological exploration. Well logging...

Use of acoustics to deter bark beetles from entering tree material.

PubMed

Aflitto, Nicholas C; Hofstetter, Richard W

2014-12-01

Acoustic technology is a potential tool to protect wood materials and eventually live trees from colonization by bark beetles. Bark beetles such as the southern pine beetle Dendroctonus frontalis, western pine beetle D. brevicomis and pine engraver Ips pini (Coleoptera: Curculionidae) use chemical and acoustic cues to communicate and to locate potential mates and host trees. In this study, the efficacy of sound treatments on D. frontalis, D. brevicomis and I. pini entry into tree materials was tested. Acoustic treatments significantly influenced whether beetles entered pine logs in the laboratory. Playback of artificial sounds reduced D. brevicomis entry into logs, and playback of stress call sounds reduced D. frontalis entry into logs. Sound treatments had no effect on I. pini entry into logs. The reduction in bark beetle entry into logs using particular acoustic treatments indicates that sound could be used as a viable management tool. © 2013 Society of Chemical Industry.

The NetLogger Toolkit V2.0

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

Gunter, Dan; Lee, Jason; Stoufer, Martin

2003-03-28

The NetLogger Toolkit is designed to monitor, under actual operating conditions, the behavior of all the elements of the application-to-application communication path in order to determine exactly where time is spent within a complex system Using NetLogger, distnbuted application components are modified to produce timestamped logs of "interesting" events at all the critical points of the distributed system Events from each component are correlated, which allov^ one to characterize the performance of all aspects of the system and network in detail. The NetLogger Toolkit itself consists of four components an API and library of functions to simplify the generation ofmore » application-level event logs, a set of tools for collecting and sorting log files, an event archive system, and a tool for visualization and analysis of the log files In order to instrument an application to produce event logs, the application developer inserts calls to the NetLogger API at all the critical points in the code, then links the application with the NetLogger library All the tools in the NetLogger Toolkit share a common log format, and assume the existence of accurate and synchronized system clocks NetLogger messages can be logged using an easy-to-read text based format based on the lETF-proposed ULM format, or a binary format that can still be used through the same API but that is several times faster and smaller, with performance comparable or better than binary message formats such as MPI, XDR, SDDF-Binary, and PBIO. The NetLogger binary format is both highly efficient and self-describing, thus optimized for the dynamic message construction and parsing of application instrumentation. NetLogger includes an "activation" API that allows NetLogger logging to be turned on, off, or modified by changing an external file This IS useful for activating logging in daemons/services (e g GndFTP server). The NetLogger reliability API provides the ability to specify backup logging locations and penodically try to reconnect broken TCP pipe. A typical use for this is to store data on local disk while net is down. An event archiver can log one or more incoming NetLogger streams to a local disk file (netlogd) or to a mySQL database (netarchd). We have found exploratory, visual analysis of the log event data to be the most useful means of determining the causes of performance anomalies The NetLogger Visualization tool, niv, has been developed to provide a flexible and interactive graphical representation of system-level and application-level events.« less

Nuclear magnetic resonance (NMR)-based metabolomics for cancer research.

PubMed

Ranjan, Renuka; Sinha, Neeraj

2018-05-07

Nuclear magnetic resonance (NMR) has emerged as an effective tool in various spheres of biomedical research, amongst which metabolomics is an important method for the study of various types of disease. Metabolomics has proved its stronghold in cancer research by the development of different NMR methods over time for the study of metabolites, thus identifying key players in the aetiology of cancer. A plethora of one-dimensional and two-dimensional NMR experiments (in solids, semi-solids and solution phases) are utilized to obtain metabolic profiles of biofluids, cell extracts and tissue biopsy samples, which can further be subjected to statistical analysis. Any alteration in the assigned metabolite peaks gives an indication of changes in metabolic pathways. These defined changes demonstrate the utility of NMR in the early diagnosis of cancer and provide further measures to combat malignancy and its progression. This review provides a snapshot of the trending NMR techniques and the statistical analysis involved in the metabolomics of diseases, with emphasis on advances in NMR methodology developed for cancer research. Copyright © 2018 John Wiley & Sons, Ltd.

Exploring high-resolution magic angle spinning (HR-MAS) NMR spectroscopy for metabonomic analysis of apples.

PubMed

Vermathen, Martina; Marzorati, Mattia; Vermathen, Peter

2012-01-01

Classical liquid-state high-resolution (HR) NMR spectroscopy has proved a powerful tool in the metabonomic analysis of liquid food samples like fruit juices. In this paper the application of (1)H high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to apple tissue is presented probing its potential for metabonomic studies. The (1)H HR-MAS NMR spectra are discussed in terms of the chemical composition of apple tissue and compared to liquid-state NMR spectra of apple juice. Differences indicate that specific metabolic changes are induced by juice preparation. The feasibility of HR-MAS NMR-based multivariate analysis is demonstrated by a study distinguishing three different apple cultivars by principal component analysis (PCA). Preliminary results are shown from subsequent studies comparing three different cultivation methods by means of PCA and partial least squares discriminant analysis (PLS-DA) of the HR-MAS NMR data. The compounds responsible for discriminating organically grown apples are discussed. Finally, an outlook of our ongoing work is given including a longitudinal study on apples.

Benchtop-NMR and MRI--a new analytical tool in drug delivery research.

PubMed

Metz, Hendrik; Mäder, Karsten

2008-12-08

During the last years, NMR spectroscopy and NMR imaging (magnetic resonance imaging, MRI) have been increasingly used to monitor drug delivery systems in vitro and in vivo. However, high installation and running costs of the commonly used superconducting magnet technology limits the application range and prevents the further spread of this non-invasive technology. Benchtop-NMR (BT-NMR) relaxometry uses permanent magnets and is much less cost intensive. BT-NMR relaxometry is commonly used in the food and chemical industry, but so far scarcely used in the pharmaceutical field. The paper shows on several examples that the application field of BT-NMR relaxometry can be extended into the field of drug delivery, including the characterisation of emulsions and lipid ingredients (e.g. the amount and physicochemical state of the lipid) and the monitoring of adsorption characteristics (e.g. oil binding of porous ingredients). The most exciting possibilities of BT-NMR technology are linked with the new development of BT-instruments with imaging capability. BT-MRI examples on the monitoring of hydration and swelling of HPMC-based monolayer and double-layer tablets are shown. BT-MRI opens new MRI opportunities for the non-invasive monitoring of drug delivery processes.

Emergency medicine clerkship encounter and procedure logging using handheld computers.

PubMed

Penciner, Rick; Siddiqui, Sanam; Lee, Shirley

2007-08-01

Tracking medical student clinical encounters is now an accreditation requirement of medical schools. The use of handheld computers for electronic logging is emerging as a strategy to achieve this. To evaluate the technical feasibility and student satisfaction of a novel electronic logging and feedback program using handheld computers in the emergency department. This was a survey study of fourth-year medical student satisfaction with the use of their handheld computers for electronic logging of patient encounters and procedures. The authors also included an analysis of this technology. Forty-six students participated in this pilot project, logging a total of 2,930 encounters. Students used the logs an average of 7.6 shifts per rotation, logging an average of 8.3 patients per shift. Twenty-nine students (63%) responded to the survey. Students generally found it easy to complete each encounter (69%) and easy to synchronize their handheld computer with the central server (83%). However, half the students (49%) never viewed the feedback Web site and most (79%) never reviewed their logs with their preceptors. Overall, only 17% found the logging program beneficial as a learning tool. Electronic logging by medical students during their emergency medicine clerkship has many potential benefits as a method to document clinical encounters and procedures performed. However, this study demonstrated poor compliance and dissatisfaction with the process. In order for electronic logging using handheld computers to be a beneficial educational tool for both learners and educators, obstacles to effective implementation need to be addressed.

Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy

PubMed Central

Kheddo, Priscilla; Cliff, Matthew J.; Uddin, Shahid; van der Walle, Christopher F.; Golovanov, Alexander P.

2016-01-01

ABSTRACT Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D 1H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins. PMID:27589351

NMR determination of an incommensurate helical antiferromagnetic structure in EuCo 2 As 2

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

Ding, Q. -P.; Higa, N.; Sangeetha, N. S.

In this paper, we report 153Eu, 75As, and 59Co nuclear magnetic resonance (NMR) results on EuCo 2As 2 single crystal. Observations of 153Eu and 75As NMR spectra in zero magnetic field at 4.3 K below an antiferromagnetic (AFM) ordering temperature T N = 45 K and its external magnetic field dependence clearly evidence an incommensurate helical AFM structure in EuCo 2As 2. Furthermore, based on 59Co NMR data in both the paramagnetic and the incommensurate AFM states, we have determined the model-independent value of the AFM propagation vector k = (0,0,0.73 ± 0.07)2π/c, where c is the c lattice parameter.more » Finally, the incommensurate helical AFM state was characterized by only NMR data with model-independent analyses, showing NMR to be a unique tool for determination of the spin structure in incommensurate helical AFMs.« less

Unambiguous Metabolite Identification in High-Throughput Metabolomics by Hybrid 1H-NMR/ESI-MS1 Approach

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

The invention improves accuracy of metabolite identification by combining direct infusion ESI-MS with one-dimensional 1H-NMR spectroscopy. First, we apply a standard 1H-NMR metabolite identification protocol by matching the chemical shift, J-coupling and intensity information of experimental NMR signals against the NMR signals of standard metabolites in a metabolomics reference libraries. This generates a list of candidate metabolites. The list contains both false positive and ambiguous identifications. The software tool (the invention) takes the list of candidate metabolites, generated from NMRbased metabolite identification, and then calculates, for each of the candidate metabolites, the monoisotopic mass-tocharge (m/z) ratios for each commonly observedmore » ion, fragment and adduct feature. These are then used to assign m/z ratios in experimental ESI-MS spectra of the same sample. Detection of the signals of a given metabolite in both NMR and MS spectra resolves the ambiguities, and therefore, significantly improves the confidence of the identification.« less

NMR determination of an incommensurate helical antiferromagnetic structure in EuCo 2 As 2

DOE PAGES

Ding, Q. -P.; Higa, N.; Sangeetha, N. S.; ...

2017-05-05

In this paper, we report 153Eu, 75As, and 59Co nuclear magnetic resonance (NMR) results on EuCo 2As 2 single crystal. Observations of 153Eu and 75As NMR spectra in zero magnetic field at 4.3 K below an antiferromagnetic (AFM) ordering temperature T N = 45 K and its external magnetic field dependence clearly evidence an incommensurate helical AFM structure in EuCo 2As 2. Furthermore, based on 59Co NMR data in both the paramagnetic and the incommensurate AFM states, we have determined the model-independent value of the AFM propagation vector k = (0,0,0.73 ± 0.07)2π/c, where c is the c lattice parameter.more » Finally, the incommensurate helical AFM state was characterized by only NMR data with model-independent analyses, showing NMR to be a unique tool for determination of the spin structure in incommensurate helical AFMs.« less

Characterizing monoclonal antibody formulations in arginine glutamate solutions using 1H NMR spectroscopy.

PubMed

Kheddo, Priscilla; Cliff, Matthew J; Uddin, Shahid; van der Walle, Christopher F; Golovanov, Alexander P

2016-10-01

Assessing how excipients affect the self-association of monoclonal antibodies (mAbs) requires informative and direct in situ measurements for highly concentrated solutions, without sample dilution or perturbation. This study explores the application of solution nuclear magnetic resonance (NMR) spectroscopy for characterization of typical mAb behavior in formulations containing arginine glutamate. The data show that the analysis of signal intensities in 1D 1 H NMR spectra, when compensated for changes in buffer viscosity, is invaluable for identifying conditions where protein-protein interactions are minimized. NMR-derived molecular translational diffusion rates for concentrated solutions are less useful than transverse relaxation rates as parameters defining optimal formulation. Furthermore, NMR reports on the solution viscosity and mAb aggregation during accelerated stability study assessment, generating data consistent with that acquired by size-exclusion chromatography. The methodology developed here offers NMR spectroscopy as a new tool providing complementary information useful to formulation development of mAbs and other large therapeutic proteins.

Quartz Crystal Temperature Sensor for MAS NMR

NASA Astrophysics Data System (ADS)

Simon, Gerald

1997-10-01

Quartz crystal temperature sensors (QCTS) were tested for the first time as wireless thermometers in NMR MAS rotors utilizing the NMR RF technique itself for exiting and receiving electro-mechanical quartz resonances. This new tool in MAS NMR has a high sensitivity, linearity, and precision. When compared to the frequently used calibration of the variable temperature in the NMR system by a solid state NMR chemical shift thermometer (CST), such as lead nitrate, QCTS shows a number of advantages. It is an inert thermometer in close contact with solid samples operating parallel to the NMR experiment. QCTS can be manufactured for any frequency to be near a NMR frequency of interest (typically 1 to 2 MHz below or above). Due to the strong response of the crystal, signal detection is possible without changing the tuning of the MAS probe. The NMR signal is not influenced due to the relative sharp crystal resonance, restricted excitation by finite pulses, high probeQvalues, and commonly used audio filters. The quadratic dependence of the temperature increase on spinning speed is the same for the QCTS and for the CST lead nitrate and is discussed in terms of frictional heat in accordance with the literature about lead nitrate and with the results of a simple rotor speed jump experiment with differently radial located lead nitrate in the rotor.

Research and development of improved geothermal well logging techniques, tools and components (current projects, goals and status). Final report

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

Lamers, M.D.

One of the key needs in the advancement of geothermal energy is availability of adequate subsurface measurements to aid the reservoir engineer in the development and operation of geothermal wells. Some current projects being sponsored by the U. S. Department of Energy's Division of Geothermal Energy pertaining to the development of improved well logging techniques, tools and components are described. An attempt is made to show how these projects contribute to improvement of geothermal logging technology in forming key elements of the overall program goals.

An Introduction to Drug Discovery by Probing Protein-Substrate Interactions Using Saturation Transfer Difference-Nuclear Magnetic Resonance (STD-NMR)

ERIC Educational Resources Information Center

Guegan, Jean-Paul; Daniellou, Richard

2012-01-01

NMR spectroscopy is a powerful tool for characterizing and identifying molecules and nowadays is even used to characterize complex systems in biology. In the experiment presented here, students learned how to apply this modern technique to probe interactions between small molecules and proteins. With the use of simple organic synthesis, students…

Can enzyme engineering benefit from the modulation of protein motions? Lessons learned from NMR relaxation dispersion experiments.

PubMed

Doucet, Nicolas

2011-04-01

Despite impressive progress in protein engineering and design, our ability to create new and efficient enzyme activities remains a laborious and time-consuming endeavor. In the past few years, intricate combinations of rational mutagenesis, directed evolution and computational methods have paved the way to exciting engineering examples and are now offering a new perspective on the structural requirements of enzyme activity. However, these structure-function analyses are usually guided by the time-averaged static models offered by enzyme crystal structures, which often fail to describe the functionally relevant 'invisible states' adopted by proteins in space and time. To alleviate such limitations, NMR relaxation dispersion experiments coupled to mutagenesis studies have recently been applied to the study of enzyme catalysis, effectively complementing 'structure-function' analyses with 'flexibility-function' investigations. In addition to offering quantitative, site-specific information to help characterize residue motion, these NMR methods are now being applied to enzyme engineering purposes, providing a powerful tool to help characterize the effects of controlling long-range networks of flexible residues affecting enzyme function. Recent advancements in this emerging field are presented here, with particular attention to mutagenesis reports highlighting the relevance of NMR relaxation dispersion tools in enzyme engineering.

STD-NMR-Based Protein Engineering of the Unique Arylpropionate-Racemase AMDase G74C.

PubMed

Gaßmeyer, Sarah Katharina; Yoshikawa, Hiroyuki; Enoki, Junichi; Hülsemann, Nadine; Stoll, Raphael; Miyamoto, Kenji; Kourist, Robert

2015-06-23

Structure-guided protein engineering achieved a variant of the unique racemase AMDase G74C, with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. Substrate binding during catalysis was investigated by saturation-transfer-difference NMR (STD-NMR) spectroscopy. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose substitutions increased the activity of G74C. Single amino acid exchanges increased the activity moderately; structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probing the stereo-electronic properties of cationic rhodium complexes bearing chiral diphosphine ligands by 103Rh NMR.

PubMed

Fabrello, Amandine; Dinoi, Chiara; Perrin, Lionel; Kalck, Philippe; Maron, Laurent; Urrutigoity, Martine; Dechy-Cabaret, Odile

2010-11-01

(103)Rh NMR represents a powerful tool to assess the global electronic and steric contribution of diphosphine ligands on [Rh(COD)(diphosphine)](+) complexes. In the case of DIOP, BINAP and MeDUPHOS, this approach proved to be more informative than classical CO-stretching frequency measurements. After validation, this method has been extended to a set of seven diphosphines. (103)Rh NMR measurements on [Rh(COD)(diphosphine)]PF(6) lead to the following order of donor properties: dppe > MeBPE > MeDUPHOS > dppb > DIOP > BINAP > Tol-BINAP. This trend has been validated by DFT in the case of DIOP, BINAP and MeDUPHOS. In conjunction, (31)P NMR chemical shift has been shown to reflect the ring constraints of the Rh-diphosphine scaffold. This contribution is a step towards a mechanistic investigation of the catalytic hydrogenation of unsaturated substrates by (103)Rh NMR and DFT. 2010 John Wiley & Sons, Ltd.

Bayesian Peak Picking for NMR Spectra

PubMed Central

Cheng, Yichen; Gao, Xin; Liang, Faming

2013-01-01

Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method. PMID:24184964

NMR spectroscopy of Group 13 metal ions: biologically relevant aspects.

PubMed

André, J P; Mäcke, H R

2003-12-01

In spite of the fact that Group 13 metal ions (Al(3+), Ga(3+), In(3+) and Tl(+/3+)) show no main biological role, they are NMR-active nuclides which can be used in magnetic resonance spectroscopy of biologically relevant systems. The fact that these metal ions are quadrupolar (with the exception of thallium) means that they are particularly sensitive to ligand type and coordination geometry. The line width of the NMR signals of their complexes shows a strong dependence on the symmetry of coordination, which constitutes an effective tool in the elucidation of structures. Here we report published NMR studies of this family of elements, applied to systems of biological importance. Special emphasis is given to binding studies of these cations to biological molecules, such as proteins, and to chelating agents of radiopharmaceutical interest. The possibility of in vivo NMR studies is also stressed, with extension to (27)Al-based MRI (magnetic resonance imaging) experiments.

On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR

PubMed Central

Mandal, Abhishek; Boatz, Jennifer C.; Wheeler, Travis; van der Wel, Patrick C. A.

2017-01-01

A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation. PMID:28229262

Parahydrogen-enhanced zero-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Theis, T.; Ganssle, P.; Kervern, G.; Knappe, S.; Kitching, J.; Ledbetter, M. P.; Budker, D.; Pines, A.

2011-07-01

Nuclear magnetic resonance, conventionally detected in magnetic fields of several tesla, is a powerful analytical tool for the determination of molecular identity, structure and function. With the advent of prepolarization methods and detection schemes using atomic magnetometers or superconducting quantum interference devices, interest in NMR in fields comparable to the Earth's magnetic field and below (down to zero field) has been revived. Despite the use of superconducting quantum interference devices or atomic magnetometers, low-field NMR typically suffers from low sensitivity compared with conventional high-field NMR. Here we demonstrate direct detection of zero-field NMR signals generated through parahydrogen-induced polarization, enabling high-resolution NMR without the use of any magnets. The sensitivity is sufficient to observe spectra exhibiting 13C-1H scalar nuclear spin-spin couplings (known as J couplings) in compounds with 13C in natural abundance, without the need for signal averaging. The resulting spectra show distinct features that aid chemical fingerprinting.

Towards a global network of gamma-ray detector calibration facilities

NASA Astrophysics Data System (ADS)

Tijs, Marco; Koomans, Ronald; Limburg, Han

2016-09-01

Gamma-ray logging tools are applied worldwide. At various locations, calibration facilities are used to calibrate these gamma-ray logging systems. Several attempts have been made to cross-correlate well known calibration pits, but this cross-correlation does not include calibration facilities in Europe or private company calibration facilities. Our aim is to set-up a framework that gives the possibility to interlink all calibration facilities worldwide by using `tools of opportunity' - tools that have been calibrated in different calibration facilities, whether this usage was on a coordinated basis or by coincidence. To compare the measurement of different tools, it is important to understand the behaviour of the tools in the different calibration pits. Borehole properties, such as diameter, fluid, casing and probe diameter strongly influence the outcome of gamma-ray borehole logging. Logs need to be properly calibrated and compensated for these borehole properties in order to obtain in-situ grades or to do cross-hole correlation. Some tool providers provide tool-specific correction curves for this purpose. Others rely on reference measurements against sources of known radionuclide concentration and geometry. In this article, we present an attempt to set-up a framework for transferring `local' calibrations to be applied `globally'. This framework includes corrections for any geometry and detector size to give absolute concentrations of radionuclides from borehole measurements. This model is used to compare measurements in the calibration pits of Grand Junction, located in the USA; Adelaide (previously known as AMDEL), located in Adelaide Australia; and Stonehenge, located at Medusa Explorations BV in the Netherlands.

Taming Log Files from Game/Simulation-Based Assessments: Data Models and Data Analysis Tools. Research Report. ETS RR-16-10

ERIC Educational Resources Information Center

Hao, Jiangang; Smith, Lawrence; Mislevy, Robert; von Davier, Alina; Bauer, Malcolm

2016-01-01

Extracting information efficiently from game/simulation-based assessment (G/SBA) logs requires two things: a well-structured log file and a set of analysis methods. In this report, we propose a generic data model specified as an extensible markup language (XML) schema for the log files of G/SBAs. We also propose a set of analysis methods for…

Detailed evaluation of gas hydrate reservoir properties using JAPEX/JNOC/GSC Mallik 2L-38 gas hydrate research well downhole well-log displays

USGS Publications Warehouse

Collett, T.S.

1999-01-01

The JAPEX/JNOC/GSC Mallik 2L-38 gas hydrate research well project was designed to investigate the occurrence of in situ natural gas hydrate in the Mallik area of the Mackenzie Delta of Canada. Because gas hydrate is unstable at surface pressure and temperature conditions, a major emphasis was placed on the downhole logging program to determine the in situ physical properties of the gas-hydrate-bearing sediments. Downhole logging tool strings deployed in the Mallik 2L-38 well included the Schlumberger Platform Express with a high resolution laterolog, Array Induction Imager Tool, Dipole Shear Sonic Imager, and a Fullbore Formation Microlmager. The downhole log data obtained from the log- and core-inferred gas-hydrate-bearing sedimentary interval (897.25-1109.5 m log depth) in the Mallik 2L-38 well is depicted in a series of well displays. Also shown are numerous reservoir parameters, including gas hydrate saturation and sediment porosity log traces, calculated from available downhole well-log and core data. The gas hydrate accumulation delineated by the Mallik 2L-38 well has been determined to contain as much as 4.15109 m3 of gas in the 1 km2 area surrounding the drill site.

Real World Experience With Ion Implant Fault Detection at Freescale Semiconductor

NASA Astrophysics Data System (ADS)

Sing, David C.; Breeden, Terry; Fakhreddine, Hassan; Gladwin, Steven; Locke, Jason; McHugh, Jim; Rendon, Michael

2006-11-01

The Freescale automatic fault detection and classification (FDC) system has logged data from over 3.5 million implants in the past two years. The Freescale FDC system is a low cost system which collects summary implant statistics at the conclusion of each implant run. The data is collected by either downloading implant data log files from the implant tool workstation, or by exporting summary implant statistics through the tool's automation interface. Compared to the traditional FDC systems which gather trace data from sensors on the tool as the implant proceeds, the Freescale FDC system cannot prevent scrap when a fault initially occurs, since the data is collected after the implant concludes. However, the system can prevent catastrophic scrap events due to faults which are not detected for days or weeks, leading to the loss of hundreds or thousands of wafers. At the Freescale ATMC facility, the practical applications of the FD system fall into two categories: PM trigger rules which monitor tool signals such as ion gauges and charge control signals, and scrap prevention rules which are designed to detect specific failure modes that have been correlated to yield loss and scrap. PM trigger rules are designed to detect shifts in tool signals which indicate normal aging of tool systems. For example, charging parameters gradually shift as flood gun assemblies age, and when charge control rules start to fail a flood gun PM is performed. Scrap prevention rules are deployed to detect events such as particle bursts and excessive beam noise, events which have been correlated to yield loss. The FDC system does have tool log-down capability, and scrap prevention rules often use this capability to automatically log the tool into a maintenance state while simultaneously paging the sustaining technician for data review and disposition of the affected product.

Deuteron NMR (Nuclear Magnetic Resonance) in relation to the glass transition in polymers

NASA Technical Reports Server (NTRS)

Roessler, E.; Sillescu, H.; Spiess, H. W.; Wallwitz, R.

1983-01-01

H-2NMR is introduced as a tool for investigating slow molecular motion in the glass transition region of amorphous polymers. In particular, we compare H-2 spin alignment echo spectra of chain deuterated polystyrene with model calculations for restricted rotational Brownian motion. Molecular motion in the polyztyrene-toluene system has been investigated by analyzing H-2NMR of partially deuterated polystyrene and toluene, respectively. The diluent mobility in the mixed glass has been decomposed into solid and liquid components where the respective average correlation times differ by more than 5 decades.

The SPORT-NMR Software: A Tool for Determining Relaxation Times in Unresolved NMR Spectra

NASA Astrophysics Data System (ADS)

Geppi, Marco; Forte, Claudia

1999-03-01

A software package which allows the correct determination of individual relaxation times for all the nonequivalent nuclei in poorly resolved NMR spectra is described. The procedure used, based on the fitting of each spectrum in the series recorded in the relaxation experiment, should improve the analysis of relaxation data in terms of quantitative dynamic information, especially in anisotropic phases. Tests on simulated data and experimental examples concerning1H and13CT1ρmeasurement in a solid copolymer and2HT1ZandT1Qmeasurement in a liquid crystal are shown and discussed.

75 FR 63506 - Logging Operations; Extension of the Office of Management and Budget's (OMB) Approval of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-15

...] Logging Operations; Extension of the Office of Management and Budget's (OMB) Approval of Information... Logging Operations (29 CFR 1910.266). DATES: Comments must be submitted (postmarked, sent, or received) by... following elements: Safe work practices, including the use, operation, and maintenance of tools, machines...

Automated method for measuring the extent of selective logging damage with airborne LiDAR data

NASA Astrophysics Data System (ADS)

Melendy, L.; Hagen, S. C.; Sullivan, F. B.; Pearson, T. R. H.; Walker, S. M.; Ellis, P.; Kustiyo; Sambodo, Ari Katmoko; Roswintiarti, O.; Hanson, M. A.; Klassen, A. W.; Palace, M. W.; Braswell, B. H.; Delgado, G. M.

2018-05-01

Selective logging has an impact on the global carbon cycle, as well as on the forest micro-climate, and longer-term changes in erosion, soil and nutrient cycling, and fire susceptibility. Our ability to quantify these impacts is dependent on methods and tools that accurately identify the extent and features of logging activity. LiDAR-based measurements of these features offers significant promise. Here, we present a set of algorithms for automated detection and mapping of critical features associated with logging - roads/decks, skid trails, and gaps - using commercial airborne LiDAR data as input. The automated algorithm was applied to commercial LiDAR data collected over two logging concessions in Kalimantan, Indonesia in 2014. The algorithm results were compared to measurements of the logging features collected in the field soon after logging was complete. The automated algorithm-mapped road/deck and skid trail features match closely with features measured in the field, with agreement levels ranging from 69% to 99% when adjusting for GPS location error. The algorithm performed most poorly with gaps, which, by their nature, are variable due to the unpredictable impact of tree fall versus the linear and regular features directly created by mechanical means. Overall, the automated algorithm performs well and offers significant promise as a generalizable tool useful to efficiently and accurately capture the effects of selective logging, including the potential to distinguish reduced impact logging from conventional logging.

Test-bench system for a borehole azimuthal acoustic reflection imaging logging tool

NASA Astrophysics Data System (ADS)

Liu, Xianping; Ju, Xiaodong; Qiao, Wenxiao; Lu, Junqiang; Men, Baiyong; Liu, Dong

2016-06-01

The borehole azimuthal acoustic reflection imaging logging tool (BAAR) is a new generation of imaging logging tool, which is able to investigate stratums in a relatively larger range of space around the borehole. The BAAR is designed based on the idea of modularization with a very complex structure, so it has become urgent for us to develop a dedicated test-bench system to debug each module of the BAAR. With the help of a test-bench system introduced in this paper, test and calibration of BAAR can be easily achieved. The test-bench system is designed based on the client/server model. The hardware system mainly consists of a host computer, an embedded controlling board, a bus interface board, a data acquisition board and a telemetry communication board. The host computer serves as the human machine interface and processes the uploaded data. The software running on the host computer is designed based on VC++. The embedded controlling board uses Advanced Reduced Instruction Set Machines 7 (ARM7) as the micro controller and communicates with the host computer via Ethernet. The software for the embedded controlling board is developed based on the operating system uClinux. The bus interface board, data acquisition board and telemetry communication board are designed based on a field programmable gate array (FPGA) and provide test interfaces for the logging tool. To examine the feasibility of the test-bench system, it was set up to perform a test on BAAR. By analyzing the test results, an unqualified channel of the electronic receiving cabin was discovered. It is suggested that the test-bench system can be used to quickly determine the working condition of sub modules of BAAR and it is of great significance in improving production efficiency and accelerating industrial production of the logging tool.

A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank.

PubMed

Smelter, Andrey; Astra, Morgan; Moseley, Hunter N B

2017-03-17

The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magnetic Resonance (NMR) spectroscopic data of biological macromolecules. It is an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties of biological macromolecules. It is primarily maintained and accessed in a flat file ASCII format known as NMR-STAR. While the format is human readable, the size of most BMRB entries makes computer readability and explicit representation a practical requirement for almost any rigorous systematic analysis. To aid in the use of this public resource, we have developed a package called nmrstarlib in the popular open-source programming language Python. The nmrstarlib's implementation is very efficient, both in design and execution. The library has facilities for reading and writing both NMR-STAR version 2.1 and 3.1 formatted files, parsing them into usable Python dictionary- and list-based data structures, making access and manipulation of the experimental data very natural within Python programs (i.e. "saveframe" and "loop" records represented as individual Python dictionary data structures). Another major advantage of this design is that data stored in original NMR-STAR can be easily converted into its equivalent JavaScript Object Notation (JSON) format, a lightweight data interchange format, facilitating data access and manipulation using Python and any other programming language that implements a JSON parser/generator (i.e., all popular programming languages). We have also developed tools to visualize assigned chemical shift values and to convert between NMR-STAR and JSONized NMR-STAR formatted files. Full API Reference Documentation, User Guide and Tutorial with code examples are also available. We have tested this new library on all current BMRB entries: 100% of all entries are parsed without any errors for both NMR-STAR version 2.1 and version 3.1 formatted files. We also compared our software to three currently available Python libraries for parsing NMR-STAR formatted files: PyStarLib, NMRPyStar, and PyNMRSTAR. The nmrstarlib package is a simple, fast, and efficient library for accessing data from the BMRB. The library provides an intuitive dictionary-based interface with which Python programs can read, edit, and write NMR-STAR formatted files and their equivalent JSONized NMR-STAR files. The nmrstarlib package can be used as a library for accessing and manipulating data stored in NMR-STAR files and as a command-line tool to convert from NMR-STAR file format into its equivalent JSON file format and vice versa, and to visualize chemical shift values. Furthermore, the nmrstarlib implementation provides a guide for effectively JSONizing other older scientific formats, improving the FAIRness of data in these formats.

Self-optimizing Monte Carlo method for nuclear well logging simulation

NASA Astrophysics Data System (ADS)

Liu, Lianyan

1997-09-01

In order to increase the efficiency of Monte Carlo simulation for nuclear well logging problems, a new method has been developed for variance reduction. With this method, an importance map is generated in the regular Monte Carlo calculation as a by-product, and the importance map is later used to conduct the splitting and Russian roulette for particle population control. By adopting a spatial mesh system, which is independent of physical geometrical configuration, the method allows superior user-friendliness. This new method is incorporated into the general purpose Monte Carlo code MCNP4A through a patch file. Two nuclear well logging problems, a neutron porosity tool and a gamma-ray lithology density tool are used to test the performance of this new method. The calculations are sped up over analog simulation by 120 and 2600 times, for the neutron porosity tool and for the gamma-ray lithology density log, respectively. The new method enjoys better performance by a factor of 4~6 times than that of MCNP's cell-based weight window, as per the converged figure-of-merits. An indirect comparison indicates that the new method also outperforms the AVATAR process for gamma-ray density tool problems. Even though it takes quite some time to generate a reasonable importance map from an analog run, a good initial map can create significant CPU time savings. This makes the method especially suitable for nuclear well logging problems, since one or several reference importance maps are usually available for a given tool. Study shows that the spatial mesh sizes should be chosen according to the mean-free-path. The overhead of the importance map generator is 6% and 14% for neutron and gamma-ray cases. The learning ability towards a correct importance map is also demonstrated. Although false-learning may happen, physical judgement can help diagnose with contributon maps. Calibration and analysis are performed for the neutron tool and the gamma-ray tool. Due to the fact that a very good initial importance map is always available after the first point has been calculated, high computing efficiency is maintained. The availability of contributon maps provides an easy way of understanding the logging measurement and analyzing for the depth of investigation.

Monitoring Object Library Usage and Changes

NASA Technical Reports Server (NTRS)

Owen, R. K.; Craw, James M. (Technical Monitor)

1995-01-01

The NASA Ames Numerical Aerodynamic Simulation program Aeronautics Consolidated Supercomputing Facility (NAS/ACSF) supercomputing center services over 1600 users, and has numerous analysts with root access. Several tools have been developed to monitor object library usage and changes. Some of the tools do "noninvasive" monitoring and other tools implement run-time logging even for object-only libraries. The run-time logging identifies who, when, and what is being used. The benefits are that real usage can be measured, unused libraries can be discontinued, training and optimization efforts can be focused at those numerical methods that are actually used. An overview of the tools will be given and the results will be discussed.

An approach to derive some simple empirical equations to calibrate nuclear and acoustic well logging tools.

PubMed

Mohammad Al Alfy, Ibrahim

2018-01-01

A set of three pads was constructed from primary materials (sand, gravel and cement) to calibrate the gamma-gamma density tool. A simple equation was devised to convert the qualitative cps values to quantitative g/cc values. The neutron-neutron porosity tool measures the qualitative cps porosity values. A direct equation was derived to calculate the porosity percentage from the cps porosity values. Cement-bond log illustrates the cement quantities, which surround well pipes. This log needs a difficult process due to the existence of various parameters, such as: drilling well diameter as well as internal diameter, thickness and type of well pipes. An equation was invented to calculate the cement percentage at standard conditions. This equation can be modified according to varying conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Unambiguous metabolite identification in high-throughput metabolomics by hybrid 1D 1 H NMR/ESI MS 1 approach: Hybrid 1D 1 H NMR/ESI MS 1 metabolomics method

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

Walker, Lawrence R.; Hoyt, David W.; Walker, S. Michael

We present a novel approach to improve accuracy of metabolite identification by combining direct infusion ESI MS1 with 1D 1H NMR spectroscopy. The new approach first applies standard 1D 1H NMR metabolite identification protocol by matching the chemical shift, J-coupling and intensity information of experimental NMR signals against the NMR signals of standard metabolites in metabolomics library. This generates a list of candidate metabolites. The list contains false positive and ambiguous identifications. Next, we constrained the list with the chemical formulas derived from high-resolution direct infusion ESI MS1 spectrum of the same sample. Detection of the signals of a metabolitemore » both in NMR and MS significantly improves the confidence of identification and eliminates false positive identification. 1D 1H NMR and direct infusion ESI MS1 spectra of a sample can be acquired in parallel in several minutes. This is highly beneficial for rapid and accurate screening of hundreds of samples in high-throughput metabolomics studies. In order to make this approach practical, we developed a software tool, which is integrated to Chenomx NMR Suite. The approach is demonstrated on a model mixture, tomato and Arabidopsis thaliana metabolite extracts, and human urine.« less

Proton Nuclear Magnetic Resonance Spectroscopy as a Technique for Gentamicin Drug Susceptibility Studies with Escherichia coli ATCC 25922

PubMed Central

García-Álvarez, Lara; Busto, Jesús H.; Avenoza, Alberto; Sáenz, Yolanda; Peregrina, Jesús Manuel

2015-01-01

Antimicrobial drug susceptibility tests involving multiple time-consuming steps are still used as reference methods. Today, there is a need for the development of new automated instruments that can provide faster results and reduce operating time, reagent costs, and labor requirements. Nuclear magnetic resonance (NMR) spectroscopy meets those requirements. The metabolism and antimicrobial susceptibility of Escherichia coli ATCC 25922 in the presence of gentamicin have been analyzed using NMR and compared with a reference method. Direct incubation of the bacteria (with and without gentamicin) into the NMR tube has also been performed, and differences in the NMR spectra were obtained. The MIC, determined by the reference method found in this study, would correspond with the termination of the bacterial metabolism observed with NMR. Experiments carried out directly into the NMR tube enabled the development of antimicrobial drug susceptibility tests to assess the effectiveness of the antibiotic. NMR is an objective and reproducible method for showing the effects of a drug on the subject bacterium and can emerge as an excellent tool for studying bacterial activity in the presence of different antibiotic concentrations. PMID:25972417

Proton Nuclear Magnetic Resonance Spectroscopy as a Technique for Gentamicin Drug Susceptibility Studies with Escherichia coli ATCC 25922.

PubMed

García-Álvarez, Lara; Busto, Jesús H; Avenoza, Alberto; Sáenz, Yolanda; Peregrina, Jesús Manuel; Oteo, José A

2015-08-01

Antimicrobial drug susceptibility tests involving multiple time-consuming steps are still used as reference methods. Today, there is a need for the development of new automated instruments that can provide faster results and reduce operating time, reagent costs, and labor requirements. Nuclear magnetic resonance (NMR) spectroscopy meets those requirements. The metabolism and antimicrobial susceptibility of Escherichia coli ATCC 25922 in the presence of gentamicin have been analyzed using NMR and compared with a reference method. Direct incubation of the bacteria (with and without gentamicin) into the NMR tube has also been performed, and differences in the NMR spectra were obtained. The MIC, determined by the reference method found in this study, would correspond with the termination of the bacterial metabolism observed with NMR. Experiments carried out directly into the NMR tube enabled the development of antimicrobial drug susceptibility tests to assess the effectiveness of the antibiotic. NMR is an objective and reproducible method for showing the effects of a drug on the subject bacterium and can emerge as an excellent tool for studying bacterial activity in the presence of different antibiotic concentrations. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Advances in solid-state NMR of cellulose.

PubMed

Foston, Marcus

2014-06-01

Nuclear magnetic resonance (NMR) spectroscopy is a well-established analytical and enabling technology in biofuel research. Over the past few decades, lignocellulosic biomass and its conversion to supplement or displace non-renewable feedstocks has attracted increasing interest. The application of solid-state NMR spectroscopy has long been seen as an important tool in the study of cellulose and lignocellulose structure, biosynthesis, and deconstruction, especially considering the limited number of effective solvent systems and the significance of plant cell wall three-dimensional microstructure and component interaction to conversion yield and rate profiles. This article reviews common and recent applications of solid-state NMR spectroscopy methods that provide insight into the structural and dynamic processes of cellulose that control bulk properties and biofuel conversion. Copyright © 2014 Elsevier Ltd. All rights reserved.

Enhanced detection of aldehydes in Extra-Virgin Olive Oil by means of band selective NMR spectroscopy

NASA Astrophysics Data System (ADS)

Dugo, Giacomo; Rotondo, Archimede; Mallamace, Domenico; Cicero, Nicola; Salvo, Andrea; Rotondo, Enrico; Corsaro, Carmelo

2015-02-01

High resolution Nuclear Magnetic Resonance (NMR) spectroscopy is a very powerful tool for comprehensive food analyses and especially for Extra-Virgin Olive Oils (EVOOs). We use the NMR technique to study the spectral region of aldehydes (8-10 ppm) for EVOOs coming from the south part of Italy. We perform novel experiments by using mono and bidimensional band selective spin-echo pulse sequences and identify four structural classes of aldehydes in EVOOs. For the first time such species are identified in EVOOs without any chemical treatment; only dilution with CDCl3 is employed. This would allow the discrimination of different EVOOs for the aldehydes content increasing the potentiality of the NMR technique in the screening of metabolites for geographical characterization of EVOOs.

High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance of Intact Zebrafish Embryos Detects Metabolic Changes Following Exposure to Teratogenic Polymethoxyalkenes from Algae

PubMed Central

Roy, Upasana; Jaja-Chimedza, Asha; Sanchez, Kristel; Matysik, Joerg

2016-01-01

Abstract Techniques based on nuclear magnetic resonance (NMR) for imaging and chemical analyses of in vivo, or otherwise intact, biological systems are rapidly emerging and finding diverse applications within a wide range of fields. Very recently, several NMR-based techniques have been developed for the zebrafish as a model animal system. In the current study, the novel application of high-resolution magic angle spinning (HR-MAS) NMR is presented as a means of metabolic profiling of intact zebrafish embryos. Toward investigating the utility of HR-MAS NMR as a toxicological tool, these studies specifically examined metabolic changes of embryos exposed to polymethoxy-1-alkenes (PMAs)—a recently identified family of teratogenic compounds from freshwater algae—as emerging environmental contaminants. One-dimensional and two-dimensional HR-MAS NMR analyses were able to effectively identify and quantify diverse metabolites in early-stage (≤36 h postfertilization) embryos. Subsequent comparison of the metabolic profiles between PMA-exposed and control embryos identified several statistically significant metabolic changes associated with subacute exposure to the teratogen, including (1) elevated inositol as a recognized component of signaling pathways involved in embryo development; (2) increases in several metabolites, including inositol, phosphoryl choline, fatty acids, and cholesterol, which are associated with lipid composition of cell membranes; (3) concomitant increase in glucose and decrease in lactate; and (4) decreases in several biochemically related metabolites associated with central nervous system development and function, including γ-aminobutyric acid, glycine, glutamate, and glutamine. A potentially unifying model/hypothesis of PMA teratogenicity based on the data is presented. These findings, taken together, demonstrate that HR-MAS NMR is a promising tool for metabolic profiling in the zebrafish embryo, including toxicological applications. PMID:27348393

Hardwood sawyer trainer

Treesearch

Luis G. Occeña; Eknarin Santitrakul; Daniel L. Schmoldt

2000-01-01

It is well understood by now that the initial breakdown of hardwood logs into lumber has a tremendous impact on the total lumber value and conversion efficiency. The focus of this research project is the development of a computer-aided sawing trainer tool for the primary breakdown of hardwood logs. Maximum lumber recovery is dependent on the proper log orientation as...

Forest management practices and the occupational safety and health administration logging standard

Treesearch

John R. Myers; David Elton Fosbroke

1995-01-01

The Occupational Safety and Health Administration (OSHA) has established safety and health regulations for the logging industry. These new regulations move beyond the prior OSHA pulpwood harvesting standard by including sawtimber harvesting operations. Because logging is a major tool used by forest managers to meet silvicultural goals, managers must be aware of what...

Best opening face system for sweepy, eccentric logs : a user’s guide

Treesearch

David W. Lewis

1985-01-01

Log breakdown simulation models have gained rapid acceptance within the sawmill industry in the last 15 years. Although they have many advantages over traditional decision making tools, the existing models do not calculate yield correctly when used to simulate the breakdown of eccentric, sweepy logs in North American sawmills producing softwood dimension lumber. In an...

Interactive NMR: A Simulation Based Teaching Tool for Fundamentals to Applications with Tangible Analogies

NASA Astrophysics Data System (ADS)

Griesse-Nascimento, Sarah; Bridger, Joshua; Brown, Keith; Westervelt, Robert

2011-03-01

Interactive computer simulations increase students' understanding of difficult concepts and their ability to explain complex ideas. We created a module of eight interactive programs and accompanying lesson plans for teaching the fundamental concepts of Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI) that we call interactive NMR (iNMR). We begin with an analogy between nuclear spins and metronomes to start to build intuition about the dynamics of spins in a magnetic field. We continue to explain T1, T2, and pulse sequences with the metronome analogy. The final three programs are used to introduce and explain the Magnetic Resonance Switch, a recent diagnostic technique based on NMR. A modern relevant application is useful to generate interest in the topic and confidence in the students' ability to apply their knowledge. The iNMR module was incorporated into a high school AP physics class. In a preliminary evaluation of implementation, students expressed enthusiasm and demonstrated enhanced understanding of the material relative to the previous year. Funded by NSF PHY-0646094 grant.

Updates in metabolomics tools and resources: 2014-2015.

PubMed

Misra, Biswapriya B; van der Hooft, Justin J J

2016-01-01

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources--in the form of tools, software, and databases--is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Long-range Li+ dynamics in the lithium argyrodite Li7PSe6 as probed by rotating-frame spin-lattice relaxation NMR.

PubMed

Epp, V; Gün, O; Deiseroth, H-J; Wilkening, M

2013-05-21

Lithium-rich argyrodites belong to a relatively new group of fast ion conducting solids. They might serve as powerful electrolytes in all-solid-state lithium-ion batteries being, from a medium-term point of view, the key technology when safe energy storage systems have to be developed. Spin-lattice relaxation (SLR) nuclear magnetic resonance (NMR) measurements carried out in the rotating frame of reference turned out to be the method of choice to study Li dynamics in argyrodites. When plotted as a function of the inverse temperature, the SLR rates log10(R1ρ) reveal an asymmetric diffusion-induced rate peak. The rate peak contains information on the Li jump rate, the activation energy of the hopping process as well as correlation effects. In particular, considering the high-temperature flank of the SLR NMR rate peak recorded in the rotating frame of reference, an activation energy of approximately 0.49 eV is found. This value represents long-range lithium jump diffusion in crystalline Li7PSe6. As an example, at 325 K the Li jump rate determined from SLR NMR is in the order of 1.4 × 10(5) s(-1). The pronounced asymmetry of the rate peak R1ρ(1/T) points to correlated Li motion. It is comparable to that which is typically found for structurally disordered materials showing a broad range of correlation times.

Density functional theory study on aqueous aluminum-fluoride complexes: exploration of the intrinsic relationship between water-exchange rate constants and structural parameters for monomer aluminum complexes.

PubMed

Jin, Xiaoyan; Qian, Zhaosheng; Lu, Bangmei; Yang, Wenjing; Bi, Shuping

2011-01-01

Density functional theory (DFT) calculation is carried out to investigate the structures, (19)F and (27)Al NMR chemical shifts of aqueous Al-F complexes and their water-exchange reactions. The following investigations are performed in this paper: (1) the microscopic properties of typical aqueous Al-F complexes are obtained at the level of B3LYP/6-311+G**. Al-OH(2) bond lengths increase with F(-) replacing inner-sphere H(2)O progressively, indicating labilizing effect of F(-) ligand. The Al-OH(2) distance trans to fluoride is longer than other Al-OH(2) distance, accounting for trans effect of F(-) ligand. (19)F and (27)Al NMR chemical shifts are calculated using GIAO method at the HF/6-311+G** level relative to F(H(2)O)(6)(-) and Al(H(2)O)(6)(3+) references, respectively. The results are consistent with available experimental values; (2) the dissociative (D) activated mechanism is observed by modeling water-exchange reaction for [Al(H(2)O)(6-i)F(i)]((3-i)+) (i = 1-4). The activation energy barriers are found to decrease with increasing F(-) substitution, which is in line with experimental rate constants (k(ex)). The log k(ex) of AlF(3)(H(2)O)(3)(0) and AlF(4)(H(2)O)(2)(-) are predicted by three ways. The results indicate that the correlation between log k(ex) and Al-O bond length as well as the given transmission coefficient allows experimental rate constants to be predicted, whereas the correlation between log k(ex) and activation free energy is poor; (3) the environmental significance of this work is elucidated by the extension toward three fields, that is, polyaluminum system, monomer Al-organic system and other metal ions system with high charge-to-radius ratio.

Humic Acid Composition and Characteristics of Soil Organic Matter in Relation to the Elevation Gradient of Moso Bamboo Plantations.

PubMed

Wang, Hsueh-Ching; Chou, Chiao-Ying; Chiou, Chyi-Rong; Tian, Guanglong; Chiu, Chih-Yu

2016-01-01

Studying the influence of climatic and/or site-specific factors on soil organic matter (SOM) along an elevation gradient is important for understanding the response of SOM to global warming. We evaluated the composition of SOM and structure of humic acids along an altitudinal gradient from 600 to 1400 m in moso bamboo (Phyllostachys edulis) plantations in central Taiwan using NMR spectroscopy and photometric analysis. Total organic C and total nitrogen (N) content increased with increasing elevation. Aromaticity decreased and ΔlogK (the logarithm of the absorbance ratio of humic acids at 400 and 600 nm) increased with increasing elevation, which suggests that SOM humification decreased with increasing elevation. High temperature at low elevations seemed to enhance the decomposition (less accumulation of total organic C and N) and humification (high aromaticity and low ΔlogK). The alkyl-C/O-alkyl-C (A/O-A) ratio of humic acids increased with increasing elevation, which suggests that SOM humification increased with increasing elevation; this finding was contrary to the trend observed for ΔlogK and aromaticity. Such a discrepancy might be due to the relatively greater remaining of SOM derived from high alkyl-C broadleaf litter of previous forest at high elevations. The ratio of recalcitrant C to total organic C was low at low elevations, possibly because of enhanced decomposition of recalcitrant SOM from the previous broadleaf forest during long-term intensive cultivation and high temperature. Overall, the change in SOM pools and in the rate of humification with elevation was primarily affected by changes in climatic conditions along the elevation gradient in these bamboo plantations. However, when the composition of SOM, as assessed by NMR spectroscopy and photometric analysis was considered, site-specific factors such as residual SOM from previous forest and intensive cultivation history could also have an important effect on the humic acid composition and humification of SOM.

Humic Acid Composition and Characteristics of Soil Organic Matter in Relation to the Elevation Gradient of Moso Bamboo Plantations

PubMed Central

Wang, Hsueh-Ching; Chou, Chiao-Ying; Chiou, Chyi-Rong; Tian, Guanglong

2016-01-01

Studying the influence of climatic and/or site-specific factors on soil organic matter (SOM) along an elevation gradient is important for understanding the response of SOM to global warming. We evaluated the composition of SOM and structure of humic acids along an altitudinal gradient from 600 to 1400 m in moso bamboo (Phyllostachys edulis) plantations in central Taiwan using NMR spectroscopy and photometric analysis. Total organic C and total nitrogen (N) content increased with increasing elevation. Aromaticity decreased and ΔlogK (the logarithm of the absorbance ratio of humic acids at 400 and 600 nm) increased with increasing elevation, which suggests that SOM humification decreased with increasing elevation. High temperature at low elevations seemed to enhance the decomposition (less accumulation of total organic C and N) and humification (high aromaticity and low ΔlogK). The alkyl-C/O-alkyl-C (A/O-A) ratio of humic acids increased with increasing elevation, which suggests that SOM humification increased with increasing elevation; this finding was contrary to the trend observed for ΔlogK and aromaticity. Such a discrepancy might be due to the relatively greater remaining of SOM derived from high alkyl-C broadleaf litter of previous forest at high elevations. The ratio of recalcitrant C to total organic C was low at low elevations, possibly because of enhanced decomposition of recalcitrant SOM from the previous broadleaf forest during long-term intensive cultivation and high temperature. Overall, the change in SOM pools and in the rate of humification with elevation was primarily affected by changes in climatic conditions along the elevation gradient in these bamboo plantations. However, when the composition of SOM, as assessed by NMR spectroscopy and photometric analysis was considered, site-specific factors such as residual SOM from previous forest and intensive cultivation history could also have an important effect on the humic acid composition and humification of SOM. PMID:27583451

Gulf of Mexico Gas Hydrate Joint Industry Project Leg II logging-while-drilling data acquisition and anaylsis

USGS Publications Warehouse

Collett, Timothy S.; Lee, Myung W.; Zyrianova, Margarita V.; Mrozewski, Stefan A.; Guerin, Gilles; Cook, Ann E.; Goldberg, Dave S.

2012-01-01

One of the objectives of the Gulf of MexicoGasHydrateJointIndustryProjectLegII (GOM JIP LegII) was the collection of a comprehensive suite of logging-while-drilling (LWD) data within gas-hydrate-bearing sand reservoirs in order to make accurate estimates of the concentration of gashydrates under various geologic conditions and to understand the geologic controls on the occurrence of gashydrate at each of the sites drilled during this expedition. The LWD sensors just above the drill bit provided important information on the nature of the sediments and the occurrence of gashydrate. There has been significant advancements in the use of downhole well-logging tools to acquire detailed information on the occurrence of gashydrate in nature: From using electrical resistivity and acoustic logs to identify gashydrate occurrences in wells to where wireline and advanced logging-while-drilling tools are routinely used to examine the petrophysical nature of gashydrate reservoirs and the distribution and concentration of gashydrates within various complex reservoir systems. Recent integrated sediment coring and well-log studies have confirmed that electrical resistivity and acoustic velocity data can yield accurate gashydrate saturations in sediment grain supported (isotropic) systems such as sand reservoirs, but more advanced log analysis models are required to characterize gashydrate in fractured (anisotropic) reservoir systems. In support of the GOM JIP LegII effort, well-log data montages have been compiled and presented in this report which includes downhole logs obtained from all seven wells drilled during this expedition with a focus on identifying and characterizing the potential gas-hydrate-bearing sedimentary section in each of the wells. Also presented and reviewed in this report are the gas-hydrate saturation and sediment porosity logs for each of the wells as calculated from available downhole well logs.

Spectroscopic techniques (Mössbauer spectrometry, NMR, ESR,…) as tools to resolve doubtful NMR images: Study of the craniopharyngioma tumor

NASA Astrophysics Data System (ADS)

Rimbert, J. N.; Dumas, F.; Lafargue, C.; Kellershohn, C.; Brunelle, F.; Lallemand, D.

1990-07-01

Craniopharyngioma, an intracranial tumor, exhibits hyperintensity in the Spin-Echo-T2-NMR image and a hyposignal in the SE-T1-image. However, in some cases (15-20% cases), hypersignals are seen in both SE-T1 and T2-MRI. Using spectroscopic techniques, Mössbauer spectrometry in particular, we have demonstrated that the T1 hypersignal is due to ferritin, dissolved in the cystic liquid, after tumor cell lysis, in the course of time. Other possible reasons inducing a shortening of the T1 relaxation time (presence of lipids, intratumoral hemorrhage) have been rejected.

Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate.

PubMed

Filip, Xenia; Miclaus, Maria; Martin, Flavia; Filip, Claudiu; Grosu, Ioana Georgeta

2017-05-10

Herein we report the preparation and solid state structural investigation of the 1,4-dioxane-quercetin solvate. NMR crystallography methods were employed for crystal structure determination of the solvate from microcrystalline powder. The stability of the compound relative to other reported quercetin solvates is discussed and found to be in perfect agreement with the hydrogen bonding networks/supra-molecular architectures formed in each case. It is also clearly shown that NMR crystallography represents an ideal analytical tool in such cases when hydrogen-bonding networks are required to be constrained at a high accuracy level. Copyright © 2017 Elsevier B.V. All rights reserved.

Performance Analysis Tool for HPC and Big Data Applications on Scientific Clusters

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

Yoo, Wucherl; Koo, Michelle; Cao, Yu

Big data is prevalent in HPC computing. Many HPC projects rely on complex workflows to analyze terabytes or petabytes of data. These workflows often require running over thousands of CPU cores and performing simultaneous data accesses, data movements, and computation. It is challenging to analyze the performance involving terabytes or petabytes of workflow data or measurement data of the executions, from complex workflows over a large number of nodes and multiple parallel task executions. To help identify performance bottlenecks or debug the performance issues in large-scale scientific applications and scientific clusters, we have developed a performance analysis framework, using state-ofthe-more » art open-source big data processing tools. Our tool can ingest system logs and application performance measurements to extract key performance features, and apply the most sophisticated statistical tools and data mining methods on the performance data. It utilizes an efficient data processing engine to allow users to interactively analyze a large amount of different types of logs and measurements. To illustrate the functionality of the big data analysis framework, we conduct case studies on the workflows from an astronomy project known as the Palomar Transient Factory (PTF) and the job logs from the genome analysis scientific cluster. Our study processed many terabytes of system logs and application performance measurements collected on the HPC systems at NERSC. The implementation of our tool is generic enough to be used for analyzing the performance of other HPC systems and Big Data workows.« less

PLAT: An Automated Fault and Behavioural Anomaly Detection Tool for PLC Controlled Manufacturing Systems.

PubMed

Ghosh, Arup; Qin, Shiming; Lee, Jooyeoun; Wang, Gi-Nam

2016-01-01

Operational faults and behavioural anomalies associated with PLC control processes take place often in a manufacturing system. Real time identification of these operational faults and behavioural anomalies is necessary in the manufacturing industry. In this paper, we present an automated tool, called PLC Log-Data Analysis Tool (PLAT) that can detect them by using log-data records of the PLC signals. PLAT automatically creates a nominal model of the PLC control process and employs a novel hash table based indexing and searching scheme to satisfy those purposes. Our experiments show that PLAT is significantly fast, provides real time identification of operational faults and behavioural anomalies, and can execute within a small memory footprint. In addition, PLAT can easily handle a large manufacturing system with a reasonable computing configuration and can be installed in parallel to the data logging system to identify operational faults and behavioural anomalies effectively.

PLAT: An Automated Fault and Behavioural Anomaly Detection Tool for PLC Controlled Manufacturing Systems

PubMed Central

Ghosh, Arup; Qin, Shiming; Lee, Jooyeoun

2016-01-01

Operational faults and behavioural anomalies associated with PLC control processes take place often in a manufacturing system. Real time identification of these operational faults and behavioural anomalies is necessary in the manufacturing industry. In this paper, we present an automated tool, called PLC Log-Data Analysis Tool (PLAT) that can detect them by using log-data records of the PLC signals. PLAT automatically creates a nominal model of the PLC control process and employs a novel hash table based indexing and searching scheme to satisfy those purposes. Our experiments show that PLAT is significantly fast, provides real time identification of operational faults and behavioural anomalies, and can execute within a small memory footprint. In addition, PLAT can easily handle a large manufacturing system with a reasonable computing configuration and can be installed in parallel to the data logging system to identify operational faults and behavioural anomalies effectively. PMID:27974882

Automating linear accelerator quality assurance.

PubMed

Eckhause, Tobias; Al-Hallaq, Hania; Ritter, Timothy; DeMarco, John; Farrey, Karl; Pawlicki, Todd; Kim, Gwe-Ya; Popple, Richard; Sharma, Vijeshwar; Perez, Mario; Park, SungYong; Booth, Jeremy T; Thorwarth, Ryan; Moran, Jean M

2015-10-01

The purpose of this study was 2-fold. One purpose was to develop an automated, streamlined quality assurance (QA) program for use by multiple centers. The second purpose was to evaluate machine performance over time for multiple centers using linear accelerator (Linac) log files and electronic portal images. The authors sought to evaluate variations in Linac performance to establish as a reference for other centers. The authors developed analytical software tools for a QA program using both log files and electronic portal imaging device (EPID) measurements. The first tool is a general analysis tool which can read and visually represent data in the log file. This tool, which can be used to automatically analyze patient treatment or QA log files, examines the files for Linac deviations which exceed thresholds. The second set of tools consists of a test suite of QA fields, a standard phantom, and software to collect information from the log files on deviations from the expected values. The test suite was designed to focus on the mechanical tests of the Linac to include jaw, MLC, and collimator positions during static, IMRT, and volumetric modulated arc therapy delivery. A consortium of eight institutions delivered the test suite at monthly or weekly intervals on each Linac using a standard phantom. The behavior of various components was analyzed for eight TrueBeam Linacs. For the EPID and trajectory log file analysis, all observed deviations which exceeded established thresholds for Linac behavior resulted in a beam hold off. In the absence of an interlock-triggering event, the maximum observed log file deviations between the expected and actual component positions (such as MLC leaves) varied from less than 1% to 26% of published tolerance thresholds. The maximum and standard deviations of the variations due to gantry sag, collimator angle, jaw position, and MLC positions are presented. Gantry sag among Linacs was 0.336 ± 0.072 mm. The standard deviation in MLC position, as determined by EPID measurements, across the consortium was 0.33 mm for IMRT fields. With respect to the log files, the deviations between expected and actual positions for parameters were small (<0.12 mm) for all Linacs. Considering both log files and EPID measurements, all parameters were well within published tolerance values. Variations in collimator angle, MLC position, and gantry sag were also evaluated for all Linacs. The performance of the TrueBeam Linac model was shown to be consistent based on automated analysis of trajectory log files and EPID images acquired during delivery of a standardized test suite. The results can be compared directly to tolerance thresholds. In addition, sharing of results from standard tests across institutions can facilitate the identification of QA process and Linac changes. These reference values are presented along with the standard deviation for common tests so that the test suite can be used by other centers to evaluate their Linac performance against those in this consortium.

NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers.

PubMed

Clos, Lawrence J; Jofre, M Fransisca; Ellinger, James J; Westler, William M; Markley, John L

2013-06-01

To facilitate the high-throughput acquisition of nuclear magnetic resonance (NMR) experimental data on large sets of samples, we have developed a simple and straightforward automated methodology that capitalizes on recent advances in Bruker BioSpin NMR spectrometer hardware and software. Given the daunting challenge for non-NMR experts to collect quality spectra, our goal was to increase user accessibility, provide customized functionality, and improve the consistency and reliability of resultant data. This methodology, NMRbot, is encoded in a set of scripts written in the Python programming language accessible within the Bruker BioSpin TopSpin ™ software. NMRbot improves automated data acquisition and offers novel tools for use in optimizing experimental parameters on the fly. This automated procedure has been successfully implemented for investigations in metabolomics, small-molecule library profiling, and protein-ligand titrations on four Bruker BioSpin NMR spectrometers at the National Magnetic Resonance Facility at Madison. The investigators reported benefits from ease of setup, improved spectral quality, convenient customizations, and overall time savings.

Recent Advances in Characterization of Lignin Polymer by Solution-State Nuclear Magnetic Resonance (NMR) Methodology

PubMed Central

Wen, Jia-Long; Sun, Shao-Long; Xue, Bai-Liang; Sun, Run-Cang

2013-01-01

The demand for efficient utilization of biomass induces a detailed analysis of the fundamental chemical structures of biomass, especially the complex structures of lignin polymers, which have long been recognized for their negative impact on biorefinery. Traditionally, it has been attempted to reveal the complicated and heterogeneous structure of lignin by a series of chemical analyses, such as thioacidolysis (TA), nitrobenzene oxidation (NBO), and derivatization followed by reductive cleavage (DFRC). Recent advances in nuclear magnetic resonance (NMR) technology undoubtedly have made solution-state NMR become the most widely used technique in structural characterization of lignin due to its versatility in illustrating structural features and structural transformations of lignin polymers. As one of the most promising diagnostic tools, NMR provides unambiguous evidence for specific structures as well as quantitative structural information. The recent advances in two-dimensional solution-state NMR techniques for structural analysis of lignin in isolated and whole cell wall states (in situ), as well as their applications are reviewed. PMID:28809313

Bayesian peak picking for NMR spectra.

PubMed

Cheng, Yichen; Gao, Xin; Liang, Faming

2014-02-01

Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein-DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method. Copyright © 2013. Production and hosting by Elsevier Ltd.

Emerging New Strategies for Successful Metabolite Identification in Metabolomics

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

Bingol, Ahmet K.; Bruschweiler-Li, Lei; Li, Dawei

2016-02-26

NMR is a very powerful tool for the identification of known and unknown (or unnamed) metabolites in complex mixtures as encountered in metabolomics. Known compounds can be reliably identified using 2D NMR methods, such as 13C-1H HSQC, for which powerful web servers with databases are available for semi-automated analysis. For the identification of unknown compounds, new combinations of NMR with MS have been developed recently that make synergistic use of the mutual strengths of the two techniques. The use of chemical additives to the NMR tube, such as reactive agents, paramagnetic ions, or charged silica nanoparticles, permit the identification ofmore » metabolites with specific physical chemical properties. In the following sections, we give an overview of some of the recent advances in metabolite identification and discuss remaining challenges.« less

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification.

PubMed

Beirnaert, Charlie; Meysman, Pieter; Vu, Trung Nghia; Hermans, Nina; Apers, Sandra; Pieters, Luc; Covaci, Adrian; Laukens, Kris

2018-03-01

Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping, thus avoiding the binning step. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using a simulated dataset and two publicly available datasets. speaq 2.0 is distributed through the existing speaq R package to provide a complete solution for NMR data processing. The package and the code for the presented case studies are freely available on CRAN (https://cran.r-project.org/package=speaq) and GitHub (https://github.com/beirnaert/speaq).

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification

PubMed Central

Pieters, Luc; Covaci, Adrian

2018-01-01

Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping, thus avoiding the binning step. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using a simulated dataset and two publicly available datasets. speaq 2.0 is distributed through the existing speaq R package to provide a complete solution for NMR data processing. The package and the code for the presented case studies are freely available on CRAN (https://cran.r-project.org/package=speaq) and GitHub (https://github.com/beirnaert/speaq). PMID:29494588

A dielectric logging tool with insulated collar for formation fluid detection around borehole

NASA Astrophysics Data System (ADS)

Wang, Bin; Li, Kang; Kong, Fan-Min; Zhao, Jia

2015-08-01

A dielectric tool with insulated collar for analyzing fluid saturation outside a borehole was introduced. The UWB (ultra-wideband) antenna mounted on the tool was optimized to launch a transient pulse. The broadband evaluation method provided more advantages when compared with traditional dielectric tools. The EM (electromagnetic) power distribution outside the borehole was studied, and it was shown that energy was propagated in two modes. Furthermore, the mechanism of the modes was discussed. In order to increase this tools' investigation depth, a novel insulated collar was introduced. In addition, operation in difference formations was discussed and this tool proved to be able to efficiently launch lateral EM waves. Response voltages indicated that the proposed scheme was able to evaluate the fluid saturation of reservoir formations and dielectric dispersion properties. It may be used as an alternative tool for imaging logging applications.

An Introduction to Biological NMR Spectroscopy*

PubMed Central

Marion, Dominique

2013-01-01

NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). PMID:23831612

Integrated Geophysical Measurements for Bioremediation Monitoring: Combining Spectral Induced Polarization, Nuclear Magnetic Resonance and Magnetic Methods

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

Keating, Kristina; Slater, Lee; Ntarlagiannis, Dimitris

2015-02-24

This documents contains the final report for the project "Integrated Geophysical Measurements for Bioremediation Monitoring: Combining Spectral Induced Polarization, Nuclear Magnetic Resonance and Magnetic Methods" (DE-SC0007049) Executive Summary: Our research aimed to develop borehole measurement techniques capable of monitoring subsurface processes, such as changes in pore geometry and iron/sulfur geochemistry, associated with remediation of heavy metals and radionuclides. Previous work has demonstrated that geophysical method spectral induced polarization (SIP) can be used to assess subsurface contaminant remediation; however, SIP signals can be generated from multiple sources limiting their interpretation value. Integrating multiple geophysical methods, such as nuclear magnetic resonance (NMR)more » and magnetic susceptibility (MS), with SIP, could reduce the ambiguity of interpretation that might result from a single method. Our research efforts entails combining measurements from these methods, each sensitive to different mineral forms and/or mineral-fluid interfaces, providing better constraints on changes in subsurface biogeochemical processes and pore geometries significantly improving our understanding of processes impacting contaminant remediation. The Rifle Integrated Field Research Challenge (IFRC) site was used as a test location for our measurements. The Rifle IFRC site is located at a former uranium ore-processing facility in Rifle, Colorado. Leachate from spent mill tailings has resulted in residual uranium contamination of both groundwater and sediments within the local aquifer. Studies at the site include an ongoing acetate amendment strategy, native microbial populations are stimulated by introduction of carbon intended to alter redox conditions and immobilize uranium. To test the geophysical methods in the field, NMR and MS logging measurements were collected before, during, and after acetate amendment. Next, laboratory NMR, MS, and SIP measurements were collected on columns of Rifle sediments during acetate amendment. The laboratory experiments were designed to simulate the field experiments; changes in geophysical signals were expected to correlate with changes in redox conditions and iron speciation. Field MS logging measurements revealed vertically stratified magnetic mineralization, likely the result of detrital magnetic fraction within the bulk alluvium. Little to no change was observed in the MS data suggesting negligible production of magnetic phases (e.g. magnetite, pyrrhotite) as a result of sulfidogenesis. Borehole NMR measurements contained high levels of noise contamination requiring significant signal processing, and analysis suggests that any changes may be difficult to differentiate from simultaneous changes in water content. Laboratory MS and NMR measurements remained relatively stable throughout the course of the acetate amendment experiment, consistent with field measurements. However, SIP measurements changed during the acetate amendment associated with the formation of iron-sulfide mineral phases; a finding that is consistent with chemical analysis of the solid phase materials in the columns.« less

Framework for Automation of Hazard Log Management on Large Critical Projects

NASA Astrophysics Data System (ADS)

Vinerbi, Lorenzo; Babu, Arun P.

2016-08-01

Hazard log is a database of all risk management activities in a project. Maintaining its correctness and consistency on large safety/mission critical projects involving multiple vendors, suppliers, and partners is critical and challenging. IBM DOORS is one of the popular tool used for hazard management in space applications. However, not all stake- holders are familiar with it. Also, It is not always feasible to expect all stake-holders to provide correct and consistent hazard data.The current work describes the process and tools to simplify the process of hazard data collection on large projects. It demonstrates how the collected data from all stake-holders is merged to form the hazard log while ensuring data consistency and correctness.The data provided by all parties are collected using a template containing scripts. The scripts check for mistakes based on internal standards of company in charge of hazard management. The collected data is then subjected to merging in DOORS, which also contain scripts to check and import data to form the hazard log. The proposed tool has been applied to a mission critical project, and has been found to save time and reduce the number of mistakes while creating the hazard log. The use of automatic checks paves the way for correct tracking of risk and hazard analysis activities for large critical projects.

The PsyLOG mobile application: development of a tool for the assessment and monitoring of side effects of psychotropic medication.

PubMed

Kuzman, Martina Rojnic; Andlauer, Olivier; Burmeister, Kai; Dvoracek, Boris; Lencer, Rebekka; Koelkebeck, Katja; Nawka, Alexander; Riese, Florian

2017-06-01

Mobile health interventions are regarded as affordable and accessible tools that can enhance standard psychiatric care. As part of the mHealth Psycho-Educational Intervention Versus Antipsychotic-Induced Side Effects (mPIVAS) project (www.psylog.eu), we developed the mobile application "PsyLOG" based on mobile "smartphone" technology to monitor antipsychotic-induced side effects. The aim of this paper is to describe the rationale and development of the PsyLOG and its clinical use. The PsyLOG application runs on smartphones with Android operating system. The application is currently available in seven languages (Croatian, Czech, English, French, German, Japanese and Serbian). It consists of several categories: "My Drug Effects", "My Life Styles", "My Charts", "My Medication", "My Strategies", "My Supporters", "Settings" and "About". The main category "My Drug Effects" includes a list of 30 side effects with the possibility to add three additional side effects. Side effects are each accompanied by an appropriate description and the possibility to rate its severity on a visual analogue scale from 0-100%. The PsyLOG application is intended to enhance the link between patients and mental health professionals, serving as a tool that more objectively monitors side-effects over certain periods of time. To the best of our knowledge, no such applications have so far been developed for patients taking antipsychotic medication or for their therapists.

HS.Register - An Audit-Trail Tool to Respond to the General Data Protection Regulation (GDPR).

PubMed

Gonçalves-Ferreira, Duarte; Leite, Mariana; Santos-Pereira, Cátia; Correia, Manuel E; Antunes, Luis; Cruz-Correia, Ricardo

2018-01-01

Introduction The new General Data Protection Regulation (GDPR) compels health care institutions and their software providers to properly document all personal data processing and provide clear evidence that their systems are inline with the GDPR. All applications involved in personal data processing should therefore produce meaningful event logs that can later be used for the effective auditing of complex processes. Aim This paper aims to describe and evaluate HS.Register, a system created to collect and securely manage at scale audit logs and data produced by a large number of systems. Methods HS.Register creates a single audit log by collecting and aggregating all kinds of meaningful event logs and data (e.g. ActiveDirectory, syslog, log4j, web server logs, REST, SOAP and HL7 messages). It also includes specially built dashboards for easy auditing and monitoring of complex processes, crossing different systems in an integrated way, as well as providing tools for helping on the auditing and on the diagnostics of difficult problems, using a simple web application. HS.Register is currently installed at five large Portuguese Hospitals and is composed of the following open-source components: HAproxy, RabbitMQ, Elasticsearch, Logstash and Kibana. Results HS.Register currently collects and analyses an average of 93 million events per week and it is being used to document and audit HL7 communications. Discussion Auditing tools like HS.Register are likely to become mandatory in the near future to allow for traceability and detailed auditing for GDPR compliance.

Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

NASA Astrophysics Data System (ADS)

Kupka, Teobald; Wieczorek, Piotr P.

2016-01-01

In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of 1H and 13C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.

Protein folding on the ribosome studied using NMR spectroscopy

PubMed Central

Waudby, Christopher A.; Launay, Hélène; Cabrita, Lisa D.; Christodoulou, John

2013-01-01

NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome–nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity. PMID:24083462

Active Wireline Heave Compensation for Ocean Drilling

NASA Astrophysics Data System (ADS)

Goldberg, D.; Liu, T.; Swain, K.; Furman, C.; Iturrino, G. J.

2014-12-01

The up-and-down heave motion of a ship causes a similar motion on any instruments tethered on wireline cable below it. If the amplitude of this motion is greater than a few tens of cm, significant discrepancy in the depth below the ship is introduced, causing uncertainty in the acquired data. Large and irregular cabled motions also increase the risk of damaging tethered instruments, particularly those with relatively delicate sensors. In 2005, Schlumberger and Deep Down, Inc built an active wireline heave compensator (AHC) system for use onboard the JOIDES Resolution to compensate for heave motion on wireline logging tools deployed in scientific drill holes. The goals for the new AHC system were to (1) design a reliable heave compensation system; and (2) devise a robust and quantitative methodology for routine assessment of compensation efficiency (CE) during wireline operations. Software programs were developed to monitor CE and the dynamics of logging tools in real-time, including system performance under variable parameters such as water depth, sea state, cable length, logging speed and direction. We present the CE results from the AHC system on the JOIDES Resolution during a 5-year period of recent IODP operations and compare the results to those from previous compensation systems deployed during ODP and IODP. Based on new data under heave conditions of ±0.2-2.0 m and water depths of 300-4,800 m in open holes, the system reduces 65-80% of downhole tool displacement under stationary conditions and 50-60% during normal logging operations. Moreover, down/up tool motion at low speeds (300-600 m/h) reduces the system's CE values by 15-20%, and logging down at higher speeds (1,000-1,200 m/h) reduces CE values by 55-65%. Furthermore, the system yields slightly lower CE values of 40-50% without tension feedback of the downhole cable while logging. These results indicate that the new system's compensation efficiency is comparable to or better than previous systems, with additional advantages that include upgradable compensation control software and the capability for continued assessment under varying environmental conditions. Future integration of downhole cable dynamics as an input feedback could further improve CE during logging operations.­

10 CFR 39.69 - Radioactive contamination control.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Radiation Safety Requirements § 39.69 Radioactive contamination control. (a) If the licensee detects... licensee shall continuously monitor, with an appropriate radiation detection instrument or a logging tool...

10 CFR 39.69 - Radioactive contamination control.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Radiation Safety Requirements § 39.69 Radioactive contamination control. (a) If the licensee detects... licensee shall continuously monitor, with an appropriate radiation detection instrument or a logging tool...

10 CFR 39.69 - Radioactive contamination control.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Radiation Safety Requirements § 39.69 Radioactive contamination control. (a) If the licensee detects... licensee shall continuously monitor, with an appropriate radiation detection instrument or a logging tool...

10 CFR 39.69 - Radioactive contamination control.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Radiation Safety Requirements § 39.69 Radioactive contamination control. (a) If the licensee detects... licensee shall continuously monitor, with an appropriate radiation detection instrument or a logging tool...

10 CFR 39.69 - Radioactive contamination control.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Radiation Safety Requirements § 39.69 Radioactive contamination control. (a) If the licensee detects... licensee shall continuously monitor, with an appropriate radiation detection instrument or a logging tool...

The Design Log: A New Informational Tool

ERIC Educational Resources Information Center

Spivak, Mayer

1978-01-01

The design log is a record of observations, diagnoses, prescriptions, and performance specifications for each space in a structure. It is a systematic approach to design that integrates information about user needs with traditional architectural programming and design. (Author/MLF)

Portable acuity screening for any school: validation of patched HOTV with amblyopic patients and Bangerter normals.

PubMed

Tsao Wu, Maya; Armitage, M Diane; Trujillo, Claire; Trujillo, Anna; Arnold, Laura E; Tsao Wu, Lauren; Arnold, Robert W

2017-12-04

We needed to validate and calibrate our portable acuity screening tools so amblyopia could be detected quickly and effectively at school entry. Spiral-bound flip cards and download pdf surround HOTV acuity test box with critical lines were combined with a matching card. Amblyopic patients performed critical line, then threshold acuity which was then compared to patched E-ETDRS acuity. 5 normal subjects wore Bangerter foil goggles to simulate blur for comparative validation. The 31 treated amblyopic eyes showed: logMAR HOTV = 0.97(logMAR E-ETDRS)-0.04 r2 = 0.88. All but two (6%) fell less than 2 lines difference. The five showed logMAR HOTV = 1.09 ((logMAR E-ETDRS) + .15 r2 = 0.63. The critical-line, test box was 98% efficient at screening within one line of 20/40. These tools reliably detected acuity in treated amblyopic patients and Bangerter blurred normal subjects. These free and affordable tools provide sensitive screening for amblyopia in children from public, private and home schools. Changing "pass" criteria to 4 out of 5 would improve sensitivity with somewhat slower testing for all students.

Acoustic testing to enhance western forest values and meet customer wood quality needs

Treesearch

Peter Carter; David Briggs; Robert J. Ross; Xiping Wang

2005-01-01

Nondestructive testing (NDT) of wood products, such as lumber and veneer, for stiffness and strength evaluation has been proven and commercialized for many years. The NDT concept has been extended and commercialized in the Director HM-200™ tool for testing logs in advance of processing so manufacturers can make more informed log purchases and better match logs to...

Well logging evaporative thermal protection system

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

Lamers, M.D.; Martelli, V.P.

1981-02-03

An evaporative thermal protection system for use in hostile environment well logging applications, the system including a downhole thermal protection cartridge disposed within a well logging sonde or tool to keep a payload such as sensors and support electronics cool, the cartridge carrying either an active evaporative system for refrigeration or a passive evaporative system, both exhausting to the surface through an armored flexible fluidic communication mechanical cable.

Measuring ecological impacts from logging in natural forests of the eastern Amazonia as a tool to assess forest degradation

Treesearch

Marco W Lentini; Johan C Zweede; Thomas P Holmes

2010-01-01

Sound forest management practices have been seen as an interesting strategy to ally forest conservation and rural economic development in Amazônia. However, the implementation of Reduced Impact Logging (RIL) techniques in the field has been incipient, while most of the Amazonian timber production is generated through predatory and illegal logging. Despite several...

A method to evaluate hydraulic fracture using proppant detection.

PubMed

Liu, Juntao; Zhang, Feng; Gardner, Robin P; Hou, Guojing; Zhang, Quanying; Li, Hu

2015-11-01

Accurate determination of the proppant placement and propped fracture height are important for evaluating and optimizing stimulation strategies. A technology using non-radioactive proppant and a pulsed neutron gamma energy spectra logging tool to determine the placement and height of propped fractures is proposed. Gd2O3 was incorporated into ceramic proppant and a Monte Carlo method was utilized to build the logging tools and formation models. Characteristic responses of the recorded information of different logging tools to fracture widths, proppant concentrations and influencing factors were studied. The results show that Gd capture gamma rays can be used to evaluate propped fractures and it has higher sensitivity to the change of fracture width and traceable proppant content compared with the exiting non-radioactive proppant evaluation techniques and only an after-fracture measurement is needed for the new method; The changes in gas saturation and borehole size have a great impact on determining propped fractures when compensated neutron and pulsed neutron capture tool are used. A field example is presented to validate the application of the new technique. Copyright © 2015 Elsevier Ltd. All rights reserved.

Assessing Competencies Needed to Engage With Digital Health Services: Development of the eHealth Literacy Assessment Toolkit.

PubMed

Karnoe, Astrid; Furstrand, Dorthe; Christensen, Karl Bang; Norgaard, Ole; Kayser, Lars

2018-05-10

To achieve full potential in user-oriented eHealth projects, we need to ensure a match between the eHealth technology and the user's eHealth literacy, described as knowledge and skills. However, there is a lack of multifaceted eHealth literacy assessment tools suitable for screening purposes. The objective of our study was to develop and validate an eHealth literacy assessment toolkit (eHLA) that assesses individuals' health literacy and digital literacy using a mix of existing and newly developed scales. From 2011 to 2015, scales were continuously tested and developed in an iterative process, which led to 7 tools being included in the validation study. The eHLA validation version consisted of 4 health-related tools (tool 1: "functional health literacy," tool 2: "health literacy self-assessment," tool 3: "familiarity with health and health care," and tool 4: "knowledge of health and disease") and 3 digitally-related tools (tool 5: "technology familiarity," tool 6: "technology confidence," and tool 7: "incentives for engaging with technology") that were tested in 475 respondents from a general population sample and an outpatient clinic. Statistical analyses examined floor and ceiling effects, interitem correlations, item-total correlations, and Cronbach coefficient alpha (CCA). Rasch models (RM) examined the fit of data. Tools were reduced in items to secure robust tools fit for screening purposes. Reductions were made based on psychometrics, face validity, and content validity. Tool 1 was not reduced in items; it consequently consists of 10 items. The overall fit to the RM was acceptable (Anderson conditional likelihood ratio, CLR=10.8; df=9; P=.29), and CCA was .67. Tool 2 was reduced from 20 to 9 items. The overall fit to a log-linear RM was acceptable (Anderson CLR=78.4, df=45, P=.002), and CCA was .85. Tool 3 was reduced from 23 to 5 items. The final version showed excellent fit to a log-linear RM (Anderson CLR=47.7, df=40, P=.19), and CCA was .90. Tool 4 was reduced from 12 to 6 items. The fit to a log-linear RM was acceptable (Anderson CLR=42.1, df=18, P=.001), and CCA was .59. Tool 5 was reduced from 20 to 6 items. The fit to the RM was acceptable (Anderson CLR=30.3, df=17, P=.02), and CCA was .94. Tool 6 was reduced from 5 to 4 items. The fit to a log-linear RM taking local dependency (LD) into account was acceptable (Anderson CLR=26.1, df=21, P=.20), and CCA was .91. Tool 7 was reduced from 6 to 4 items. The fit to a log-linear RM taking LD and differential item functioning into account was acceptable (Anderson CLR=23.0, df=29, P=.78), and CCA was .90. The eHLA consists of 7 short, robust scales that assess individual's knowledge and skills related to digital literacy and health literacy. ©Astrid Karnoe, Dorthe Furstrand, Karl Bang Christensen, Ole Norgaard, Lars Kayser. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 10.05.2018.

Fragment-Linking Approach Using (19)F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of β-Secretase.

PubMed

Jordan, John B; Whittington, Douglas A; Bartberger, Michael D; Sickmier, E Allen; Chen, Kui; Cheng, Yuan; Judd, Ted

2016-04-28

Fragment-based drug discovery (FBDD) has become a widely used tool in small-molecule drug discovery efforts. One of the most commonly used biophysical methods in detecting weak binding of fragments is nuclear magnetic resonance (NMR) spectroscopy. In particular, FBDD performed with (19)F NMR-based methods has been shown to provide several advantages over (1)H NMR using traditional magnetization-transfer and/or two-dimensional methods. Here, we demonstrate the utility and power of (19)F-based fragment screening by detailing the identification of a second-site fragment through (19)F NMR screening that binds to a specific pocket of the aspartic acid protease, β-secretase (BACE-1). The identification of this second-site fragment allowed the undertaking of a fragment-linking approach, which ultimately yielded a molecule exhibiting a more than 360-fold increase in potency while maintaining reasonable ligand efficiency and gaining much improved selectivity over cathepsin-D (CatD). X-ray crystallographic studies of the molecules demonstrated that the linked fragments exhibited binding modes consistent with those predicted from the targeted screening approach, through-space NMR data, and molecular modeling.

NMR studies of the incommensurate helical antiferromagnet EuCo 2 P 2 : Determination of antiferromagnetic propagation vector

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

Higa, Nonoka; Ding, Qing -Ping; Yogi, Mamoru

Recently, Q.-P. Ding et al. reported that their nuclear magnetic resonance (NMR) study on EuCo 2As 2 successfully characterized the antiferromagnetic (AFM) propagation vector of the incommensurate helix AFM state, showing that NMR is a unique tool for determination of the spin structures in incommensurate helical AFMs. Motivated by this work, we have carried out 153Eu, 31P, and 59Co NMR measurements on the helical antiferromagnet EuCo 2P 2 with an AFM ordering temperature T N = 66.5 K. An incommensurate helical AFM structure was clearly confirmed by 153Eu and 31P NMR spectra on single-crystalline EuCo 2P 2 in zero magneticmore » field at 1.6 K and its external magnetic field dependence. Furthermore, based on 59Co NMR data in both the paramagnetic and incommensurate AFM states, we have determined the model-independent value of the AFM propagation vector k = (0,0,0.73±0.09)2π/c, where c is the c-axis lattice parameter. As a result, the temperature dependence of k is also discussed.« less

NMR studies of the incommensurate helical antiferromagnet EuCo 2 P 2 : Determination of antiferromagnetic propagation vector

DOE PAGES

Higa, Nonoka; Ding, Qing -Ping; Yogi, Mamoru; ...

2017-07-06

Recently, Q.-P. Ding et al. reported that their nuclear magnetic resonance (NMR) study on EuCo 2As 2 successfully characterized the antiferromagnetic (AFM) propagation vector of the incommensurate helix AFM state, showing that NMR is a unique tool for determination of the spin structures in incommensurate helical AFMs. Motivated by this work, we have carried out 153Eu, 31P, and 59Co NMR measurements on the helical antiferromagnet EuCo 2P 2 with an AFM ordering temperature T N = 66.5 K. An incommensurate helical AFM structure was clearly confirmed by 153Eu and 31P NMR spectra on single-crystalline EuCo 2P 2 in zero magneticmore » field at 1.6 K and its external magnetic field dependence. Furthermore, based on 59Co NMR data in both the paramagnetic and incommensurate AFM states, we have determined the model-independent value of the AFM propagation vector k = (0,0,0.73±0.09)2π/c, where c is the c-axis lattice parameter. As a result, the temperature dependence of k is also discussed.« less

Understanding Unimer Exchange Processes in Block Copolymer Micelles using NMR Diffusometry, Time-Resolved NMR, and SANS

NASA Astrophysics Data System (ADS)

Madsen, Louis; Kidd, Bryce; Li, Xiuli; Miller, Katherine; Cooksey, Tyler; Robertson, Megan

Our team seeks to understand dynamic behaviors of block copolymer micelles and their interplay with encapsulated cargo molecules. Quantifying unimer and cargo exchange rates micelles can provide critical information for determining mechanisms of unimer exchange as well as designing systems for specific cargo release dynamics. We are exploring the utility of NMR spectroscopy and diffusometry techniques as complements to existing SANS and fluorescence methods. One promising new method involves time-resolved NMR spin relaxation measurements, wherein mixing of fully protonated and 2H-labeled PEO-b-PCL micelles solutions shows an increase in spin-lattice relaxation time (T1) with time after mixing. This is due to a weakening in magnetic environment surrounding 1H spins as 2H-bearing unimers join fully protonated micelles. We are measuring time constants for unimer exchange of minutes to hours, and we expect to resolve times of <1 min. This method can work on any solution NMR spectrometer and with minimal perturbation to chemical structure (as in dye-labelled fluorescence methods). Multimodal NMR can complement existing characterization tools, expanding and accelerating dynamics measurements for polymer micelle, nanogel, and nanoparticle developers.

Bacterial cell wall composition and the influence of antibiotics by cell-wall and whole-cell NMR

PubMed Central

Romaniuk, Joseph A. H.; Cegelski, Lynette

2015-01-01

The ability to characterize bacterial cell-wall composition and structure is crucial to understanding the function of the bacterial cell wall, determining drug modes of action and developing new-generation therapeutics. Solid-state NMR has emerged as a powerful tool to quantify chemical composition and to map cell-wall architecture in bacteria and plants, even in the context of unperturbed intact whole cells. In this review, we discuss solid-state NMR approaches to define peptidoglycan composition and to characterize the modes of action of old and new antibiotics, focusing on examples in Staphylococcus aureus. We provide perspectives regarding the selected NMR strategies as we describe the exciting and still-developing cell-wall and whole-cell NMR toolkit. We also discuss specific discoveries regarding the modes of action of vancomycin analogues, including oritavancin, and briefly address the reconsideration of the killing action of β-lactam antibiotics. In such chemical genetics approaches, there is still much to be learned from perturbations enacted by cell-wall assembly inhibitors, and solid-state NMR approaches are poised to address questions of cell-wall composition and assembly in S. aureus and other organisms. PMID:26370936

A dynamic nuclear polarization strategy for multi-dimensional Earth's field NMR spectroscopy.

PubMed

Halse, Meghan E; Callaghan, Paul T

2008-12-01

Dynamic nuclear polarization (DNP) is introduced as a powerful tool for polarization enhancement in multi-dimensional Earth's field NMR spectroscopy. Maximum polarization enhancements, relative to thermal equilibrium in the Earth's magnetic field, are calculated theoretically and compared to the more traditional prepolarization approach for NMR sensitivity enhancement at ultra-low fields. Signal enhancement factors on the order of 3000 are demonstrated experimentally using DNP with a nitroxide free radical, TEMPO, which contains an unpaired electron which is strongly coupled to a neighboring (14)N nucleus via the hyperfine interaction. A high-quality 2D (19)F-(1)H COSY spectrum acquired in the Earth's magnetic field with DNP enhancement is presented and compared to simulation.

High-resolution NMR spectroscopy of encapsulated proteins dissolved in low-viscosity fluids

PubMed Central

Nucci, Nathaniel V.; Valentine, Kathleen G.; Wand, A. Joshua

2014-01-01

High-resolution multi-dimensional solution NMR is unique as a biophysical and biochemical tool in its ability to examine both the structure and dynamics of macromolecules at atomic resolution. Conventional solution NMR approaches, however, are largely limited to examinations of relatively small (< 25 kDa) molecules, mostly due to the spectroscopic consequences of slow rotational diffusion. Encapsulation of macromolecules within the protective nanoscale aqueous interior of reverse micelles dissolved in low viscosity fluids has been developed as a means through which the ‘slow tumbling problem’ can be overcome. This approach has been successfully applied to diverse proteins and nucleic acids ranging up to 100 kDa, considerably widening the range of biological macromolecules to which conventional solution NMR methodologies may be applied. Recent advances in methodology have significantly broadened the utility of this approach in structural biology and molecular biophysics. PMID:24656086

In vivo nuclear magnetic resonance imaging

NASA Technical Reports Server (NTRS)

Leblanc, A.; Evans, H.; Bryan, R. N.; Johnson, P.; Schonfeld, E.; Jhingran, S. G.

1984-01-01

A number of physiological changes have been demonstrated in bone, muscle and blood after exposure of humans and animals to microgravity. Determining mechanisms and the development of effective countermeasures for long duration space missions is an important NASA goal. The advent of tomographic nuclear magnetic resonance imaging (NMR or MRI) gives NASA a way to greatly extend early studies of this phenomena in ways not previously possible; NMR is also noninvasive and safe. NMR provides both superb anatomical images for volume assessments of individual organs and quantification of chemical/physical changes induced in the examined tissues. The feasibility of NMR as a tool for human physiological research as it is affected by microgravity is demonstrated. The animal studies employed the rear limb suspended rat as a model of mucle atrophy that results from microgravity. And bedrest of normal male subjects was used to simulate the effects of microgravity on bone and muscle.

Optimization of cell disruption methods for efficient recovery of bioactive metabolites via NMR of three freshwater microalgae (chlorophyta).

PubMed

Ma, Nyuk Ling; Teh, Kit Yinn; Lam, Su Shiung; Kaben, Anne Marie; Cha, Thye San

2015-08-01

This study demonstrates the use of NMR techniques coupled with chemometric analysis as a high throughput data mining method to identify and examine the efficiency of different disruption techniques tested on microalgae (Chlorella variabilis, Scenedesmus regularis and Ankistrodesmus gracilis). The yield and chemical diversity from the disruptions together with the effects of pre-oven and pre-freeze drying prior to disruption techniques were discussed. HCl extraction showed the highest recovery of oil compounds from the disrupted microalgae (up to 90%). In contrast, NMR analysis showed the highest intensity of bioactive metabolites obtained for homogenized extracts pre-treated with freeze-drying, indicating that homogenizing is a more favorable approach to recover bioactive substances from the disrupted microalgae. The results show the potential of NMR as a useful metabolic fingerprinting tool for assessing compound diversity in complex microalgae extracts. Copyright © 2015 Elsevier Ltd. All rights reserved.

Two-dimensional nuclear magnetic resonance structure determination module for introductory biochemistry: synthesis and structural characterization of lyso-glycerophospholipids.

PubMed

Garrett, Teresa A; Rose, Rebecca L; Bell, Sidney M

2013-01-01

In this laboratory module, introductory biochemistry students are exposed to two-dimensional (1) H-nuclear magnetic resonance of glycerophospholipids (GPLs). Working in groups of three, students enzymatically synthesized and purified a variety of 2-acyl lyso GPLs. The structure of the 2-acyl lyso GPL was verified using (1) H-correlation spectroscopy. Students scored significantly higher on an assessment of NMR knowledge after having participated in this lab module and in comparison to a similar cohort who did not participate. Inaddition, student confidence in their NMR knowledge and abilities increased 62% following the module and correlated with their ability to apply their NMR knowledge. Based on these results, the laboratory module was very effective at providing students with a more extensive understanding of the underlying concepts of NMR as a tool for structural determination. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Combined In Situ Illumination-NMR-UV/Vis Spectroscopy: A New Mechanistic Tool in Photochemistry.

PubMed

Seegerer, Andreas; Nitschke, Philipp; Gschwind, Ruth M

2018-06-18

Synthetic applications in photochemistry are booming. Despite great progress in the development of new reactions, mechanistic investigations are still challenging. Therefore, we present a fully automated in situ combination of NMR spectroscopy, UV/Vis spectroscopy, and illumination to allow simultaneous and time-resolved detection of paramagnetic and diamagnetic species. This optical fiber-based setup enables the first acquisition of combined UV/Vis and NMR spectra in photocatalysis, as demonstrated on a conPET process. Furthermore, the broad applicability of combined UVNMR spectroscopy for light-induced processes is demonstrated on a structural and quantitative analysis of a photoswitch, including rate modulation and stabilization of transient species by temperature variation. Owing to the flexibility regarding the NMR hardware, temperature, and light sources, we expect wide-ranging applications of this setup in various research fields. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.

PubMed

Kuhn, Stefan; Schlörer, Nils E

2015-08-01

nmrshiftdb2 supports with its laboratory information management system the integration of an electronic lab administration and management into academic NMR facilities. Also, it offers the setup of a local database, while full access to nmrshiftdb2's World Wide Web database is granted. This freely available system allows on the one hand the submission of orders for measurement, transfers recorded data automatically or manually, and enables download of spectra via web interface, as well as the integrated access to prediction, search, and assignment tools of the NMR database for lab users. On the other hand, for the staff and lab administration, flow of all orders can be supervised; administrative tools also include user and hardware management, a statistic functionality for accounting purposes, and a 'QuickCheck' function for assignment control, to facilitate quality control of assignments submitted to the (local) database. Laboratory information management system and database are based on a web interface as front end and are therefore independent of the operating system in use. Copyright © 2015 John Wiley & Sons, Ltd.

Observations from borehole dilution logging experiments in fractured crystalline rock under variable hydraulic conditions

USGS Publications Warehouse

Harte, Philip T.; Anderson, Alton; Williams, John H.

2014-01-01

Identifying hydraulically active fractures in low permeability, crystalline-bedrock aquifers requires a variety of geophysical and hydrogeophysical borehole tools and approaches. One such approach is Single Borehole Dilution Tests (SBDT), which in some low flow cases have been shown to provide greater resolution of borehole flow than other logging procedures, such as vertical differential Heat Pulse Flowmeter (HPFM) logging. Because the tools used in SBDT collect continuous profiles of water quality or dye changes, they can identify horizontal flow zones and vertical flow. We used SBDT with a food grade blue dye as a tracer and dual photometer-nephelometer measurements to identify low flow zones.SBDT were conducted at seven wells with open boreholes (exceeding 300 ft). At most of the wells HPFM logs were also collected. The seven wells are set in low-permeability, fractured granite and gneiss rocks underlying a former tetrachloroeythylene (PCE) source area at the Savage Municipal Well Superfund site in Milford, NH. Time series SBDT logs were collected at each of the seven wells under three distinct hydraulic conditions: (1) ambient conditions prior to a pump test at an adjacent well, (2) mid test, after 2-3 days of the start of the pump test, and (3) at the end of the test, after 8-9 days of the pump test. None of the SBDT were conducted under pumping conditions in the logged well. For each condition, wells were initially passively spiked with blue dye once and subsequent time series measurements were made.Measurement accuracy and precision of the photometer tool is important in SBDT when attempting to detect low rates of borehole flow. Tests indicate that under ambient conditions, none of the wells had detectable flow as measured with HPFM logging. With SBDT, 4 of the 7 showed the presence of some very low flow. None of 5 (2 of the 7 wells initially logged with HPFM under ambient conditions were not re-logged) wells logged with the HPFM during the pump test had detectable flow. However, 3 of the 5 wells showed the patterns of very low flow with SBDT during the pump test including pumping induced changes of inflow and outflow patterns at one well.

The PAW/GIPAW approach for computing NMR parameters: a new dimension added to NMR study of solids.

PubMed

Charpentier, Thibault

2011-07-01

In 2001, Mauri and Pickard introduced the gauge including projected augmented wave (GIPAW) method that enabled for the first time the calculation of all-electron NMR parameters in solids, i.e. accounting for periodic boundary conditions. The GIPAW method roots in the plane wave pseudopotential formalism of the density functional theory (DFT), and avoids the use of the cluster approximation. This method has undoubtedly revitalized the interest in quantum chemical calculations in the solid-state NMR community. It has quickly evolved and improved so that the calculation of the key components of NMR interactions, namely the shielding and electric field gradient tensors, has now become a routine for most of the common nuclei studied in NMR. Availability of reliable implementations in several software packages (CASTEP, Quantum Espresso, PARATEC) make its usage more and more increasingly popular, maybe indispensable in near future for all material NMR studies. The majority of nuclei of the periodic table have already been investigated by GIPAW, and because of its high accuracy it is quickly becoming an essential tool for interpreting and understanding experimental NMR spectra, providing reliable assignments of the observed resonances to crystallographic sites or enabling a priori prediction of NMR data. The continuous increase of computing power makes ever larger (and thus more realistic) systems amenable to first-principles analysis. In the near future perspectives, as the incorporation of dynamical effects and/or disorder are still at their early developments, these areas will certainly be the prime target. Copyright © 2011 Elsevier Inc. All rights reserved.

Geophysical Parameter Estimation of Near Surface Materials Using Nuclear Magnetic Resonance

NASA Astrophysics Data System (ADS)

Keating, K.

2017-12-01

Proton nuclear magnetic resonance (NMR), a mature geophysical technology used in petroleum applications, has recently emerged as a promising tool for hydrogeophysicists. The NMR measurement, which can be made in the laboratory, in boreholes, and using a surface based instrument, are unique in that it is directly sensitive to water, via the initial signal magnitude, and thus provides a robust estimate of water content. In the petroleum industry rock physics models have been established that relate NMR relaxation times to pore size distributions and permeability. These models are often applied directly for hydrogeophysical applications, despite differences in the material in these two environments (e.g., unconsolidated versus consolidated, and mineral content). Furthermore, the rock physics models linking NMR relaxation times to pore size distributions do not account for partially saturated systems that are important for understanding flow in the vadose zone. In our research, we are developing and refining quantitative rock physics models that relate NMR parameters to hydrogeological parameters. Here we highlight the limitations of directly applying established rock physics models to estimate hydrogeological parameters from NMR measurements, and show some of the successes we have had in model improvement. Using examples drawn from both laboratory and field measurements, we focus on the use of NMR in partial saturated systems to estimate water content, pore-size distributions, and the water retention curve. Despite the challenges in interpreting the measurements, valuable information about hydrogeological parameters can be obtained from NMR relaxation data, and we conclude by outlining pathways for improving the interpretation of NMR data for hydrogeophysical investigations.

A possible glycosidic benzophenone with full substitution on B-ring from Psidium guajava leaves.

PubMed

Venditti, Alessandro; Ukwueze, Stanley E

2017-04-01

Bidimensional NMR analysis may be a useful tool to resolve the structure of chemical compounds also in mixture. This letter would demonstrate how these techniques could be applied e.g. to the reported case on identification of benzophenone glycoside from Psidium guajava. A tentative structure for the secondary component, not yet described, was possibly proposed on the basis of observation and critic review of available 1D and 2D NMR spectra.

Automatic differential analysis of NMR experiments in complex samples.

PubMed

Margueritte, Laure; Markov, Petar; Chiron, Lionel; Starck, Jean-Philippe; Vonthron-Sénécheau, Catherine; Bourjot, Mélanie; Delsuc, Marc-André

2018-06-01

Liquid state nuclear magnetic resonance (NMR) is a powerful tool for the analysis of complex mixtures of unknown molecules. This capacity has been used in many analytical approaches: metabolomics, identification of active compounds in natural extracts, and characterization of species, and such studies require the acquisition of many diverse NMR measurements on series of samples. Although acquisition can easily be performed automatically, the number of NMR experiments involved in these studies increases very rapidly, and this data avalanche requires to resort to automatic processing and analysis. We present here a program that allows the autonomous, unsupervised processing of a large corpus of 1D, 2D, and diffusion-ordered spectroscopy experiments from a series of samples acquired in different conditions. The program provides all the signal processing steps, as well as peak-picking and bucketing of 1D and 2D spectra, the program and its components are fully available. In an experiment mimicking the search of a bioactive species in a natural extract, we use it for the automatic detection of small amounts of artemisinin added to a series of plant extracts and for the generation of the spectral fingerprint of this molecule. This program called Plasmodesma is a novel tool that should be useful to decipher complex mixtures, particularly in the discovery of biologically active natural products from plants extracts but can also in drug discovery or metabolomics studies. Copyright © 2017 John Wiley & Sons, Ltd.

Development of an 19F NMR method for the analysis of fluorinated acids in environmental water samples.

PubMed

Ellis, D A; Martin, J W; Muir, D C; Mabury, S A

2000-02-15

This investigation was carried out to evaluate 19F NMR as an analytical tool for the measurement of trifluoroacetic acid (TFA) and other fluorinated acids in the aquatic environment. A method based upon strong anionic exchange (SAX) chromatography was also optimized for the concentration of the fluoro acids prior to NMR analysis. Extraction of the analyte from the SAX column was carried out directly in the NMR solvent in the presence of the strong organic base, DBU. The method allowed the analysis of the acid without any prior cleanup steps being involved. Optimal NMR sensitivity based upon T1 relaxation times was investigated for seven fluorinated compounds in four different NMR solvents. The use of the relaxation agent chromium acetylacetonate, Cr(acac)3, within these solvent systems was also evaluated. Results show that the optimal NMR solvent differs for each fluorinated analyte. Cr(acac)3 was shown to have pronounced effects on the limits of detection of the analyte. Generally, the optimal sensitivity condition appears to be methanol-d4/2M DBU in the presence of 4 mg/mL of Cr-(acac)3. The method was validated through spike and recovery for five fluoro acids from environmentally relevant waters. Results are presented for the analysis of TFA in Toronto rainwater, which ranged from < 16 to 850 ng/L. The NMR results were confirmed by GC-MS selected-ion monitoring of the fluoroanalide derivative.

Modeling CO 2 Sequestration in Saline Aquifer and Depleted Oil Reservoir To Evaluate Regional CO 2 Sequestration Potential of Ozark Plateau Aquifer System, South-Central Kansas

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

Watney, W. Lynn

2014-09-30

1. Drilled, cored, and logged three wells to the basement and collecting more than 2,700 ft of conventional core; obtained 20 m i2 of multicomponent 3D seismic imaging and merged and reprocessed more than 125 mi 2 of existing 3D seismic data for use in modeling CO 2- EOR oil recovery and CO 2 storage in five oil fields in southern Kansas. 2. Determined the technical feasibility of injecting and sequestering CO 2 in a set of four depleted oil reservoirs in the Cutter, Pleasant Prairie South, Eubank, and Shuck fields in southwest Kansas; of concurrently recovering oil from thosemore » fields; and of quantifying the volumes of CO2 sequestered and oil recovered during the process. 3. Formed a consortium of six oil operating companies, five of which own and operate the four fields. The consortium became part of the Southwest Kansas CO 2-EOR Initiative for the purpose of sharing data, knowledge, and interest in understanding the potential for CO 2-EOR in Kansas. 4. Built a regional well database covering 30,000 mi 2 and containing stratigraphic tops from ~90,000 wells; correlated 30 major stratigraphic horizons; digitized key wells, including wireline logs and sample logs; and analyzed more than 3,000 drill stem tests to establish that fluid levels in deep aquifers below the Permian evaporites are not connected to the surface and therefore pressures are not hydrostatic. Connectivity with the surface aquifers is lacking because shale aquitards and impermeable evaporite layers consist of both halite and anhydrite. 5. Developed extensive web applications and an interactive mapping system that do the following: a. Facilitate access to a wide array of data obtained in the study, including core descriptions and analyses, sample logs, digital (LAS) well logs, seismic data, gravity and magnetics maps, structural and stratigraphic maps, inferred fault traces, earthquakes, Class I and II disposal wells, and surface lineaments. b. Provide real-time analysis of the project dataset, including automated integration and viewing of well logs, core, core analyses, brine chemistry, and stratigraphy using the Java Profile app. A cross-section app allows for the display of log data for up to four wells at a time. 6. Integrated interpretations from the project’s interactive web-based mapping system to gain insights to aid in assessing the efficacy of geologic CO 2 storage in Kansas and insights toward understanding recent seismicity to aid in evaluating induced vs. naturally occurring earthquakes. 7. Developed a digital type-log system, including web-based software to modify and refine stratigraphic nomenclature to provide stakeholders a common means for communication about the subsurface. 8. Contracted use of a nuclear magnetic resonance (NMR) log and ran it slowly to capture response and characterize larger pores common for carbonate reservoirs. Used NMR to extend core analyses to apply permeability, relative permeability to CO 2, and capillary pressure to the major rock types, each uniquely expressed as a reservoir quality index (RQI), present in the Mississippian and Arbuckle rocks. 9. Characterized and evaluated the possible role of microbes in dense brines. Used microbes to compliment H/O stable isotopes to fingerprint brine systems. Used perforation/swabbing to obtain samples from multiple hydrostratigraphic units and confirmed equivalent results using less expensive drill stem tests (DST). 10. Used an integrated approach from whole core, logs, tests, and seismic to verify and quantify properties of vuggy, brecciated, and fractured carbonate intervals. 11. Used complex geocellular static and dynamic models to evaluate regional storage capacity using large parallel processing. 12. Carbonates are complex reservoirs and CO 2-EOR needs to move to the next generation to increase effectiveness of CO 2 and efficiency and safety of the injection.« less

High-resolution well-log derived dielectric properties of gas-hydrate-bearing sediments, Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

USGS Publications Warehouse

Sun, Y.; Goldberg, D.; Collett, T.; Hunter, R.

2011-01-01

A dielectric logging tool, electromagnetic propagation tool (EPT), was deployed in 2007 in the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well (Mount Elbert Well), North Slope, Alaska. The measured dielectric properties in the Mount Elbert well, combined with density log measurements, result in a vertical high-resolution (cm-scale) estimate of gas hydrate saturation. Two hydrate-bearing sand reservoirs about 20 m thick were identified using the EPT log and exhibited gas-hydrate saturation estimates ranging from 45% to 85%. In hydrate-bearing zones where variation of hole size and oil-based mud invasion are minimal, EPT-based gas hydrate saturation estimates on average agree well with lower vertical resolution estimates from the nuclear magnetic resonance logs; however, saturation and porosity estimates based on EPT logs are not reliable in intervals with substantial variations in borehole diameter and oil-based invasion.EPT log interpretation reveals many thin-bedded layers at various depths, both above and below the thick continuous hydrate occurrences, which range from 30-cm to about 1-m thick. Such thin layers are not indicated in other well logs, or from the visual observation of core, with the exception of the image log recorded by the oil-base microimager. We also observe that EPT dielectric measurements can be used to accurately detect fine-scale changes in lithology and pore fluid properties of hydrate-bearing sediments where variation of hole size is minimal. EPT measurements may thus provide high-resolution in-situ hydrate saturation estimates for comparison and calibration with laboratory analysis. ?? 2010 Elsevier Ltd.

Defining genetic and chemical diversity in wheat grain by 1H‐NMR spectroscopy of polar metabolites

PubMed Central

Corol, Delia I.; Jones, Huw D.; Beale, Michael H.; Ward, Jane L.

2017-01-01

Scope The application of high‐throughput 1H nuclear magnetic resonance (1H‐NMR) of unpurified extracts to determine genetic diversity and the contents of polar components in grain of wheat. Methods and results Milled whole wheat grain was extracted with 80:20 D2O:CD3OD containing 0.05% d4–trimethylsilylpropionate. 1H‐NMR spectra were acquired under automation at 300°K using an Avance Spectrometer operating at 600.0528 MHz. Regions for individual metabolites were identified by comparison to a library of known standards run under identical conditions. The individual 1H‐NMR peaks or levels of known metabolites were then compared by Principal Component Analysis using SIMCA‐P software. Conclusions High‐throughput 1H‐NMR is an excellent tool to compare the extent of genetic diversity within and between wheat species, and to quantify specific components (including glycine betaine, choline, and asparagine) in individual genotypes. It can also be used to monitor changes in composition related to environmental factors and to support comparisons of the substantial equivalence of transgenic lines. PMID:28087883

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.

Gulf of Mexico Gas Hydrate Joint Industry Project Leg II logging-while-drilling data acquisition and analysis

USGS Publications Warehouse

Collett, Timothy S.; Lee, Wyung W.; Zyrianova, Margarita V.; Mrozewski, Stefan A.; Guerin, Gilles; Cook, Ann E.; Goldberg, Dave S.

2012-01-01

One of the objectives of the Gulf of Mexico Gas Hydrate Joint Industry Project Leg II (GOM JIP Leg II) was the collection of a comprehensive suite of logging-while-drilling (LWD) data within gas-hydrate-bearing sand reservoirs in order to make accurate estimates of the concentration of gas hydrates under various geologic conditions and to understand the geologic controls on the occurrence of gas hydrate at each of the sites drilled during this expedition. The LWD sensors just above the drill bit provided important information on the nature of the sediments and the occurrence of gas hydrate. There has been significant advancements in the use of downhole well-logging tools to acquire detailed information on the occurrence of gas hydrate in nature: From using electrical resistivity and acoustic logs to identify gas hydrate occurrences in wells to where wireline and advanced logging-while-drilling tools are routinely used to examine the petrophysical nature of gas hydrate reservoirs and the distribution and concentration of gas hydrates within various complex reservoir systems. Recent integrated sediment coring and well-log studies have confirmed that electrical resistivity and acoustic velocity data can yield accurate gas hydrate saturations in sediment grain supported (isotropic) systems such as sand reservoirs, but more advanced log analysis models are required to characterize gas hydrate in fractured (anisotropic) reservoir systems. In support of the GOM JIP Leg II effort, well-log data montages have been compiled and presented in this report which includes downhole logs obtained from all seven wells drilled during this expedition with a focus on identifying and characterizing the potential gas-hydrate-bearing sedimentary section in each of the wells. Also presented and reviewed in this report are the gas-hydrate saturation and sediment porosity logs for each of the wells as calculated from available downhole well logs.

Nuclear Tools For Oilfield Logging-While-Drilling Applications

NASA Astrophysics Data System (ADS)

Reijonen, Jani

2011-06-01

Schlumberger is an international oilfield service company with nearly 80,000 employees of 140 nationalities, operating globally in 80 countries. As a market leader in oilfield services, Schlumberger has developed a suite of technologies to assess the downhole environment, including, among others, electromagnetic, seismic, chemical, and nuclear measurements. In the past 10 years there has been a radical shift in the oilfield service industry from traditional wireline measurements to logging-while-drilling (LWD) analysis. For LWD measurements, the analysis is performed and the instruments are operated while the borehole is being drilled. The high temperature, high shock, and extreme vibration environment of LWD imposes stringent requirements for the devices used in these applications. This has a significant impact on the design of the components and subcomponents of a downhole tool. Another significant change in the past few years for nuclear-based oilwell logging tools is the desire to replace the sealed radioisotope sources with active, electronic ones. These active radiation sources provide great benefits compared to the isotopic sources, ranging from handling and safety to nonproliferation and well contamination issues. The challenge is to develop electronic generators that have a high degree of reliability for the entire lifetime of a downhole tool. LWD tool testing and operations are highlighted with particular emphasis on electronic radiation sources and nuclear detectors for the downhole environment.

NMRbox: A Resource for Biomolecular NMR Computation.

PubMed

Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

2017-04-25

Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

A personal computer-based nuclear magnetic resonance spectrometer

NASA Astrophysics Data System (ADS)

Job, Constantin; Pearson, Robert M.; Brown, Michael F.

1994-11-01

Nuclear magnetic resonance (NMR) spectroscopy using personal computer-based hardware has the potential of enabling the application of NMR methods to fields where conventional state of the art equipment is either impractical or too costly. With such a strategy for data acquisition and processing, disciplines including civil engineering, agriculture, geology, archaeology, and others have the possibility of utilizing magnetic resonance techniques within the laboratory or conducting applications directly in the field. Another aspect is the possibility of utilizing existing NMR magnets which may be in good condition but unused because of outdated or nonrepairable electronics. Moreover, NMR applications based on personal computer technology may open up teaching possibilities at the college or even secondary school level. The goal of developing such a personal computer (PC)-based NMR standard is facilitated by existing technologies including logic cell arrays, direct digital frequency synthesis, use of PC-based electrical engineering software tools to fabricate electronic circuits, and the use of permanent magnets based on neodymium-iron-boron alloy. Utilizing such an approach, we have been able to place essentially an entire NMR spectrometer console on two printed circuit boards, with the exception of the receiver and radio frequency power amplifier. Future upgrades to include the deuterium lock and the decoupler unit are readily envisioned. The continued development of such PC-based NMR spectrometers is expected to benefit from the fast growing, practical, and low cost personal computer market.

Characterization of Two Distinct Amorphous Forms of Valsartan by Solid-State NMR.

PubMed

Skotnicki, Marcin; Apperley, David C; Aguilar, Juan A; Milanowski, Bartłomiej; Pyda, Marek; Hodgkinson, Paul

2016-01-04

Valsartan (VAL) is an antihypertensive drug marketed in an amorphous form. Amorphous materials can have different physicochemical properties depending on preparation method, thermal history, etc., but the nature of such materials is difficult to study by diffraction techniques. This study characterizes two different amorphous forms of valsartan (AR and AM) using solid-state NMR (SSNMR) as a primary investigation tool, supported by solution-state NMR, FT-IR, TMDSC, and dissolution tests. The two forms are found to be clearly distinct, with a significantly higher level of structural arrangement in the AR form, as observed in (13)C, (15)N, and (1)H SSNMR. (13)C and (15)N NMR indicates that the fully amorphous material (AM) contains an approximately equal ratio of cis-trans conformers about the amide bond, whereas the AR form exists mainly as one conformer, with minor conformational "defects". (1)H ultrafast MAS NMR shows significant differences in the hydrogen bonding involving the tetrazole and acid hydrogens between the two materials, while (15)N NMR shows that both forms exist as a 1,2,3,4-tetrazole tautomer. NMR relaxation times show subtle differences in local and bulk molecular mobility, which can be connected with the glass transition, the stability of the glassy material, and its response to aging. Counterintuitively the fully amorphous material is found to have a significantly lower dissolution rate than the apparently more ordered AR material.

Studies on thermophysical properties at New Jersey Shallow Shelf (IODP Expedition 313)

NASA Astrophysics Data System (ADS)

Fehr, A.; Pechnig, R.; Inwood, J.; LOFI, J.; Bosch, F. P.; Clauser, C.

2011-12-01

The IODP drilling expedition 313 New Jersey Shallow Shelf was proposed for obtaining deep sub-seafloor samples and downhole logging measurements in the crucial inner shelf region.The inner to central shelf off-shore New Jersey is an ideal location for studying the history of sea-level changes and its relationship to sequence stratigraphy and onshore/offshore groundwater flows. The region features rapid depositional rates, tectonic stability, and well-preserved, cosmopolitan age control fossils suitable for characterizing the sediments of this margin throughout the time interval of interest. Past sea-level rise and fall is documented in sedimentary layers deposited during Earth's history. In addition, the inner shelf is characterised by relatively fresh pore water intervals alternating vertically with saltier intervals (Mountain et al., 2010). Therefore, three boreholes were drilled in the so-called New Jersey/Mid-Atlantic transect during IODP Expedition 313 New Jersey Shallow Shelf. Numerous questions have arisen concerning the age and origin of the brackish waters recovered offshore at depth. Here we present an analysis of thermophysical properties to be used as input parameters in constructing numerical models for future groundwater flow simulations. Our study is based mainly on Nuclear Magnetic Resonance (NMR) measurements for inferring porosity and permeability, and thermal conductivity. We performed NMR measurements on samples from boreholes M0027A, M0028A and M0029A and thermal conductivity measurements on the whole round cores prior to the Onshore Party. These results are compared with data from alternative laboratory measurements and with petrophysical properties inferred from downhole logging data.

Chemical Exchange Saturation Transfer in Chemical Reactions: A Mechanistic Tool for NMR Detection and Characterization of Transient Intermediates.

PubMed

Lokesh, N; Seegerer, Andreas; Hioe, Johnny; Gschwind, Ruth M

2018-02-07

The low sensitivity of NMR and transient key intermediates below detection limit are the central problems studying reaction mechanisms by NMR. Sensitivity can be enhanced by hyperpolarization techniques such as dynamic nuclear polarization or the incorporation/interaction of special hyperpolarized molecules. However, all of these techniques require special equipment, are restricted to selective reactions, or undesirably influence the reaction pathways. Here, we apply the chemical exchange saturation transfer (CEST) technique for the first time to NMR detect and characterize previously unobserved transient reaction intermediates in organocatalysis. The higher sensitivity of CEST and chemical equilibria present in the reaction pathway are exploited to access population and kinetics information on low populated intermediates. The potential of the method is demonstrated on the proline-catalyzed enamine formation for unprecedented in situ detection of a DPU stabilized zwitterionic iminium species, the elusive key intermediate between enamine and oxazolidinones. The quantitative analysis of CEST data at 250 K revealed the population ratio of [Z-iminium]/[exo-oxazolidinone] 0.02, relative free energy +8.1 kJ/mol (calculated +7.3 kJ/mol), and free energy barrier of +45.9 kJ/mol (ΔG ⧧ calc. (268 K) = +42.2 kJ/mol) for Z-iminium → exo-oxazolidinone. The findings underpin the iminium ion participation in enamine formation pathway corroborating our earlier theoretical prediction and help in better understanding. The reliability of CEST is validated using 1D EXSY-build-up techniques at low temperature (213 K). The CEST method thus serves as a new tool for mechanistic investigations in organocatalysis to access key information, such as chemical shifts, populations, and reaction kinetics of intermediates below the standard NMR detection limit.

High-Resolution Flow Logging for Hydraulic Characterization of Boreholes and Aquifer Flow Zones at Contaminated Bedrock Sites

NASA Astrophysics Data System (ADS)

Williams, J. H.; Johnson, C. D.; Paillet, F. L.

2004-05-01

In the past, flow logging was largely restricted to the application of spinner flowmeters to determine flow-zone contributions in large-diameter production wells screened in highly transmissive aquifers. Development and refinement of tool-measurement technology, field methods, and analysis techniques has greatly extended and enhanced flow logging to include the hydraulic characterization of boreholes and aquifer flow zones at contaminated bedrock sites. State-of-the-art in flow logging will be reviewed, and its application to bedrock-contamination investigations will be presented. In open bedrock boreholes, vertical flows are measured with high-resolution flowmeters equipped with flexible rubber-disk diverters fitted to the nominal borehole diameters to concentrate flow through the measurement throat of the tools. Heat-pulse flowmeters measure flows in the range of 0.05 to 5 liters per minute, and electromagnetic flowmeters measure flows in the range of 0.3 to 30 liters per minute. Under ambient and low-rate stressed (either extraction or injection) conditions, stationary flowmeter measurements are collected in competent sections of the borehole between fracture zones identified on borehole-wall images. Continuous flow, fluid-resistivity, and temperature logs are collected under both sets of conditions while trolling with a combination electromagnetic flowmeter and fluid tool. Electromagnetic flowmeters are used with underfit diverters to measure flow rates greater than 30 liters per minute and suppress effects of diameter variations while trolling. A series of corrections are applied to the flow-log data to account for the zero-flow response, bypass, trolling, and borehole-diameter biases and effects. The flow logs are quantitatively analyzed by matching simulated flows computed with a numerical model to measured flows by varying the hydraulic properties (transmissivity and hydraulic head) of the flow zones. Several case studies will be presented that demonstrate the integration of flow logging in site-characterization activities framework; 2) evaluate cross-connection effects and determine flow-zone contributions to water-quality samples from open boreholes; and 3) design discrete-zone hydraulic tests and monitoring-well completions.

Phosphorus Imaging as a Tool for Studying the pH Metabolism in Living Insects

NASA Astrophysics Data System (ADS)

Skibbe, U.; Christeller, J. T.; Eccles, C. D.; Laing, W. A.; Callaghan, P. T.

1995-09-01

Comparative 31P NMR and 1H NMR imaging experiments at submillimeter pixel resolution were carried out, using a specially constructed solenoidal RF coil. Chemical-shift imaging is used to provide pH maps from the midgut of a Lepidopteran larvae and to demonstrate physiological dependence in the resulting images, The titration curve of pH versus chemical shift for inorganic phosphate is extended beyond the "normal" biological range to the strong alkaline limit.

Solid state nuclear magnetic resonance studies of prion peptides and proteins

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

Heller, Jonathan

1997-08-01

High-resolution structural studies using x-ray diffraction and solution nuclear magnetic resonance (NMR) are not feasible for proteins of low volubility and high tendency to aggregate. Solid state NMR (SSNMR) is in principle capable of providing structural information in such systems, however to do this efficiently and accurately, further SSNMR tools must be developed This dissertation describes the development of three new methods and their application to a biological system of interest, the priori protein (PrP).

NMR clinical imaging and spectroscopy: Its impact on nuclear medicine

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

Not Available

1990-02-02

This is a collection of four papers describing aspects of past and future use of nuclear magnetic resonance as a clinical diagnostic tool. The four papers are entitled (1) What Does NMR Offer that Nuclear Medicine Does Not by Jerry W. Froelich, (2) Oncological Imaging: Now, Future and Impact Jerry W. Froelich, (3) Magnetic Resonance Spectroscopy/Spectroscopic Imaging and Nuclear Medicine: Past, Present and Future by H. Cecil Charles, and (4) MR Cardiology: Now, Future and Impact by Robert J. Herfkens.

NMR clinical imaging and spectroscopy: Its impact on nuclear medicine

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

Not Available

1990-02-02

This is a collection of four papers describing aspects of past and future use of nuclear magnetic resonance as a clinical diagnostic tool. The four papers are entitled (1) What Does NMR Offer that Nuclear Medicine Does Not? by Jerry W. Froelich, (2) Oncological Imaging: Now, Future and Impact Jerry W. Froelich, (3) Magnetic Resonance Spectroscopy/Spectroscopic Imaging and Nuclear Medicine: Past, Present and Future by H. Cecil Charles, and (4) MR Cardiology: Now, Future and Impact by Robert J. Herfkens.

Development of Enabling Scientific Tools to Characterize the Geologic Subsurface at Hanford

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

Kenna, Timothy C.; Herron, Michael M.

2014-07-08

This final report to the Department of Energy provides a summary of activities conducted under our exploratory grant, funded through U.S. DOE Subsurface Biogeochemical Research Program in the category of enabling scientific tools, which covers the period from July 15, 2010 to July 14, 2013. The main goal of this exploratory project is to determine the parameters necessary to translate existing borehole log data into reservoir properties following scientifically sound petrophysical relationships. For this study, we focused on samples and Ge-based spectral gamma logging system (SGLS) data collected from wells located in the Hanford 300 Area. The main activities consistedmore » of 1) the analysis of available core samples for a variety of mineralogical, chemical and physical; 2) evaluation of selected spectral gamma logs, environmental corrections, and calibration; 3) development of algorithms and a proposed workflow that permits translation of log responses into useful reservoir properties such as lithology, matrix density, porosity, and permeability. These techniques have been successfully employed in the petroleum industry; however, the approach is relatively new when applied to subsurface remediation. This exploratory project has been successful in meeting its stated objectives. We have demonstrated that our approach can lead to an improved interpretation of existing well log data. The algorithms we developed can utilize available log data, in particular gamma, and spectral gamma logs, and continued optimization will improve their application to ERSP goals of understanding subsurface properties.« less

Investigation of hydrogenation of toluene to methylcyclohexane in a trickle bed reactor by low-field nuclear magnetic resonance spectroscopy.

PubMed

Guthausen, Gisela; von Garnier, Agnes; Reimert, Rainer

2009-10-01

Low-field nuclear magnetic resonance (NMR) spectroscopy is applied to study the hydrogenation of toluene in a lab-scale reactor. A conventional benchtop NMR system was modified to achieve chemical shift resolution. After an off-line validity check of the approach, the reaction product is analyzed on-line during the process, applying chemometric data processing. The conversion of toluene to methylcyclohexane is compared with off-line gas chromatographic analysis. Both classic analytical and chemometric data processing was applied. As the results, which are obtained within a few tens of seconds, are equivalent within the experimental accuracy of both methods, low-field NMR spectroscopy was shown to provide an analytical tool for reaction characterization and immediate feedback.

Automation of NMR structure determination of proteins.

PubMed

Altieri, Amanda S; Byrd, R Andrew

2004-10-01

The automation of protein structure determination using NMR is coming of age. The tedious processes of resonance assignment, followed by assignment of NOE (nuclear Overhauser enhancement) interactions (now intertwined with structure calculation), assembly of input files for structure calculation, intermediate analyses of incorrect assignments and bad input data, and finally structure validation are all being automated with sophisticated software tools. The robustness of the different approaches continues to deal with problems of completeness and uniqueness; nevertheless, the future is very bright for automation of NMR structure generation to approach the levels found in X-ray crystallography. Currently, near completely automated structure determination is possible for small proteins, and the prospect for medium-sized and large proteins is good. Copyright 2004 Elsevier Ltd.

High-resolution nuclear magnetic resonance studies of proteins.

PubMed

Jonas, Jiri

2002-03-25

The combination of advanced high-resolution nuclear magnetic resonance (NMR) techniques with high-pressure capability represents a powerful experimental tool in studies of protein folding. This review is organized as follows: after a general introduction of high-pressure, high-resolution NMR spectroscopy of proteins, the experimental part deals with instrumentation. The main section of the review is devoted to NMR studies of reversible pressure unfolding of proteins with special emphasis on pressure-assisted cold denaturation and the detection of folding intermediates. Recent studies investigating local perturbations in proteins and the experiments following the effects of point mutations on pressure stability of proteins are also discussed. Ribonuclease A, lysozyme, ubiquitin, apomyoglobin, alpha-lactalbumin and troponin C were the model proteins investigated.

PATHA: Performance Analysis Tool for HPC Applications

DOE PAGES

Yoo, Wucherl; Koo, Michelle; Cao, Yi; ...

2016-02-18

Large science projects rely on complex workflows to analyze terabytes or petabytes of data. These jobs are often running over thousands of CPU cores and simultaneously performing data accesses, data movements, and computation. It is difficult to identify bottlenecks or to debug the performance issues in these large workflows. In order to address these challenges, we have developed Performance Analysis Tool for HPC Applications (PATHA) using the state-of-art open source big data processing tools. Our framework can ingest system logs to extract key performance measures, and apply the most sophisticated statistical tools and data mining methods on the performance data.more » Furthermore, it utilizes an efficient data processing engine to allow users to interactively analyze a large amount of different types of logs and measurements. To illustrate the functionality of PATHA, we conduct a case study on the workflows from an astronomy project known as the Palomar Transient Factory (PTF). This study processed 1.6 TB of system logs collected on the NERSC supercomputer Edison. Using PATHA, we were able to identify performance bottlenecks, which reside in three tasks of PTF workflow with the dependency on the density of celestial objects.« less

Increasing rigor in NMR-based metabolomics through validated and open source tools

PubMed Central

Eghbalnia, Hamid R; Romero, Pedro R; Westler, William M; Baskaran, Kumaran; Ulrich, Eldon L; Markley, John L

2016-01-01

The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism’s phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies. PMID:27643760

Increasing rigor in NMR-based metabolomics through validated and open source tools.

PubMed

Eghbalnia, Hamid R; Romero, Pedro R; Westler, William M; Baskaran, Kumaran; Ulrich, Eldon L; Markley, John L

2017-02-01

The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism's phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies. Copyright © 2016. Published by Elsevier Ltd.

The specific purpose Monte Carlo code McENL for simulating the response of epithermal neutron lifetime well logging tools

NASA Astrophysics Data System (ADS)

Prettyman, T. H.; Gardner, R. P.; Verghese, K.

1993-08-01

A new specific purpose Monte Carlo code called McENL for modeling the time response of epithermal neutron lifetime tools is described. The weight windows technique, employing splitting and Russian roulette, is used with an automated importance function based on the solution of an adjoint diffusion model to improve the code efficiency. Complete composition and density correlated sampling is also included in the code, and can be used to study the effect on tool response of small variations in the formation, borehole, or logging tool composition and density. An illustration of the latter application is given for the density of a thermal neutron filter. McENL was benchmarked against test-pit data for the Mobil pulsed neutron porosity tool and was found to be very accurate. Results of the experimental validation and details of code performance are presented.

Accuracy and borehole influences in pulsed neutron gamma density logging while drilling.

PubMed

Yu, Huawei; Sun, Jianmeng; Wang, Jiaxin; Gardner, Robin P

2011-09-01

A new pulsed neutron gamma density (NGD) logging has been developed to replace radioactive chemical sources in oil logging tools. The present paper describes studies of near and far density measurement accuracy of NGD logging at two spacings and the borehole influences using Monte-Carlo simulation. The results show that the accuracy of near density is not as good as far density. It is difficult to correct this for borehole effects by using conventional methods because both near and far density measurement is significantly sensitive to standoffs and mud properties. Copyright © 2011 Elsevier Ltd. All rights reserved.

Solution nuclear magnetic resonance spectroscopy on a nanostructured diamond chip.

PubMed

Kehayias, P; Jarmola, A; Mosavian, N; Fescenko, I; Benito, F M; Laraoui, A; Smits, J; Bougas, L; Budker, D; Neumann, A; Brueck, S R J; Acosta, V M

2017-08-04

Sensors using nitrogen-vacancy centers in diamond are a promising tool for small-volume nuclear magnetic resonance (NMR) spectroscopy, but the limited sensitivity remains a challenge. Here we show nearly two orders of magnitude improvement in concentration sensitivity over previous nitrogen-vacancy and picoliter NMR studies. We demonstrate NMR spectroscopy of picoliter-volume solutions using a nanostructured diamond chip with dense, high-aspect-ratio nanogratings, enhancing the surface area by 15 times. The nanograting sidewalls are doped with nitrogen-vacancies located a few nanometers from the diamond surface to detect the NMR spectrum of roughly 1 pl of fluid lying within adjacent nanograting grooves. We perform 1 H and 19 F nuclear magnetic resonance spectroscopy at room temperature in magnetic fields below 50 mT. Using a solution of CsF in glycerol, we determine that 4 ± 2 × 10 12 19 F spins in a 1 pl volume can be detected with a signal-to-noise ratio of 3 in 1 s of integration.Nitrogen vacancy (NV) centres in diamond can be used for NMR spectroscopy, but increased sensitivity is needed to avoid long measurement times. Kehayias et al. present a nanostructured diamond grating with a high density of NV centres, enabling NMR spectroscopy of picoliter-volume solutions.

Dynamic NMR Study of Model CMP Slurry Containing Silica Particles as Abrasives

NASA Astrophysics Data System (ADS)

Odeh, F.; Al-Bawab, A.; Li, Y.

2018-02-01

Chemical mechanical planarization (CMP) should provide a good surface planarity with minimal surface defectivity. Since CMP slurries are multi-component systems, it is very important to understand the various processes and interactions taking place in such slurries. Several techniques have been employed for such task, however, most of them lack the molecular recognition to investigate molecular interactions without adding probes which in turn increase complexity and might alter the microenvironment of the slurry. Nuclear magnetic resonance (NMR) is a powerful technique that can be employed in such study. The longitudinal relaxation times (T1) of the different components of CMP slurries were measured using Spin Echo-NMR (SE-NMR) at a constant temperature. The fact that NMR is non-invasive and gives information on the molecular level gives more advantage to the technique. The model CMP slurry was prepared in D2O to enable monitoring of T1 for the various components' protons. SE-NMR provide a very powerful tool to study the various interactions and adsorption processes that take place in a model CMP silica based slurry which contains BTA and/or glycine and/or Cu+2 ions. It was found that BTA is very competitive towards complexation with Cu+2 ions and BTA-Cu complex adsorbs on silica surface.

Novel NMR tools to study structure and dynamics of biomembranes.

PubMed

Gawrisch, Klaus; Eldho, Nadukkudy V; Polozov, Ivan V

2002-06-01

Nuclear magnetic resonance (NMR) studies on biomembranes have benefited greatly from introduction of magic angle spinning (MAS) NMR techniques. Improvements in MAS probe technology, combined with the higher magnetic field strength of modern instruments, enables almost liquid-like resolution of lipid resonances. The cross-relaxation rates measured by nuclear Overhauser enhancement spectroscopy (NOESY) provide new insights into conformation and dynamics of lipids with atomic-scale resolution. The data reflect the tremendous motional disorder in the lipid matrix. Transfer of magnetization by spin diffusion along the proton network of lipids is of secondary relevance, even at a long NOESY mixing time of 300 ms. MAS experiments with re-coupling of anisotropic interactions, like the 13C-(1)H dipolar couplings, benefit from the excellent resolution of 13C shifts that enables assignment of the couplings to specific carbon atoms. The traditional 2H NMR experiments on deuterated lipids have higher sensitivity when conducted on oriented samples at higher magnetic field strength. A very large number of NMR parameters from lipid bilayers is now accessible, providing information about conformation and dynamics for every lipid segment. The NMR methods have the sensitivity and resolution to study lipid-protein interaction, lateral lipid organization, and the location of solvents and drugs in the lipid matrix.

Crystallinity and compositional changes in carbonated apatites: Evidence from 31P solid-state NMR, Raman, and AFM analysis

NASA Astrophysics Data System (ADS)

McElderry, John-David P.; Zhu, Peizhi; Mroue, Kamal H.; Xu, Jiadi; Pavan, Barbara; Fang, Ming; Zhao, Guisheng; McNerny, Erin; Kohn, David H.; Franceschi, Renny T.; Holl, Mark M. Banaszak; Tecklenburg, Mary M. J.; Ramamoorthy, Ayyalusamy; Morris, Michael D.

2013-10-01

Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and 31P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse 31P NMR linewidth and inverse Raman PO43-ν1 bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3-10.3 wt% CO32- range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the 31P NMR chemical shift frequency and the Raman phosphate ν1 band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals.

Prediction of recrystallization behavior of troglitazone/polyvinylpyrrolidone solid dispersion by solid-state NMR.

PubMed

Ito, Atsutoshi; Watanabe, Tomoyuki; Yada, Shuichi; Hamaura, Takeshi; Nakagami, Hiroaki; Higashi, Kenjirou; Moribe, Kunikazu; Yamamoto, Keiji

2010-01-04

The purpose of this study was to elaborate the relationship between the (13)C CP/MAS NMR spectra and the recrystallization behavior during the storage of troglitazone solid dispersions. The solid dispersions were prepared by either the solvent method or by co-grinding. The recrystallization behavior under storage conditions at 40 degrees C/94% RH was evaluated by the Kolmogorov-Johnson-Mehl-Avrami (KJMA) equation. Solid dispersions prepared by the solvent method or by prolonged grinding brought about inhibition of the nucleation and the nuclei growth at the same time. No differences in the PXRD profiles were found in the samples prepared by the co-grinding and solvent methods, however, (13)C CP/MAS NMR showed significant differences in the spectra. The correlation coefficients using partial least square regression analysis between the PXRD profiles and the apparent nuclei-growth constant or induction period to nucleation were 0.1305 or 0.6350, respectively. In contrast, those between the (13)C CP/MAS NMR spectra and the constant or the period were 0.9916 or 0.9838, respectively. The (13)C CP/MAS NMR spectra had good correlation with the recrystallization kinetic parameters evaluated by the KJMA equation. Consequently, solid-state NMR was judged to be a useful tool for the prediction of the recrystallization behavior of solid dispersions.

Application of quantitative 1H NMR for the calibration of protoberberine alkaloid reference standards.

PubMed

Wu, Yan; He, Yi; He, Wenyi; Zhang, Yumei; Lu, Jing; Dai, Zhong; Ma, Shuangcheng; Lin, Ruichao

2014-03-01

Quantitative nuclear magnetic resonance spectroscopy (qNMR) has been developed into an important tool in the drug analysis, biomacromolecule detection, and metabolism study. Compared with mass balance method, qNMR method bears some advantages in the calibration of reference standard (RS): it determines the absolute amount of a sample; other chemical compound and its certified reference material (CRM) can be used as internal standard (IS) to obtain the purity of the sample. Protoberberine alkaloids have many biological activities and have been used as reference standards for the control of many herbal drugs. In present study, the qNMR methods were developed for the calibration of berberine hydrochloride, palmatine hydrochloride, tetrahydropalmatine, and phellodendrine hydrochloride with potassium hydrogen phthalate as IS. Method validation was carried out according to the guidelines for the method validation of Chinese Pharmacopoeia. The results of qNMR were compared with those of mass balance method and the differences between the results of two methods were acceptable based on the analysis of estimated measurement uncertainties. Therefore, qNMR is an effective and reliable analysis method for the calibration of RS and can be used as a good complementarity to the mass balance method. Copyright © 2013 Elsevier B.V. All rights reserved.

Lithotype characterizations by Nuclear Magnetic Resonance (NMR): A case study on limestone and associated rocks from the eastern Dahomey Basin, Nigeria

NASA Astrophysics Data System (ADS)

Olatinsu, O. B.; Olorode, D. O.; Clennell, B.; Esteban, L.; Josh, M.

2017-05-01

Three representative rock types (limestone, sandstone, and shale) and glauconite samples collected from Ewekoro Quarry, eastern Dahomey Basin in Nigeria were characterized using low field 2 MHz and 20 MHz Nuclear Magnetic Resonance (NMR) techniques. NMR T2 relaxation time decay measurement was conducted on disc samples under partial water-saturation and full water-saturation conditions using CPMG spin-echo routine. The T2 relaxation decay was converted into T2 distribution in the time domain to assess and evaluate the pore size distribution of the samples. Good agreement exists between water content from T2 NMR distributions and water imbibition porosity (WIP) technique. Results show that the most useful characteristics to discriminate the different facies come from full saturation NMR 2 MHz pore size distribution (PSD). Shale facies depict a quasi-unimodal distribution with greater than 90% contribution from clay bound water component (T2s) coupled to capillary bound water component (T2i) centred on 2 ms. The other facies with well connected pore structure show either bimodal or trimodal T2 distribution composed of the similar clay bound water component centred on 0.3 ms and quasi-capillary bound water component centred on 10 ms. But their difference depends on the movable water T2 component (T2l) that does not exist in the glauconite facies (bimodal distribution) while it exists in both the sandstone and limestone facies. The basic difference between the limestone and sandstone facies is related to the longer T2 coupling: T2i and T2l populations are coupled in sandstone generating a single population which convolves both populations (bimodal distribution). Limestone with a trimodal distribution attests to the fact that carbonate rocks have more complex pore system than siliclastic rocks. The degree of pore connectivity is highest in sandstone, followed by limestone and least in glauconite. Therefore a basic/quick NMR log run on samples along a geological formation can provide precise lithofacies characterization with quantitative information on pore size, structure and distributions.

Optical pumping and xenon NMR

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

Raftery, M. Daniel

1991-11-01

Nuclear Magnetic Resonance (NMR) spectroscopy of xenon has become an important tool for investigating a wide variety of materials, especially those with high surface area. The sensitivity of its chemical shift to environment, and its chemical inertness and adsorption properties make xenon a particularly useful NMR probe. This work discusses the application of optical pumping to enhance the sensitivity of xenon NMR experiments, thereby allowing them to be used in the study of systems with lower surface area. A novel method of optically-pumping 129Xe in low magnetic field below an NMR spectrometer and subsequent transfer of the gas to highmore » magnetic field is described. NMR studies of the highly polarized gas adsorbed onto powdered samples with low to moderate surface areas are now possible. For instance, NMR studies of optically-pumped xenon adsorbed onto polyacrylic acid show that xenon has a large interaction with the surface. By modeling the low temperature data in terms of a sticking probability and the gas phase xenon-xenon interaction, the diffusion coefficient for xenon at the surface of the polymer is determined. The sensitivity enhancement afforded by optical pumping also allows the NMR observation of xenon thin films frozen onto the inner surfaces of different sample cells. The geometry of the thin films results in interesting line shapes that are due to the bulk magnetic susceptibility of xenon. Experiments are also described that combine optical pumping with optical detection for high sensitivity in low magnetic field to observe the quadrupoler evolution of 131 Xe spins at the surface of the pumping cells. In cells with macroscopic asymmetry, a residual quadrupolar interaction causes a splitting in the 131Xe NMR frequencies in bare Pyrex glass cells and cells with added hydrogen.« less

Optical pumping and xenon NMR

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

Raftery, M.D.

1991-11-01

Nuclear Magnetic Resonance (NMR) spectroscopy of xenon has become an important tool for investigating a wide variety of materials, especially those with high surface area. The sensitivity of its chemical shift to environment, and its chemical inertness and adsorption properties make xenon a particularly useful NMR probe. This work discusses the application of optical pumping to enhance the sensitivity of xenon NMR experiments, thereby allowing them to be used in the study of systems with lower surface area. A novel method of optically-pumping [sup 129]Xe in low magnetic field below an NMR spectrometer and subsequent transfer of the gas tomore » high magnetic field is described. NMR studies of the highly polarized gas adsorbed onto powdered samples with low to moderate surface areas are now possible. For instance, NMR studies of optically-pumped xenon adsorbed onto polyacrylic acid show that xenon has a large interaction with the surface. By modeling the low temperature data in terms of a sticking probability and the gas phase xenon-xenon interaction, the diffusion coefficient for xenon at the surface of the polymer is determined. The sensitivity enhancement afforded by optical pumping also allows the NMR observation of xenon thin films frozen onto the inner surfaces of different sample cells. The geometry of the thin films results in interesting line shapes that are due to the bulk magnetic susceptibility of xenon. Experiments are also described that combine optical pumping with optical detection for high sensitivity in low magnetic field to observe the quadrupoler evolution of 131 Xe spins at the surface of the pumping cells. In cells with macroscopic asymmetry, a residual quadrupolar interaction causes a splitting in the [sup 131]Xe NMR frequencies in bare Pyrex glass cells and cells with added hydrogen.« less

Transformation of meta-stable calcium silicate hydrates to tobermorite: reaction kinetics and molecular structure from XRD and NMR spectroscopy

PubMed Central

2009-01-01

Understanding the integrity of well-bore systems that are lined with Portland-based cements is critical to the successful storage of sequestered CO2 in gas and oil reservoirs. As a first step, we investigate reaction rates and mechanistic pathways for cement mineral growth in the absence of CO2 by coupling water chemistry with XRD and NMR spectroscopic data. We find that semi-crystalline calcium (alumino-)silicate hydrate (Al-CSH) forms as a precursor solid to the cement mineral tobermorite. Rate constants for tobermorite growth were found to be k = 0.6 (± 0.1) × 10-5 s-1 for a solution:solid of 10:1 and 1.6 (± 0.8) × 10-4 s-1 for a solution:solid of 5:1 (batch mode; T = 150°C). This data indicates that reaction rates for tobermorite growth are faster when the solution volume is reduced by half, suggesting that rates are dependent on solution saturation and that the Gibbs free energy is the reaction driver. However, calculated solution saturation indexes for Al-CSH and tobermorite differ by less than one log unit, which is within the measured uncertainty. Based on this data, we consider both heterogeneous nucleation as the thermodynamic driver and internal restructuring as possible mechanistic pathways for growth. We also use NMR spectroscopy to characterize the site symmetry and bonding environment of Al and Si in a reacted tobermorite sample. We find two [4]Al coordination structures at δiso = 59.9 ppm and 66.3 ppm with quadrupolar product parameters (PQ) of 0.21 MHz and 0.10 MHz (± 0.08) from 27Al 3Q-MAS NMR and speculate on the Al occupancy of framework sites by probing the protonation environment of Al metal centers using 27Al{1H}CP-MAS NMR. PMID:19144195

Teacher Logs: A Tool for Gaining a Comprehensive Understanding of Classroom Practices

ERIC Educational Resources Information Center

Glennie, Elizabeth J.; Charles, Karen J.; Rice, Olivia N.

2017-01-01

Examining repeated classroom encounters over time provides a comprehensive picture of activities. Studies of instructional practices in classrooms have traditionally relied on two methods: classroom observations, which are expensive, and surveys, which are limited in scope and accuracy. Teacher logs provide a "real-time" method for…

Quantitative analysis of amygdalin and prunasin in Prunus serotina Ehrh. using (1) H-NMR spectroscopy.

PubMed

Santos Pimenta, Lúcia P; Schilthuizen, Menno; Verpoorte, Robert; Choi, Young Hae

2014-01-01

Prunus serotina is native to North America but has been invasively introduced in Europe since the seventeenth century. This plant contains cyanogenic glycosides that are believed to be related to its success as an invasive plant. For these compounds, chromatographic- or spectrometric-based (targeting on HCN hydrolysis) methods of analysis have been employed so far. However, the conventional methods require tedious preparation steps and a long measuring time. To develop a fast and simple method to quantify the cyanogenic glycosides, amygdalin and prunasin in dried Prunus serotina leaves without any pre-purification steps using (1) H-NMR spectroscopy. Extracts of Prunus serotina leaves using CH3 OH-d4 and KH2 PO4 buffer in D2 O (1:1) were quantitatively analysed for amygdalin and prunasin using (1) H-NMR spectroscopy. Different internal standards were evaluated for accuracy and stability. The purity of quantitated (1) H-NMR signals was evaluated using several two-dimensional NMR experiments. Trimethylsilylpropionic acid sodium salt-d4 proved most suitable as the internal standard for quantitative (1) H-NMR analysis. Two-dimensional J-resolved NMR was shown to be a useful tool to confirm the structures and to check for possible signal overlapping with the target signals for the quantitation. Twenty-two samples of P. serotina were subsequently quantitatively analysed for the cyanogenic glycosides prunasin and amygdalin. The NMR method offers a fast, high-throughput analysis of cyanogenic glycosides in dried leaves permitting simultaneous quantification and identification of prunasin and amygdalin in Prunus serotina. Copyright © 2013 John Wiley & Sons, Ltd.

Label-free quantitative 1H NMR spectroscopy to study low-affinity ligand–protein interactions in solution: A contribution to the mechanism of polyphenol-mediated astringency

PubMed Central

Delius, Judith; Frank, Oliver

2017-01-01

Nuclear magnetic resonance (NMR) spectroscopy is well-established in assessing the binding affinity between low molecular weight ligands and proteins. However, conventional NMR-based binding assays are often limited to small proteins of high purity and may require elaborate isotopic labeling of one of the potential binding partners. As protein–polyphenol complexation is assumed to be a key event in polyphenol-mediated oral astringency, here we introduce a label-free, ligand-focused 1H NMR titration assay to estimate binding affinities and characterize soluble complex formation between proteins and low molecular weight polyphenols. The method makes use of the effects of NMR line broadening due to protein–ligand interactions and quantitation of the non-bound ligand at varying protein concentrations by quantitative 1H NMR spectroscopy (qHNMR) using electronic reference to access in vivo concentration (ERETIC 2). This technique is applied to assess the interaction kinetics of selected astringent tasting polyphenols and purified mucin, a major lubricating glycoprotein of human saliva, as well as human whole saliva. The protein affinity values (BC50) obtained are subsequently correlated with the intrinsic mouth-puckering, astringent oral sensation imparted by these compounds. The quantitative NMR method is further exploited to study the effect of carboxymethyl cellulose, a candidate “anti-astringent” protein binding antagonist, on the polyphenol–protein interaction. Consequently, the NMR approach presented here proves to be a versatile tool to study the interactions between proteins and low-affinity ligands in solution and may find promising applications in the discovery of bioactives. PMID:28886151

High Temperature Logging and Monitoring Instruments to Explore and Drill Deep into Hot Oceanic Crust.

NASA Astrophysics Data System (ADS)

Denchik, N.; Pezard, P. A.; Ragnar, A.; Jean-Luc, D.; Jan, H.

2014-12-01

Drilling an entire section of the oceanic crust and through the Moho has been a goal of the scientific community for more than half of a century. On the basis of ODP and IODP experience and data, this will require instruments and strategies working at temperature far above 200°C (reached, for example, at the bottom of DSDP/ODP Hole 504B), and possibly beyond 300°C. Concerning logging and monitoring instruments, progress were made over the past ten years in the context of the HiTI ("High Temperature Instruments") project funded by the european community for deep drilling in hot Icelandic geothermal holes where supercritical conditions and a highly corrosive environment are expected at depth (with temperatures above 374 °C and pressures exceeding 22 MPa). For example, a slickline tool (memory tool) tolerating up to 400°C and wireline tools up to 300°C were developed and tested in Icelandic high-temperature geothermal fields. The temperature limitation of logging tools was defined to comply with the present limitation in wireline cables (320°C). As part of this new set of downhole tools, temperature, pressure, fluid flow and casing collar location might be measured up to 400°C from a single multisensor tool. Natural gamma radiation spectrum, borehole wall ultrasonic images signal, and fiber optic cables (using distributed temperature sensing methods) were also developed for wireline deployment up to 300°C and tested in the field. A wireline, dual laterolog electrical resistivity tool was also developed but could not be field tested as part of HiTI. This new set of tools constitutes a basis for the deep exploration of the oceanic crust in the future. In addition, new strategies including the real-time integration of drilling parameters with modeling of the thermo-mechanical status of the borehole could be developed, using time-lapse logging of temperature (for heat flow determination) and borehole wall images (for hole stability and in-situ stress determination) as boundary conditions for the models. In all, and with limited integration of existing tools, to deployment of high-temperature downhole tools could contribute largely to the success of the long awaited Mohole project.

Quantitative estimation of massive gas hydrate in gas chimney structures, the eastern margin of Japan Sea, from the physical property anomalies obtained by LWD.

NASA Astrophysics Data System (ADS)

Tanahashi, M.; Morita, S.; Matsumoto, R.

2017-12-01

Two dedicated LWD (Logging While Drilling) cruises, GR14 and HR15, were conducted in summers of 2014 and 2015, respectively, by Meiji University and Geological Survey of Japan, AIST to explore the gas chimney structures, which are characterized by the columnar acoustic blanking below the topographic mound and/or pockmarks in eastern margin of Japan Sea. Shallow (33 to 172m-bsf, average 136m-bsf) 33 LWD drillings were carried out generally in and around gas chimney structures which are in Oki Trough, Off-Joetsu, and Mogami Trough areas, eastern margin of Japan Sea, during two cruises. Schlumberger LWD tools, GeoVISION (resistivity), TeleScope, ProVISION (NMR) and SonicVISION (sonic) were applied during GR14. NeoScope (neutron) was added and SonicScope was replaced for SonicVISION during HR15. The presence of thick highly-anomalous intervals within the LWD data at site J24L suggests the development of massive gas hydrate within Off-Joetsu, by very high resistivity ( 10,000 Ωm), high Vp ( 3,700 m/s) and Vs (370-1,839 m/s), high neutron porosity ( 1.2), low natural gamma ray intensity ( 0 API), low neutron gamma density ( 0.8 g/cm3), low NMR porosity ( 0.0), low permeability (10-2-10-4 mD), low formation neutron sigma (26-28). The extreme physical properties intervals suggest the development of the almost pure hydrate. Because of the clear contrast between pure hydrate and seawater saturated fine sediments, the hydrate amount can be estimated quantitatively based on the assumptions as the two component system of pure hydrate and the monotonous seawater saturated fine sediments. This study was conducted as a part of the methane hydrate research project funded by METI (the Ministry of Economy, Trade and Industry, Japan).

REAL-TIME TRACER MONITORING OF RESERVOIR STIMULATION PROCEDURES VIA ELECTRONIC WIRELINE AND TELEMETRY DATA TRANSMISSION

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

George L. Scott III

2005-01-01

Finalized Phase 2-3 project work has field-proven two separate real-time reservoir processes that were co-developed via funding by the National Energy Technology Laboratory (NETL). Both technologies are presently patented in the United States and select foreign markets; a downhole-commingled reservoir stimulation procedure and a real-time tracer-logged fracturing diagnostic system. Phase 2 and early Phase 3 project work included the research, development and well testing of a U.S. patented gamma tracer fracturing diagnostic system. This stimulation logging process was successfully field-demonstrated; real-time tracer measurement of fracture height while fracturing was accomplished and proven technically possible. However, after the initial well tests,more » there were several licensing issues that developed between service providers that restricted and minimized Realtimezone's (RTZ) ability to field-test the real-time gamma diagnostic system as was originally outlined for this project. Said restrictions were encountered after when one major provider agreed to license their gamma logging tools to another. Both of these companies previously promised contributory support toward Realtimezone's DE-FC26-99FT40129 project work, however, actual support was less than desired when newly-licensed wireline gamma logging tools from one company were converted by the other from electric wireline into slickline, batter-powered ''memory'' tools for post-stimulation logging purposes. Unfortunately, the converted post-fracture measurement memory tools have no applications in experimentally monitoring real-time movement of tracers in the reservoir concurrent with the fracturing treatment. RTZ subsequently worked with other tracer gamma-logging tool companies for basic gamma logging services, but with lessened results due to lack of multiple-isotope detection capability. In addition to real-time logging system development and well testing, final Phase 2 and Phase 3 project work included the development of a real-time reservoir stimulation procedure, which was successfully field-demonstrated and is presently patented in the U.S. and select foreign countries, including Venezuela, Brazil and Canada. Said patents are co-owned by RTZ and the National Energy Technology Lab (NETL). In 2002, Realtimezone and the NETL licensed said patents to Halliburton Energy Services (HES). Additional licensing agreements (LA) are anticipated with other service industry companies in 2005. Final Phase 3 work has led to commercial applications of the real-time reservoir stimulation procedure. Four successfully downhole-mixed well tests were conducted with commercially expected production results. The most recent, fourth field test was a downhole-mixed stimulated well completed in June, 2004, which currently produces 11 BOPD with 90 barrels of water per day. Conducted Phase 2 and Phase 3 field-test work to date has resulted in the fine-tuning of a real-time enhanced stimulation system that will significantly increase future petroleum well recoveries in the United States and foreign petroleum fields, both onshore and offshore, and in vertical and horizontal wells.« less

Solid-state 13C NMR studies of a large fossil gymnosperm from the Yallourn Open Cut, Latrobe Valley, Australia

USGS Publications Warehouse

Bates, A.L.; Hatcher, P.G.

1989-01-01

A series of samples taken from the cross section of a 3-m-diameter fossilized gymnospermous log (Araucariaceae) in the Yallourn Seam of the Australian brown coals was examined by solid state 13C nuclear magnetic resonance to delineate chemical changes related to the combined processes of peatification and coalification. The results show that cellulosic materials were degraded and lost on the periphery of the log, however, the degree of such degradation in the central core is substantially less. The lignin is uniformly altered by coalification reactions to a macromolecular substance displaying decreased aryl ether linkages but significantly greater amounts of carbon linkages compared to modern lignin. Changes in the methoxyl carbon contents of lignin in cross section reveal demethylation reactions, but these do not appear to be related to degree of carbon linking. Both the degredation of cellulosic materials and demethylation of lignin appear to be early diagenetic processes occurring during peatification independently of the coalification reactions. ?? 1989.

Experimental and theoretical investigation of [Al(PCr)(H2O)] complex in aqueous solution

NASA Astrophysics Data System (ADS)

Tenório, Thaís; Lopes, Damiana C. N.; Silva, Andréa M.; Ramos, Joanna Maria; Buarque, Camilla D.

2014-01-01

Phosphocreatine is a phosphorylated creatine molecule synthesized in the liver and transported to muscle cells where it is used for the temporary storage of energy. In Alzheimer's disease, the capture of glucose by cells is impaired, which negatively affects the Krebs cycle, leading to problems with the generation of phosphocreatine. Furthermore, the creatine-phosphocreatine system, regulated by creatine kinase, is affected in the brains of Alzheimer's disease patients. Aluminum ions are associated with Alzheimer's disease. Al(III) decreases cell viability and increases the fluidity of the plasma membrane, profoundly altering cell morphology. In this study, one of the complexes formed by Al(III) and phosphocreatine in aqueous solution was investigated by potentiometry, 31P and 27Al NMR, Raman spectroscopy and density functional theory (DFT) calculations. The log KAlPCr value was 11.37 ± 0.03. Phosphocreatine should act as a tridentate ligand in this complex. The 27Al NMR peak at 48.92 ppm indicated a tetrahedral molecule. The fourth position in the arrangement was occupied by a coordinated water molecule. Raman spectroscopy, 31P NMR and DFT calculations (DFT:B3LYP/6-311++G**) indicated that the donor atoms are oxygen in the phosphate group, the nitrogen of the guanidine group and the oxygen of the carboxylate group. Mulliken charges, NBO charges, frontier molecular orbitals, electrostatic potential contour surfaces and mapped electrostatic potential were also examined.

31P and 1H NMR Studies of the Molecular Organization of Lipids in the Parallel Artificial Membrane Permeability Assay.

PubMed

Assmus, Frauke; Ross, Alfred; Fischer, Holger; Seelig, Joachim; Seelig, Anna

2017-01-03

The parallel artificial membrane permeability assay (PAMPA) has emerged as a widely used primary in vitro screen for passive permeability of potential drug candidates. However, the molecular structure of the permeation barrier (consisting of a filter-supported dodecane-egg lecithin mixture) has never been characterized. Here, we investigated the long-range order of phospholipids in the PAMPA barrier by means of 31 P static solid-state NMR. Diffusion constants of PAMPA membrane components were derived from liquid state NMR and, in addition, drug distribution between the PAMPA lipid phase and buffer (log D PAMPA at pH 7.4) was systematically investigated. Increasing concentration of n-dodecane to the system egg lecithin-water (lamellar phase, L α ) induces formation of inverted hexagonal (H ii ) and isotropic phases. At n-dodecane concentrations matching those used in PAMPA (9%, w/v) a purely "isotropic" phase was observed corresponding to lipid aggregates with a diameter in the range 4-7 nm. Drug distribution studies indicate that these reverse micelles facilitate the binding to, and in turn the permeation across, the PAMPA dodecane barrier, in particular for amphiphilic solutes. The proposed model for the molecular architecture and function of the PAMPA barrier provides a fundamental, hitherto missing framework to evaluate the scope but also limitations of PAMPA for the prediction of in vivo membrane permeability.

Biorelevant physicochemical profiling of (E)- and (Z)-resveratrol determined from isomeric mixtures.

PubMed

Orgován, Gábor; Gonda, Imre; Noszál, Béla

2017-05-10

Biorelevant, isomer-specific physicochemical parameters of resveratrol, a multifunctional component in red wines, with cardioprotective, anti-Alzheimer and several other pharmacologic activities were determined. The parameters include site-specific basicities, lipophilicities, solubilities and diffusion constants for the two geometric isomers. The protonation equilibria of (E)- and (Z)-resveratrol were monitored by 1 H NMR-pH titrations. Five closely related auxiliary compounds ((E)-pinostilbene, (Z)-pinostilbene, (E)-pterostilbene, (Z)-pterostilbene and resorcinol) were also studied. Combining the datasets, the group-specific protonation constants of resveratrol isomers were determined. The results show that (Z)-resveratrol is more basic at every protonation site than the (E)-isomer. Lipophilicities are quantified in terms of logP values and were determined by octanol/water partition experiments and quantitative NMR spectroscopy: (E)-resveratrol was found to be more lipophilic. Since the molecular geometries of the isomers differ, diffusion ordered NMR spectroscopy (DOSY) experiments were also carried out to quantify the diffusion capabilities of the isomers: (Z)-resveratrol of bent shape has a slightly higher diffusion coefficient than its extended (E) counterpart. A striking 10-fold difference of water solubility was found in favor of the (Z) isomer, due obviously to the reduced water-repellent character in the more compact molecule. This is so far the greatest recorded solubility difference between geometric isomers of any compounds. Copyright © 2016. Published by Elsevier B.V.

Bioinformatics tools for the analysis of NMR metabolomics studies focused on the identification of clinically relevant biomarkers.

PubMed

Puchades-Carrasco, Leonor; Palomino-Schätzlein, Martina; Pérez-Rambla, Clara; Pineda-Lucena, Antonio

2016-05-01

Metabolomics, a systems biology approach focused on the global study of the metabolome, offers a tremendous potential in the analysis of clinical samples. Among other applications, metabolomics enables mapping of biochemical alterations involved in the pathogenesis of diseases, and offers the opportunity to noninvasively identify diagnostic, prognostic and predictive biomarkers that could translate into early therapeutic interventions. Particularly, metabolomics by Nuclear Magnetic Resonance (NMR) has the ability to simultaneously detect and structurally characterize an abundance of metabolic components, even when their identities are unknown. Analysis of the data generated using this experimental approach requires the application of statistical and bioinformatics tools for the correct interpretation of the results. This review focuses on the different steps involved in the metabolomics characterization of biofluids for clinical applications, ranging from the design of the study to the biological interpretation of the results. Particular emphasis is devoted to the specific procedures required for the processing and interpretation of NMR data with a focus on the identification of clinically relevant biomarkers. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Laplace Inversion of Low-Resolution NMR Relaxometry Data Using Sparse Representation Methods

PubMed Central

Berman, Paula; Levi, Ofer; Parmet, Yisrael; Saunders, Michael; Wiesman, Zeev

2013-01-01

Low-resolution nuclear magnetic resonance (LR-NMR) relaxometry is a powerful tool that can be harnessed for characterizing constituents in complex materials. Conversion of the relaxation signal into a continuous distribution of relaxation components is an ill-posed inverse Laplace transform problem. The most common numerical method implemented today for dealing with this kind of problem is based on L2-norm regularization. However, sparse representation methods via L1 regularization and convex optimization are a relatively new approach for effective analysis and processing of digital images and signals. In this article, a numerical optimization method for analyzing LR-NMR data by including non-negativity constraints and L1 regularization and by applying a convex optimization solver PDCO, a primal-dual interior method for convex objectives, that allows general linear constraints to be treated as linear operators is presented. The integrated approach includes validation of analyses by simulations, testing repeatability of experiments, and validation of the model and its statistical assumptions. The proposed method provides better resolved and more accurate solutions when compared with those suggested by existing tools. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 72–88, 2013. PMID:23847452

1H NMR-based metabolic profiling for evaluating poppy seed rancidity and brewing.

PubMed

Jawień, Ewa; Ząbek, Adam; Deja, Stanisław; Łukaszewicz, Marcin; Młynarz, Piotr

2015-12-01

Poppy seeds are widely used in household and commercial confectionery. The aim of this study was to demonstrate the application of metabolic profiling for industrial monitoring of the molecular changes which occur during minced poppy seed rancidity and brewing processes performed on raw seeds. Both forms of poppy seeds were obtained from a confectionery company. Proton nuclear magnetic resonance (1H NMR) was applied as the analytical method of choice together with multivariate statistical data analysis. Metabolic fingerprinting was applied as a bioprocess control tool to monitor rancidity with the trajectory of change and brewing progressions. Low molecular weight compounds were found to be statistically significant biomarkers of these bioprocesses. Changes in concentrations of chemical compounds were explained relative to the biochemical processes and external conditions. The obtained results provide valuable and comprehensive information to gain a better understanding of the biology of rancidity and brewing processes, while demonstrating the potential for applying NMR spectroscopy combined with multivariate data analysis tools for quality control in food industries involved in the processing of oilseeds. This precious and versatile information gives a better understanding of the biology of these processes.

Laplace Inversion of Low-Resolution NMR Relaxometry Data Using Sparse Representation Methods.

PubMed

Berman, Paula; Levi, Ofer; Parmet, Yisrael; Saunders, Michael; Wiesman, Zeev

2013-05-01

Low-resolution nuclear magnetic resonance (LR-NMR) relaxometry is a powerful tool that can be harnessed for characterizing constituents in complex materials. Conversion of the relaxation signal into a continuous distribution of relaxation components is an ill-posed inverse Laplace transform problem. The most common numerical method implemented today for dealing with this kind of problem is based on L 2 -norm regularization. However, sparse representation methods via L 1 regularization and convex optimization are a relatively new approach for effective analysis and processing of digital images and signals. In this article, a numerical optimization method for analyzing LR-NMR data by including non-negativity constraints and L 1 regularization and by applying a convex optimization solver PDCO, a primal-dual interior method for convex objectives, that allows general linear constraints to be treated as linear operators is presented. The integrated approach includes validation of analyses by simulations, testing repeatability of experiments, and validation of the model and its statistical assumptions. The proposed method provides better resolved and more accurate solutions when compared with those suggested by existing tools. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 72-88, 2013.

Metabolic fingerprint of Brazilian maize landraces silk (stigma/styles) using NMR spectroscopy and chemometric methods.

PubMed

Kuhnen, Shirley; Bernardi Ogliari, Juliana; Dias, Paulo Fernando; da Silva Santos, Maiara; Ferreira, Antônio Gilberto; Bonham, Connie C; Wood, Karl Vernon; Maraschin, Marcelo

2010-02-24

Aqueous extract from maize silks is used by traditional medicine for the treatment of several ailments, mainly related to the urinary system. This work focuses on the application of NMR spectroscopy and chemometric analysis for the determination of metabolic fingerprint and pattern recognition of silk extracts from seven maize landraces cultivated in southern Brazil. Principal component analysis (PCA) of the (1)H NMR data set showed clear discrimination among the maize varieties by PC1 and PC2, pointing out three distinct metabolic profiles. Target compounds analysis showed significant differences (p < 0.05) in the contents of protocatechuic acid, gallic acid, t-cinnamic acid, and anthocyanins, corroborating the discrimination of the genotypes in this study as revealed by PCA analysis. Thus the combination of (1)H NMR and PCA is a useful tool for the discrimination of maize silks in respect to their chemical composition, including rapid authentication of the raw material of current pharmacological interest.

Isotopic 13C NMR spectrometry to assess counterfeiting of active pharmaceutical ingredients: site-specific 13C content of aspirin and paracetamol.

PubMed

Silvestre, Virginie; Mboula, Vanessa Maroga; Jouitteau, Catherine; Akoka, Serge; Robins, Richard J; Remaud, Gérald S

2009-10-15

Isotope profiling is a well-established technique to obtain information about the chemical history of a given compound. However, the current methodology using IRMS can only determine the global (13)C content, leading to the loss of much valuable data. The development of quantitative isotopic (13)C NMR spectrometry at natural abundance enables the measurement of the (13)C content of each carbon within a molecule, thus giving simultaneous access to a number of isotopic parameters. When it is applied to active pharmaceutical ingredients, each manufactured batch can be characterized better than by IRMS. Here, quantitative isotopic (13)C NMR is shown to be a very promising and effective tool for assessing the counterfeiting of medicines, as exemplified by an analysis of aspirin (acetylsalicylic acid) and paracetamol (acetaminophen) samples collected from pharmacies in different countries. It is proposed as an essential complement to (2)H NMR and IRMS.

Quantitative (13)C Solid-State NMR Spectra by Multiple-Contact Cross-polarization for Drug Delivery: From Active Principles to Excipients and Drug Carriers.

PubMed

Saïdi, Fadila; Taulelle, Francis; Martineau, Charlotte

2016-08-01

In this contribution, we present an analysis of the main parameters influencing the efficiency of the (1)H → (13)C multiple-contact cross-polarization nuclear magnetic resonance (NMR) experiment in the context of solid pharmaceutical materials. Using the optimum experimental conditions, quantitative (13)C NMR spectra are then obtained for porous metal-organic frameworks (potential drug carriers) and for components present in drug formulations (active principle ingredient and excipients, amorphous or crystalline). Finally, we show that mixtures of components can also be quantified with this method and, hence, that it represents an ideal tool for quantification of pharmaceutical formulations by (13)C cross-polarization under magic-angle spinning NMR in the industry as it is robust and easy to set up, much faster than direct (13)C polarization and is efficient for samples at natural abundance. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Paramagnetic NMR Investigation of Dendrimer-Based Host-Guest Interactions

PubMed Central

Wang, Fei; Shao, Naimin; Cheng, Yiyun

2013-01-01

In this study, the host-guest behavior of poly(amidoamine) (PAMAM) dendrimers bearing amine, hydroxyl, or carboxylate surface functionalities were investigated by paramagnetic NMR studies. 2,2,6,6-Tetramethylpiperidinyloxy (TEMPO) derivatives were used as paramagnetic guest molecules. The results showed that TEMPO-COOH significantly broaden the 1H NMR peaks of amine- and hydroxyl-terminated PAMAM dendrimers. In comparison, no paramagnetic relaxation enhancement (PRE) was observed between TEMPO-NH2, TEMPO-OH and the three types of PAMAM dendrimers. The PRE phenomenon observed is correlated with the encapsulation of TEMPO-COOH within dendrimer pockets. Protonation of the tertiary amine groups within PAMAM dendrimers plays an important role during this process. Interestingly, the absence of TEMPO-COOH encapsulation within carboxylate-terminated PAMAM dendrimer is observed due to the repulsion of TEMPO-COO- anion and anionic dendrimer surface. The combination of paramagnetic probes and 1H NMR linewidth analysis can be used as a powerful tool in the analysis of dendrimer-based host-guest systems. PMID:23762249

{sup 1}H NMR-based spectroscopy detects metabolic alterations in serum of patients with early-stage ulcerative colitis

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

Zhang, Ying; Lin, Lianjie; Xu, Yanbin

2013-04-19

Highlights: •Twenty ulcerative colitis patients and nineteen healthy controls were enrolled. •Increased 3-hydroxybutyrate, glucose, phenylalanine, and decreased lipid were found. •We report early stage diagnosis of ulcerative colitis using NMR-based metabolomics. -- Abstract: Ulcerative colitis (UC) has seriously impaired the health of citizens. Accurate diagnosis of UC at an early stage is crucial to improve the efficiency of treatment and prognosis. In this study, proton nuclear magnetic resonance ({sup 1}H NMR)-based metabolomic analysis was performed on serum samples collected from active UC patients (n = 20) and healthy controls (n = 19), respectively. The obtained spectral profiles were subjected tomore » multivariate data analysis. Our results showed that consistent metabolic alterations were present between the two groups. Compared to healthy controls, UC patients displayed increased 3-hydroxybutyrate, β-glucose, α-glucose, and phenylalanine, but decreased lipid in serum. These findings highlight the possibilities of NMR-based metabolomics as a non-invasive diagnostic tool for UC.« less

Use of qNMR for speciation of flaxseeds (Linum usitatissimum) and quantification of cyanogenic glycosides.

PubMed

Roulard, Romain; Fontaine, Jean-Xavier; Jamali, Arash; Cailleu, Dominique; Tavernier, Reynald; Guillot, Xavier; Rhazi, Larbi; Petit, Emmanuel; Molinie, Roland; Mesnard, François

2017-12-01

This report describes a routine method taking less than 20 min to quantify cyanogenic glycosides such as linustatin and neolinustatin from flaxseeds (Linum usitatissimum L.) using 1 H nuclear magnetic resonance. After manual dehulling, a higher linustatin content was shown in the almond fraction, while neolinustatin and total cyanogenic glycoside contents were significantly higher in hulls. Linustatin and neolinustatin were quantified in seven cultivars grown in two locations in three different years. Linustatin, neolinustatin, and total cyanogenic glycosides ranged between 91 and 267 mg/100 g, 78-272 mg/100 g, and 198-513 mg/100 g dry weight flaxseeds, respectively. NMR revealed differences of up to 70% between samples with standard deviation variations lower than 6%. This study shows that NMR is a very suitable tool to perform flaxseed varietal selection for the cyanogenic glycoside content. Graphical abstract qNMR can be used to perform flaxseed varietal selection for the cyanogenic glycoside content.

Logging while fishing technique results in substantial savings

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

Tollefsen, E.; Everett, M.

1996-12-01

During wireline logging operations, tools occasionally become stuck in the borehole and require fishing. A typical fishing job can take anywhere from 1{1/2}--4 days. In the Gulf of Mexico, a fishing job can easily cost between $100,000 and $500,000. These costs result from nonproductive time during the fishing trip, associated wiper trip and relogging the well. Logging while fishing (LWF) technology is a patented system capable of retrieving a stuck fish and completing the logging run during the same pipe descent. Completing logging operations using LWF method saves time and money. The technique also provides well information where data maymore » not otherwise have been obtained. Other benefits include reduced fishing time and an increased level of safety.« less

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

NASA Astrophysics Data System (ADS)

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time.

Progression of coronary artery calcification seems to be inevitable, but predictable - results of the Heinz Nixdorf Recall (HNR) study.

PubMed

Erbel, Raimund; Lehmann, Nils; Churzidse, Sofia; Rauwolf, Michael; Mahabadi, Amir A; Möhlenkamp, Stefan; Moebus, Susanne; Bauer, Marcus; Kälsch, Hagen; Budde, Thomas; Montag, Michael; Schmermund, Axel; Stang, Andreas; Führer-Sakel, Dagmar; Weimar, Christian; Roggenbuck, Ulla; Dragano, Nico; Jöckel, Karl-Heinz

2014-11-07

Coronary artery calcification (CAC), as a sign of atherosclerosis, can be detected and progression quantified using computed tomography (CT). We develop a tool for predicting CAC progression. In 3481 participants (45-74 years, 53.1% women) CAC percentiles at baseline (CACb) and after five years (CAC₅y) were evaluated, demonstrating progression along gender-specific percentiles, which showed exponentially shaped age-dependence. Using quantile regression on the log-scale (log(CACb+1)) we developed a tool to individually predict CAC₅y, and compared to observed CAC₅y. The difference between observed and predicted CAC₅y (log-scale, mean±SD) was 0.08±1.11 and 0.06±1.29 in men and women. Agreement reached a kappa-value of 0.746 (95% confidence interval: 0.732-0.760) and concordance correlation (log-scale) of 0.886 (0.879-0.893). Explained variance of observed by predicted log(CAC₅y+1) was 80.1% and 72.0% in men and women, and 81.0 and 73.6% including baseline risk factors. Evaluating the tool in 1940 individuals with CACb>0 and CACb<400 at baseline, of whom 242 (12.5%) developed CAC₅y>400, yielded a sensitivity of 59.5%, specificity 96.1%, (+) and (-) predictive values of 68.3% and 94.3%. A pre-defined acceptance range around predicted CAC₅y contained 68.1% of observed CAC₅y; only 20% were expected by chance. Age, blood pressure, lipid-lowering medication, diabetes, and smoking contributed to progression above the acceptance range in men and, excepting age, in women. CAC nearly inevitably progresses with limited influence of cardiovascular risk factors. This allowed the development of a mathematical tool for prediction of individual CAC progression, enabling anticipation of the age when CAC thresholds of high risk are reached. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Cardiology.

Comprehensive Interpretation of the Laboratory Experiments Results to Construct Model of the Polish Shale Gas Rocks

NASA Astrophysics Data System (ADS)

Jarzyna, Jadwiga A.; Krakowska, Paulina I.; Puskarczyk, Edyta; Wawrzyniak-Guz, Kamila; Zych, Marcin

2018-03-01

More than 70 rock samples from so-called sweet spots, i.e. the Ordovician Sa Formation and Silurian Ja Member of Pa Formation from the Baltic Basin (North Poland) were examined in the laboratory to determine bulk and grain density, total and effective/dynamic porosity, absolute permeability, pore diameters size, total surface area, and natural radioactivity. Results of the pyrolysis, i.e., TOC (Total Organic Carbon) together with S1 and S2 - parameters used to determine the hydrocarbon generation potential of rocks, were also considered. Elemental composition from chemical analyses and mineral composition from XRD measurements were also included. SCAL analysis, NMR experiments, Pressure Decay Permeability measurements together with water immersion porosimetry and adsorption/ desorption of nitrogen vapors method were carried out along with the comprehensive interpretation of the outcomes. Simple and multiple linear statistical regressions were used to recognize mutual relationships between parameters. Observed correlations and in some cases big dispersion of data and discrepancies in the property values obtained from different methods were the basis for building shale gas rock model for well logging interpretation. The model was verified by the result of the Monte Carlo modelling of spectral neutron-gamma log response in comparison with GEM log results.

icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

NASA Astrophysics Data System (ADS)

Savorani, F.; Tomasi, G.; Engelsen, S. B.

2010-02-01

The increasing scientific and industrial interest towards metabonomics takes advantage from the high qualitative and quantitative information level of nuclear magnetic resonance (NMR) spectroscopy. However, several chemical and physical factors can affect the absolute and the relative position of an NMR signal and it is not always possible or desirable to eliminate these effects a priori. To remove misalignment of NMR signals a posteriori, several algorithms have been proposed in the literature. The icoshift program presented here is an open source and highly efficient program designed for solving signal alignment problems in metabonomic NMR data analysis. The icoshift algorithm is based on correlation shifting of spectral intervals and employs an FFT engine that aligns all spectra simultaneously. The algorithm is demonstrated to be faster than similar methods found in the literature making full-resolution alignment of large datasets feasible and thus avoiding down-sampling steps such as binning. The algorithm uses missing values as a filling alternative in order to avoid spectral artifacts at the segment boundaries. The algorithm is made open source and the Matlab code including documentation can be downloaded from www.models.life.ku.dk.

Using high-performance ¹H NMR (HP-qNMR®) for the certification of organic reference materials under accreditation guidelines--describing the overall process with focus on homogeneity and stability assessment.

PubMed

Weber, Michael; Hellriegel, Christine; Rueck, Alexander; Wuethrich, Juerg; Jenks, Peter

2014-05-01

Quantitative NMR spectroscopy (qNMR) is gaining interest across both analytical and industrial research applications and has become an essential tool for the content assignment and quantitative determination of impurities. The key benefits of using qNMR as measurement method for the purity determination of organic molecules are discussed, with emphasis on the ability to establish traceability to "The International System of Units" (SI). The work describes a routine certification procedure from the point of view of a commercial producer of certified reference materials (CRM) under ISO/IEC 17025 and ISO Guide 34 accreditation, that resulted in a set of essential references for (1)H qNMR measurements, and the relevant application data for these substances are given. The overall process includes specific selection criteria, pre-tests, experimental conditions, homogeneity and stability studies. The advantages of an accelerated stability study over the classical stability-test design are shown with respect to shelf-life determination and shipping conditions. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Defining genetic and chemical diversity in wheat grain by 1H-NMR spectroscopy of polar metabolites.

PubMed

Shewry, Peter R; Corol, Delia I; Jones, Huw D; Beale, Michael H; Ward, Jane L

2017-07-01

The application of high-throughput 1H nuclear magnetic resonance (1H-NMR) of unpurified extracts to determine genetic diversity and the contents of polar components in grain of wheat. Milled whole wheat grain was extracted with 80:20 D 2 O:CD 3 OD containing 0.05% d 4 -trimethylsilylpropionate. 1H-NMR spectra were acquired under automation at 300°K using an Avance Spectrometer operating at 600.0528 MHz. Regions for individual metabolites were identified by comparison to a library of known standards run under identical conditions. The individual 1H-NMR peaks or levels of known metabolites were then compared by Principal Component Analysis using SIMCA-P software. High-throughput 1H-NMR is an excellent tool to compare the extent of genetic diversity within and between wheat species, and to quantify specific components (including glycine betaine, choline, and asparagine) in individual genotypes. It can also be used to monitor changes in composition related to environmental factors and to support comparisons of the substantial equivalence of transgenic lines. © 2017 Rothamsted Research. Molecular Nutrition & Food Research Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

In vivo carbon-13 nuclear magnetic resonance studies of heart metabolism.

PubMed Central

Neurohr, K J; Barrett, E J; Shulman, R G

1983-01-01

Guinea pig heart metabolism was studied in vivo by 13C NMR at 20.18 MHz. High-quality proton-decoupled 13C NMR spectra with excellent signal-to-noise ratios and resolution could be obtained in 6 min. Natural-abundance spectra showed resonances that could be assigned to fatty acids, but glycogen was not seen. During intravenous infusion of D-[1-13C]glucose and insulin, the time course of myocardial glycogen synthesis was followed serially for up to 4 hr. Anoxia resulted in degradation of the labeled glycogen within 6 min and appearance of 13C label in lactic acid. Infusion of sodium [2-13C]acetate resulted in incorporation of label into the C-4, C-2, and C-3 positions of glutamate and glutamine, reflecting "scrambling" of the label expected from tricarboxylic acid cycle activity. Examination of the 31P NMR spectrum of the guinea pig heart in vivo demonstrated no change in the high-energy phosphates during the time periods of the 13C NMR experiments. Our studies indicate that 13C NMR is a unique non-destructive tool for the study of heart metabolism in vivo. PMID:6572924

Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations

PubMed Central

Pastor, Nina; Amero, Carlos

2015-01-01

Proteins participate in information pathways in cells, both as links in the chain of signals, and as the ultimate effectors. Upon ligand binding, proteins undergo conformation and motion changes, which can be sensed by the following link in the chain of information. Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations represent powerful tools for examining the time-dependent function of biological molecules. The recent advances in NMR and the availability of faster computers have opened the door to more detailed analyses of structure, dynamics, and interactions. Here we briefly describe the recent applications that allow NMR spectroscopy and MD simulations to offer unique insight into the basic motions that underlie information transfer within and between cells. PMID:25999971

Computer planning tools applied to a cable logging research study

Treesearch

Chris B. LeDoux; Penn A. Peters

1985-01-01

Contemporary harvest planning software was used in planning the layout of cable logging units for a production study of the Clearwater Yarder in upstate New York. Planning software, including payload analysis and digital terrain models, allowed researchers to identify layout and yarding problems before the experiment. Analysis of proposed ground profiles pinpointed the...

Acoustic measurements on trees and logs: a review and analysis

Treesearch

Xiping Wang

2013-01-01

Acoustic technologies have been well established as material evaluation tools in the past several decades, and their use has become widely accepted in the forest products industry for online quality control and products grading. Recent research developments on acoustic sensing technology offer further opportunities to evaluate standing trees and logs for general wood...

Simpler ISS Flight Control Communications and Log Keeping via Social Tools and Techniques

NASA Technical Reports Server (NTRS)

Scott, David W.; Cowart, Hugh; Stevens, Dan

2012-01-01

The heart of flight operations control involves a) communicating effectively in real time with other controllers in the room and/or in remote locations and b) tracking significant events, decisions, and rationale to support the next set of decisions, provide a thorough shift handover, and troubleshoot/improve operations. International Space Station (ISS) flight controllers speak with each other via multiple voice circuits or loops, each with a particular purpose and constituency. Controllers monitor and/or respond to several loops concurrently. The primary tracking tools are console logs, typically kept by a single operator and not visible to others in real-time. Information from telemetry, commanding, and planning systems also plays into decision-making. Email is very secondary/tertiary due to timing and archival considerations. Voice communications and log entries supporting ISS operations have increased by orders of magnitude because the number of control centers, flight crew, and payload operations have grown. This paper explores three developmental ground system concepts under development at Johnson Space Center s (JSC) Mission Control Center Houston (MCC-H) and Marshall Space Flight Center s (MSFC) Payload Operations Integration Center (POIC). These concepts could reduce ISS control center voice traffic and console logging yet increase the efficiency and effectiveness of both. The goal of this paper is to kindle further discussion, exploration, and tool development.

Monitoring of NMR porosity changes in the full-size core salvage through the drying process

NASA Astrophysics Data System (ADS)

Fattakhov, Artur; Kosarev, Victor; Doroginitskii, Mikhail; Skirda, Vladimir

2015-04-01

Currently the principle of nuclear magnetic resonance (NMR) is one of the most popular technologies in the field of borehole geophysics and core analysis. Results of NMR studies allow to calculate the values of the porosity and permeability of sedimentary rocks with sufficient reliability. All standard tools for the study of core salvage on the basis of NMR have significant limitations: there is considered only long relaxation times corresponding to the mobile formation fluid. Current trends in energy obligate to move away from conventional oil to various alternative sources of energy. One of these sources are deposits of bitumen and high-viscosity oil. In Kazan (Volga Region) Federal University (Russia) there was developed a mobile unit for the study of the full-length core salvage by the NMR method ("NMR-Core") together with specialists of "TNG-Group" (a company providing maintenance services to oil companies). This unit is designed for the study of core material directly on the well, after removing it from the core receiver. The maximum diameter of the core sample may be up to 116 mm, its length (or length of the set of samples) may be up to 1000 mm. Positional precision of the core sample relative to the measurement system is 1 mm, and the spatial resolution along the axis of the core is 10 mm. Acquisition time of the 1 m core salvage varies depending on the mode of research and is at least 20 minutes. Furthermore, there is implemented a special investigation mode of the core samples with super small relaxation times (for example, heavy oil) is in the tool. The aim of this work is tracking of the NMR porosity changes in the full-size core salvage in time. There was used a water-saturated core salvage from the shallow educational well as a sample. The diameter of the studied core samples is 93 mm. There was selected several sections length of 1m from the 200-meter coring interval. The studied core samples are being measured several times. The time interval between the measurements is from 1 hour to 48 hours. Making the measurements it possible to draw conclusions about that the processes of NMR porosity changes in time as a result of evaporation of the part of fluid from the surface layer of the core salvage and suggest a core analysis technique directly on the well. This work is supported by the grant of Ministry of Education and Science of the Russian Federation (project No. 02.G25.31.0029).

Tannin structural elucidation and quantitative ³¹P NMR analysis. 2. Hydrolyzable tannins and proanthocyanidins.

PubMed

Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

2013-10-02

An unprecedented analytical method that allows simultaneous structural and quantitative characterization of all functional groups present in tannins is reported. In situ labeling of all labile H groups (aliphatic and phenolic hydroxyls and carboxylic acids) with a phosphorus-containing reagent (Cl-TMDP) followed by quantitative ³¹P NMR acquisition constitutes a novel fast and reliable analytical tool for the analysis of tannins and proanthocyanidins with significant implications for the fields of food and feed analyses, tannery, and the development of natural polyphenolics containing products.

Console Log Keeping Made Easier - Tools and Techniques for Improving Quality of Flight Controller Activity Logs

NASA Technical Reports Server (NTRS)

Scott, David W.; Underwood, Debrah (Technical Monitor)

2002-01-01

At the Marshall Space Flight Center's (MSFC) Payload Operations Integration Center (POIC) for International Space Station (ISS), each flight controller maintains detailed logs of activities and communications at their console position. These logs are critical for accurately controlling flight in real-time as well as providing a historical record and troubleshooting tool. This paper describes logging methods and electronic formats used at the POIC and provides food for thought on their strengths and limitations, plus proposes some innovative extensions. It also describes an inexpensive PC-based scheme for capturing and/or transcribing audio clips from communications consoles. Flight control activity (e.g. interpreting computer displays, entering data/issuing electronic commands, and communicating with others) can become extremely intense. It's essential to document it well, but the effort to do so may conflict with actual activity. This can be more than just annoying, as what's in the logs (or just as importantly not in them) often feeds back directly into the quality of future operations, whether short-term or long-term. In earlier programs, such as Spacelab, log keeping was done on paper, often using position-specific shorthand, and the other reader was at the mercy of the writer's penmanship. Today, user-friendly software solves the legibility problem and can automate date/time entry, but some content may take longer to finish due to individual typing speed and less use of symbols. File layout can be used to great advantage in making types of information easy to find, and creating searchable master logs for a given position is very easy and a real lifesaver in reconstructing events or researching a given topic. We'll examine log formats from several console position, and the types of information that are included and (just as importantly) excluded. We'll also look at when a summary or synopsis is effective, and when extensive detail is needed.

Determining the spatial altitude of the hydraulic fractures.

NASA Astrophysics Data System (ADS)

Khamiev, Marsel; Kosarev, Victor; Goncharova, Galina

2016-04-01

Mathematical modeling and numerical simulation are the most widely used approaches for the solving geological problems. They imply software tools which are based on Monte Carlo method. The results of this project presents shows the possibility of using PNL tool to determine fracturing location. The modeled media is a homogeneous rock (limestone) cut by a vertical borehole (d=216 mm) with metal casing 9 mm thick. The cement sheath is 35 mm thick. The borehole is filled with fresh water. The rock mass is cut by crack, filled with a mixture of doped (gadolinium oxide Gd2O3) proppant (75%) and water (25%). A pulse neutron logging (PNL) tool is used for quality control in hydraulic fracturing operations. It includes a fast neutron source (so-called "neutron generator") and a set of thermal (or epithermal) neutron-sensing devices, forming the so-called near (ND) and far (FD) detectors. To evaluate neutron properties various segments (sectors) of the rock mass, the detector must register only neutrons that come from this very formation. It's possible if detecting block includes some (6 for example) thermal neutron detectors arranged circumferentially inside the tool. As a result we get few independent well logs, each accords with define rock sector. Afterwards synthetic logs processing we can determine spatial position of the hydraulic fracture.

The experiences of undergraduate nursing students with bots in Second LifeRTM

NASA Astrophysics Data System (ADS)

Rose, Lesele H.

As technology continues to transform education from the status quo of traditional lecture-style instruction to an interactive engaging learning experience, students' experiences within the learning environment continues to change as well. This dissertation addressed the need for continuing research in advancing implementation of technology in higher education. The purpose of this phenomenological study was to discover more about the experiences of undergraduate nursing students using standardized geriatric evaluation tools when interacting with scripted geriatric patient bots tools in a simulated instructional intake setting. Data was collected through a Demographics questionnaire, an Experiential questionnaire, and a Reflection questionnaire. Triangulation of data collection occurred through an automatically created log of the interactions with the two bots, and by an automatically recorded log of the participants' movements while in the simulated geriatric intake interview. The data analysis consisted of an iterative review of the questionnaires and the participants' logs in an effort to identify common themes, recurring comments, and issues which would benefit from further exploration. Findings revealed that the interactions with the bots were perceived as a valuable experience for the participants from the perspective of interacting with the Geriatric Evaluation Tools in the role of an intake nurse. Further research is indicated to explore instructional interactions with bots in effectively mastering the use of established Geriatric Evaluation Tools.

Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

PubMed

Jeannerat, Damien

2017-01-01

The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Critical Zone structure inferred from multiscale near surface geophysical and hydrological data across hillslopes at the Eel River CZO

NASA Astrophysics Data System (ADS)

Lee, S. S.; Rempe, D. M.; Holbrook, W. S.; Schmidt, L.; Hahm, W. J.; Dietrich, W. E.

2017-12-01

Except for boreholes and road cut, landslide, and quarry exposures, the subsurface structure of the critical zone (CZ) of weathered bedrock is relatively invisible and unmapped, yet this structure controls the short and long term fluxes of water and solutes. Non-invasive geophysical methods such as seismic refraction are widely applied to image the structure of the CZ at the hillslope scale. However, interpretations of such data are often limited due to heterogeneity and anisotropy contributed from fracturing, moisture content, and mineralogy on the seismic signal. We develop a quantitative framework for using seismic refraction tomography from intersecting geophysical surveys and hydrologic data obtained at the Eel River Critical Zone Observatory (ERCZO) in Northern California to help quantify the nature of subsurface structure across multiple hillslopes of varying topography in the area. To enhance our understanding of modeled velocity gradients and boundaries in relation to lithological properties, we compare refraction tomography results with borehole logs of nuclear magnetic resonance (NMR), gamma and neutron density, standard penetration testing, and observation drilling logs. We also incorporate laboratory scale rock characterization including mineralogical and elemental analyses as well as porosity and density measurements made via pycnometry, helium and mercury porosimetry, and laboratory scale NMR. We evaluate the sensitivity of seismically inferred saprolite-weathered bedrock and weathered-unweathered bedrock boundaries to various velocity and inversion parameters in relation with other macro scale processes such as gravitational and tectonic forces in influencing weathered bedrock velocities. Together, our sensitivity analyses and multi-method data comparison provide insight into the interpretation of seismic refraction tomography for the quantification of CZ structure and hydrologic dynamics.

Resource Assessment of Methane Hydrate in the Eastern Nankai Trough, Japan

NASA Astrophysics Data System (ADS)

Fujii, T.; Saeki, T.; Kobayashi, T.; Inamori, T.; Hayashi, M.; Takano, O.

2007-12-01

Resource assessment of methane hydrate (MH) in the eastern Nankai Trough was conducted through probabilistic approach using 2D/3D seismic survey data and drilling survey data from METI exploratory test wells 'Tokai-oki to Kumano-nada' [1, 2, 3]. We have extracted several prospective 'MH concentrated zones' [4] characterized by high resistivity in well log, strong seismic reflector, seismic high velocity, and turbidite deposit delineated by sedimentary facies analysis. The amount of methane gas contained in MH bearing layers was calculated using volumetric method for each zone. Each parameter, such as Gross Rock Volume (GRV), net-to-gross ratio (N/G), MH pore saturation (Sh), porosity, cage occupancy, and volume ratio was given as probabilistic distribution for Monte Carlo simulation, considering the uncertainly of these values. The GRV for each hydrate bearing zones was calculated from both strong seismic amplitude anomaly and velocity anomaly. Time-to-depth conversion was conducted using interval velocity derived from SVWD (Seismic Vision While Drilling). Risk factor was applied for the estimation of the GRV in 2D seismic area considering the uncertainty of seismic interpretation. The N/G was determined based on the relationship between LWD (Logging While Drilling) resistivity and grain size in zones with existing wells. 3ohm-m was used for typical cut off value to determine net intervals. Seismic facies map created by sequence stratigraphic approach [5] was also used for the determination of the N/G in zone without well controls. Porosity was estimated using density log, together with calibration by core analysis. The Sh was estimated by the combination of density log and NMR log (DMR method), together with the calibration by observed gas volume from onboard MH dissociation tests using PTCS (Pressure Temperature Core Sampler) [6]. The Sh in zone without well control was estimated using relationship between seismic P-wave interval velocity and Sh from NMR log at well location. Cage occupancy was determined to be around 0.95 by refereeing recent field observations. Total amount of methane gas in place contained in MH in the eastern Nankai Trough within survey area was estimated to be 40 tcf as Pmean value (10 tcf as P90 value, 82 tcf as P10 value). Total gas in place for MH concentrated zone was estimated to be 20 tcf (Half of total amount) as Pmean value. Sensitivity analysis indicated that the N/G and Sh have higher sensitivity than other parameters, and they are important for further detail analysis. This study was carried out as a part of Research Consortium for Methane Hydrate Resource in Japan (MH21). [1] Takahashi et al. (2005): Proc. Of 2005 OTC, 2-5 May, Houston, Texas, U.S.A. [2] Fujii et al. (2005): Proc. Of 5th ICGH, Trondheim, Norway, 974-979. [3] Tsuji et al. (2007): AAPG Special Publication (in press). [4] Saeki et al. (2007): Abst. of 2007 Technical Meeting of the JAPT, June 5-7, 2007, Tokyo, p49. [5] Takano et al. (2007): Abst. of 2007 Technical Meeting of the JAPT, June 5-7, 2007, Tokyo, p34. [6] Fujii et al. (2007): AAPG Special Publication (in press).

Application of accelerator sources for pulsed neutron logging of oil and gas wells

NASA Astrophysics Data System (ADS)

Randall, R. R.

1985-05-01

Dresser Atlas introduced the first commercial pulsed neutron oil well log in the early 1960s. This log had the capability of differentiating oil from salt water in a completed well. In the late 1970s the first continuous carbon/oxygen (C/O) log capable of differentiating oil from fresh water was introduced. The sources used in these commercial logs are radial geometry deuterium-tritium reaction devices with Cockcroft-Walton voltage multipliers providing the accelerator voltage. The commercial logging tools using these accelerators are comprised of scintillators detectors, power supplies, line drivers and receivers, and various timing and communications electronics. They are used to measure either the time decay or energy spectra of neutron-induced gamma events. The time decay information is useful in determining the neutron capture cross section, and the energy spectra is used to characterize inelastic neutron events.

Computational Diffusion Magnetic Resonance Imaging Based on Time-Dependent Bloch NMR Flow Equation and Bessel Functions.

PubMed

Awojoyogbe, Bamidele O; Dada, Michael O; Onwu, Samuel O; Ige, Taofeeq A; Akinwande, Ninuola I

2016-04-01

Magnetic resonance imaging (MRI) uses a powerful magnetic field along with radio waves and a computer to produce highly detailed "slice-by-slice" pictures of virtually all internal structures of matter. The results enable physicians to examine parts of the body in minute detail and identify diseases in ways that are not possible with other techniques. For example, MRI is one of the few imaging tools that can see through bones, making it an excellent tool for examining the brain and other soft tissues. Pulsed-field gradient experiments provide a straightforward means of obtaining information on the translational motion of nuclear spins. However, the interpretation of the data is complicated by the effects of restricting geometries as in the case of most cancerous tissues and the mathematical concept required to account for this becomes very difficult. Most diffusion magnetic resonance techniques are based on the Stejskal-Tanner formulation usually derived from the Bloch-Torrey partial differential equation by including additional terms to accommodate the diffusion effect. Despite the early success of this technique, it has been shown that it has important limitations, the most of which occurs when there is orientation heterogeneity of the fibers in the voxel of interest (VOI). Overcoming this difficulty requires the specification of diffusion coefficients as function of spatial coordinate(s) and such a phenomenon is an indication of non-uniform compartmental conditions which can be analyzed accurately by solving the time-dependent Bloch NMR flow equation analytically. In this study, a mathematical formulation of magnetic resonance flow sequence in restricted geometry is developed based on a general second order partial differential equation derived directly from the fundamental Bloch NMR flow equations. The NMR signal is obtained completely in terms of NMR experimental parameters. The process is described based on Bessel functions and properties that can make it possible to distinguish cancerous cells from normal cells. A typical example of liver distinguished from gray matter, white matter and kidney is demonstrated. Bessel functions and properties are specifically needed to show the direct effect of the instantaneous velocity on the NMR signal originating from normal and abnormal tissues.

An empirical model for estimating annual consumption by freshwater fish populations

USGS Publications Warehouse

Liao, H.; Pierce, C.L.; Larscheid, J.G.

2005-01-01

Population consumption is an important process linking predator populations to their prey resources. Simple tools are needed to enable fisheries managers to estimate population consumption. We assembled 74 individual estimates of annual consumption by freshwater fish populations and their mean annual population size, 41 of which also included estimates of mean annual biomass. The data set included 14 freshwater fish species from 10 different bodies of water. From this data set we developed two simple linear regression models predicting annual population consumption. Log-transformed population size explained 94% of the variation in log-transformed annual population consumption. Log-transformed biomass explained 98% of the variation in log-transformed annual population consumption. We quantified the accuracy of our regressions and three alternative consumption models as the mean percent difference from observed (bioenergetics-derived) estimates in a test data set. Predictions from our population-size regression matched observed consumption estimates poorly (mean percent difference = 222%). Predictions from our biomass regression matched observed consumption reasonably well (mean percent difference = 24%). The biomass regression was superior to an alternative model, similar in complexity, and comparable to two alternative models that were more complex and difficult to apply. Our biomass regression model, log10(consumption) = 0.5442 + 0.9962??log10(biomass), will be a useful tool for fishery managers, enabling them to make reasonably accurate annual population consumption predictions from mean annual biomass estimates. ?? Copyright by the American Fisheries Society 2005.

Linking downhole logging data with geology and drilling /coring operations - Example from Chicxulub Expedition 364.

NASA Astrophysics Data System (ADS)

Lofi, Johanna; Smith, Dave; Delahunty, Chris; Le Ber, Erwan; Mellet, Claire; Brun, Laurent; Henry, Gilles; Paris, Jehanne

2017-04-01

Expedition 364 was a joint IODP/ICDP mission specific platform expedition to explore the Chicxulub impact crater buried below the Yucatán continental shelf. In April and May 2016, our Expedition drilled a single borehole at Site M0077A into the crater's peak ring. It allowed recovering 303 excellent quality cores from 505.7 to 1334.7 meters below sea floor and acquiring more than 5.8 km of high resolution open hole logs. Downhole logs are rapidly collected, continuous with depth, and measured in situ; these data are classically interpreted in terms of stratigraphy, lithology, porosity, fluid content, geochemical composition and structure of the formation drilled. Downhole logs also allow assessing borehole quality (eg. shape and trajectory), and can provide assistance for decision support during drilling operations. In this work, Expedition 364 downhole logs are used to improve our understanding of the drilling/coring operation history. Differentiating between natural geological features and borehole artifacts are also critical for data quality assessment. The set of downhole geophysical tools used during Expedition 364 was constrained by the scientific objectives, drilling/coring technique, hole conditions and temperature at the drill site. Wireline logging data were acquired with slimline tools in three logging phases at intervals 0-503, 506-699 and 700-1334 mbsf. Logs were recorded either with standalone logging tools or, for the first time in IODP, with stackable slimline tools. Log data included total gamma radiation, sonic velocity, acoustic and optical borehole images, resistivity, conductivity, magnetic susceptibility, caliper and borehole fluid parameters. The majority of measurements were performed in open borehole conditions. During the drilling operations some problems were encountered directly linked to the geology of the drilled formation. For example, two zones of mud circulation losses correlate in depth with the presence of karst cavities or open faults, as evidenced from borehole wall images. Both form conduits probably open at a large scale as suggested by associated anomalies in the borehole fluid temperature profiles. When coring the basement, pieces of metal trapped outside the drill bit apparently led to an increase of the borehole tilt as well as to an enlargement of the hole, although this later remained sub-circular. In the post impact carbonates, 6-7 m long apparent cyclic oscillations in the magnetic field coupled to a spiral shape trajectory of the same wavelength suggest drilling induced artifacts and formation re-magnetization. Acknowledgements: Expedition 364 was funded by IODP with co-funding from ICDP and implemented by ECORD, with contributions and logistical support from the Yucatán state government and Universidad Nacional Autónoma de México. Drilling Services were provided by DOSECC Exploration Services. The downhole logging program was coordinated by EPC, as part of ESO. Expedition 364 Scientists: S. Gulick, J.V. Morgan, E. Chenot, G. Christeson, P. Claeys, C. Cockell, M.J. L. Coolen, L. Ferrière, C. Gebhardt, K. Goto, H. Jones, D.A. Kring, J. Lofi, X. Long, C. Lowery, C. Mellett, R. Ocampo-Torres, L. Perez-Cruz, A. Pickersgill, M. Poelchau, A. Rae, C. Rasmussen, M. Rebolledo-Vieyra, U. Riller, H. Sato, J. Smit, S. Tikoo, N. Tomioka, M. Whalen, A. Wittmann, J. Urrutia-Fucugauchi, K.E. Yamaguchi, W. Zylberman.

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

Ilsche, Thomas; Schuchart, Joseph; Cope, Joseph

Event tracing is an important tool for understanding the performance of parallel applications. As concurrency increases in leadership-class computing systems, the quantity of performance log data can overload the parallel file system, perturbing the application being observed. In this work we present a solution for event tracing at leadership scales. We enhance the I/O forwarding system software to aggregate and reorganize log data prior to writing to the storage system, significantly reducing the burden on the underlying file system for this type of traffic. Furthermore, we augment the I/O forwarding system with a write buffering capability to limit the impactmore » of artificial perturbations from log data accesses on traced applications. To validate the approach, we modify the Vampir tracing tool to take advantage of this new capability and show that the approach increases the maximum traced application size by a factor of 5x to more than 200,000 processors.« less

Bidentate urea derivatives of p-tert-butyldihomooxacalix[4]arene: neutral receptors for anion complexation.

PubMed

Marcos, Paula M; Teixeira, Filipa A; Segurado, Manuel A P; Ascenso, José R; Bernardino, Raul J; Michel, Sylvia; Hubscher-Bruder, Véronique

2014-01-17

Three new bidentate ureidodihomooxacalix[4]arene derivatives (phenyl 5a, n-propyl 5b, and tert-butyl 5c) were synthesized in four steps from the parent compound p-tert-butyldihomooxacalix[4]arene and obtained in the cone conformation, as shown by NMR studies. The binding ability of these neutral receptors toward spherical, linear, trigonal planar, and tetrahedrical anions was assessed by (1)H NMR and UV-vis titrations. The structures and complexation energies of some complexes were also studied by DFT methods. The data showed that the association constants are strongly dependent on the nature of the substituent (aryl/alkyl) at the urea moiety. In general, for all the receptors, the association constants decrease with decrease of anion basicity. Ph-urea 5a is the best anion receptor, showing the strongest complexation for F(-) (log K(assoc) = 3.10 in CDCl3) and also high binding affinity for the carboxylates AcO(-) and BzO(-). Similar results were obtained by UV-vis studies and were also corroborated by DFT calculations.

Forensic timber identification: It's time to integrate disciplines to combat illegal logging

Treesearch

Eleanor E. Dormontt; Markus Boner; Birgit Braun; Gerhard Breulmann; Bernd Degen; Edgard Espinoza; Shelley Gardner; Phil Guillery; John C. Hermanson; Gerald Koch; Soon Leong Lee; Milton Kanashiro; Anto Rimbawanto; Darren Thomas; Alex C. Wiedenhoeft; Yafang Yin; Johannes Zahnen; Andrew J. Lowe

2015-01-01

The prosecution of illegal logging crimes is hampered by a lack of available forensic timber identification tools, both for screening of suspectmaterial and definitive identification of illegally sourcedwood. Reputable timber traders are also struggling to police their own supply chains and comply with the growing requirement for due diligence with respect to timber...

Educational Data Mining and Problem-Based Learning

ERIC Educational Resources Information Center

Walldén, Sari; Mäkinen, Erkki

2014-01-01

This paper considers the use of log data provided by learning management systems when studying whether students obey the problem-based learning (PBL) method. Log analysis turns out to be a valuable tool in measuring the use of the learning material of interest. It gives reliable figures concerning not only the number of use sessions but also the…

Beyond Logging of Fingertip Actions: Analysis of Collaborative Learning Using Multiple Sources of Data

ERIC Educational Resources Information Center

Avouris, N.; Fiotakis, G.; Kahrimanis, G.; Margaritis, M.; Komis, V.

2007-01-01

In this article, we discuss key requirements for collecting behavioural data concerning technology-supported collaborative learning activities. It is argued that the common practice of analysis of computer generated log files of user interactions with software tools is not enough for building a thorough view of the activity. Instead, more…

Diameter sensors for tree-length harvesting systems

Treesearch

T.P. McDonald; Robert B. Rummer; T.E. Grift

2003-01-01

Most cut-to-length (CTL) harvesters provide sensors for measuring diameter of trees as they are cut and processed. Among other uses, this capability provides a data collection tool for marketing of logs in real time. Logs can be sorted and stacked based on up-to-date market information, then transportation systems optimized to route wood to proper destinations at...

CT Imaging, Data Reduction, and Visualization of Hardwood Logs

Treesearch

Daniel L. Schmoldt

1996-01-01

Computer tomography (CT) is a mathematical technique that, combined with noninvasive scanning such as x-ray imaging, has become a powerful tool to nondestructively test materials prior to use or to evaluate materials prior to processing. In the current context, hardwood lumber processing can benefit greatly by knowing what a log looks like prior to initial breakdown....

Automated clustering-based workload characterization

NASA Technical Reports Server (NTRS)

Pentakalos, Odysseas I.; Menasce, Daniel A.; Yesha, Yelena

1996-01-01

The demands placed on the mass storage systems at various federal agencies and national laboratories are continuously increasing in intensity. This forces system managers to constantly monitor the system, evaluate the demand placed on it, and tune it appropriately using either heuristics based on experience or analytic models. Performance models require an accurate workload characterization. This can be a laborious and time consuming process. It became evident from our experience that a tool is necessary to automate the workload characterization process. This paper presents the design and discusses the implementation of a tool for workload characterization of mass storage systems. The main features of the tool discussed here are: (1)Automatic support for peak-period determination. Histograms of system activity are generated and presented to the user for peak-period determination; (2) Automatic clustering analysis. The data collected from the mass storage system logs is clustered using clustering algorithms and tightness measures to limit the number of generated clusters; (3) Reporting of varied file statistics. The tool computes several statistics on file sizes such as average, standard deviation, minimum, maximum, frequency, as well as average transfer time. These statistics are given on a per cluster basis; (4) Portability. The tool can easily be used to characterize the workload in mass storage systems of different vendors. The user needs to specify through a simple log description language how the a specific log should be interpreted. The rest of this paper is organized as follows. Section two presents basic concepts in workload characterization as they apply to mass storage systems. Section three describes clustering algorithms and tightness measures. The following section presents the architecture of the tool. Section five presents some results of workload characterization using the tool.Finally, section six presents some concluding remarks.

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

PubMed Central

2011-01-01

Background Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments. Description MeRy-B, the first platform for plant 1H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues. Conclusion MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php. PMID:21668943

Solution NMR views of dynamical ordering of biomacromolecules.

PubMed

Ikeya, Teppei; Ban, David; Lee, Donghan; Ito, Yutaka; Kato, Koichi; Griesinger, Christian

2018-02-01

To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Online monitoring of fermentation processes via non-invasive low-field NMR.

PubMed

Kreyenschulte, Dirk; Paciok, Eva; Regestein, Lars; Blümich, Bernhard; Büchs, Jochen

2015-09-01

For the development of biotechnological processes in academia as well as in industry new techniques are required which enable online monitoring for process characterization and control. Nuclear magnetic resonance (NMR) spectroscopy is a promising analytical tool, which has already found broad applications in offline process analysis. The use of online monitoring, however, is oftentimes constrained by high complexity of custom-made NMR bioreactors and considerable costs for high-field NMR instruments (>US$200,000). Therefore, low-field (1) H NMR was investigated in this study in a bypass system for real-time observation of fermentation processes. The new technique was validated with two microbial systems. For the yeast Hansenula polymorpha glycerol consumption could accurately be assessed in spite of the presence of high amounts of complex constituents in the medium. During cultivation of the fungal strain Ustilago maydis, which is accompanied by the formation of several by-products, the concentrations of glucose, itaconic acid, and the relative amount of glycolipids could be quantified. While low-field spectra are characterized by reduced spectral resolution compared to high-field NMR, the compact design combined with the high temporal resolution (15 s-8 min) of spectra acquisition allowed online monitoring of the respective processes. Both applications clearly demonstrate that the investigated technique is well suited for reaction monitoring in opaque media while at the same time it is highly robust and chemically specific. It can thus be concluded that low-field NMR spectroscopy has a great potential for non-invasive online monitoring of biotechnological processes at the research and practical industrial scales. © 2015 Wiley Periodicals, Inc.

Diagnosis of coinfection by schistosomiasis and viral hepatitis B or C using 1H NMR-based metabonomics.

PubMed

Gouveia, Liana Ribeiro; Santos, Joelma Carvalho; Silva, Ronaldo Dionísio; Batista, Andrea Dória; Domingues, Ana Lúcia Coutinho; Lopes, Edmundo Pessoa de Almeida; Silva, Ricardo Oliveira

2017-01-01

Diagnosis of liver involvement due to schistosomiasis in asymptomatic patients from endemic areas previously diagnosed with chronic hepatitis B (HBV) or C (HCV) and periportal fibrosis is challenging. H-1 Nuclear Magnetic Resonance (NMR)-based metabonomics strategy is a powerful tool for providing a profile of endogenous metabolites of low molecular weight in biofluids in a non-invasive way. The aim of this study was to diagnose periportal fibrosis due to schistosomiasis mansoni in patients with chronic HBV or HCV infection through NMR-based metabonomics models. The study included 40 patients divided into two groups: (i) 18 coinfected patients with schistosomiasis mansoni and HBV or HCV; and (ii) 22 HBV or HCV monoinfected patients. The serum samples were analyzed through H-1 NMR spectroscopy and the models were based on Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA). Ultrasonography examination was used to ascertain the diagnosis of periportal fibrosis. Exploratory analysis showed a clear separation between coinfected and monoinfected samples. The supervised model built from PLS-DA showed accuracy, R2 and Q2 values equal to 100%, 98.1% and 97.5%, respectively. According to the variable importance in the projection plot, lactate serum levels were higher in the coinfected group, while the signals attributed to HDL serum cholesterol were more intense in the monoinfected group. The metabonomics models constructed in this study are promising as an alternative tool for diagnosis of periportal fibrosis by schistosomiasis in patients with chronic HBV or HCV infection from endemic areas for Schistosoma mansoni.

Formation pressure testing at the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope: Operational summary, history matching, and interpretations

USGS Publications Warehouse

Anderson, B.; Hancock, S.; Wilson, S.; Enger, C.; Collett, T.; Boswell, R.; Hunter, R.

2011-01-01

In February 2007, the U.S. Department of Energy, BP Exploration (Alaska), and the U.S. Geological Survey, collected open-hole pressure-response data, as well as gas and water sample collection, in a gas hydrate reservoir (the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well) using Schlumberger's Modular Dynamics Formation Tester (MDT) wireline tool. Four such MDT tests, ranging from six to twelve hours duration, and including a series of flow, sampling, and shut-in periods of various durations, were conducted. Locations for the testing were selected based on NMR and other log data to assure sufficient isolation from reservoir boundaries and zones of excess free water. Test stages in which pressure was reduced sufficiently to mobilize free water in the formation (yet not cause gas hydrate dissociation) produced readily interpretable pressure build-up profiles. Build-ups following larger drawdowns consistently showed gas-hydrate dissociation and gas release (as confirmed by optical fluid analyzer data), as well as progressive dampening of reservoir pressure build-up during sequential tests at a given MDT test station.History matches of one multi-stage, 12-h test (the C2 test) were accomplished using five different reservoir simulators: CMG-STARS, HydrateResSim, MH21-HYDRES, STOMP-HYD, and TOUGH. +. HYDRATE. Simulations utilized detailed information collected across the reservoir either obtained or determined from geophysical well logs, including thickness (11.3. m, 37 ft.), porosity (35%), hydrate saturation (65%), both mobile and immobile water saturations, intrinsic permeability (1000 mD), pore water salinity (5 ppt), and formation temperature (3.3-3.9 ??C). This paper will present the approach and preliminary results of the history-matching efforts, including estimates of initial formation permeability and analyses of the various unique features exhibited by the MDT results. ?? 2010 Elsevier Ltd.

New LWD tools are just in time to probe for baby elephants

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

Ghiselin, D.

Development of sophisticated formation evaluation instrumentation for use while drilling has led to a stratification of while-drilling services. Measurements while drilling (MWD) comprises measurements of mechanical parameters like weight-on-bit, mud pressures, torque, vibration, hole angle and direction. Logging while drilling (LWD) describes resistivity, sonic, and radiation logging which rival wireline measurements in accuracy. A critical feature of LWD is the rate that data can be telemetered to the surface. Early tools could only transmit 3 bits per second one way. In the last decade, the data rate has more than tripled. Despite these improvements, LWD tools have the ability tomore » make many more measurements than can be telemetered in real-time. The paper discusses the development of this technology and its applications.« less

Radiotracer properties determined by high performance liquid chromatography: a potential tool for brain radiotracer discovery.

PubMed

Tavares, Adriana Alexandre S; Lewsey, James; Dewar, Deborah; Pimlott, Sally L

2012-01-01

Previously, development of novel brain radiotracers has largely relied on simple screening tools. Improved selection methods at the early stages of radiotracer discovery and an increased understanding of the relationships between in vitro physicochemical and in vivo radiotracer properties are needed. We investigated if high performance liquid chromatography (HPLC) methodologies could provide criteria for lead candidate selection by comparing HPLC measurements with radiotracer properties in humans. Ten molecules, previously used as radiotracers in humans, were analysed to obtain the following measures: partition coefficient (Log P); permeability (P(m)); percentage of plasma protein binding (%PPB); and membrane partition coefficient (K(m)). Relationships between brain entry measurements (Log P, P(m) and %PPB) and in vivo brain percentage injected dose (%ID); and K(m) and specific binding in vivo (BP(ND)) were investigated. Log P values obtained using in silico packages and flask methods were compared with Log P values obtained using HPLC. The modelled associations with %ID were stronger for %PPB (r(2)=0.65) and P(m) (r(2)=0.77) than for Log P (r(2)=0.47) while 86% of BP(ND) variance was explained by K(m). Log P values were variable dependant on the methodology used. Log P should not be relied upon as a predictor of blood-brain barrier penetration during brain radiotracer discovery. HPLC measurements of permeability, %PPB and membrane interactions may be potentially useful in predicting in vivo performance and hence allow evaluation and ranking of compound libraries for the selection of lead radiotracer candidates at early stages of radiotracer discovery. Copyright © 2012 Elsevier Inc. All rights reserved.

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.

NMR methods for metabolomics of mammalian cell culture bioreactors.

PubMed

Aranibar, Nelly; Reily, Michael D

2014-01-01

Metabolomics has become an important tool for measuring pools of small molecules in mammalian cell cultures expressing therapeutic proteins. NMR spectroscopy has played an important role, largely because it requires minimal sample preparation, does not require chromatographic separation, and is quantitative. The concentrations of large numbers of small molecules in the extracellular media or within the cells themselves can be measured directly on the culture supernatant and on the supernatant of the lysed cells, respectively, and correlated with endpoints such as titer, cell viability, or glycosylation patterns. The observed changes can be used to generate hypotheses by which these parameters can be optimized. This chapter focuses on the sample preparation, data acquisition, and analysis to get the most out of NMR metabolomics data from CHO cell cultures but could easily be extended to other in vitro culture systems.

GRASP - A Prototype Interactive Graphic Sawing Program - (Forest Products Journal)

Treesearch

Luis G. Occeña; Daniel L. Schmoldt

1996-01-01

A versatile microcomputer-based interactive graphics sawing program has been developed as a tool for modeling various hardwood processes, from bucking and topping to log sawing, lumber edging, secondary processing, and even veneering. The microcomputer platform makes the tool affordable and accessible. A solid modeling basis provides the tool with a sound geometrical...

GRASP - A Prototype Interactive Graphic Sawing Program - (MU-IE Technical Report)

Treesearch

Luis G. Occeña; Daniel L. Schmoldt

1995-01-01

A versatile microcomputer-based interactive graphics program has been developed as a tool for modeling various hardwood processes, from bucking and topping to log sawing, lumber edging, secondary processing, even veneering. The microcomputer platform makes the tool affordable and accessible.A solid modeling basis provides the tool with a sound geometrical and...

Is Low-field NMR a Complementary Tool to GC-MS in Quality Control of Essential Oils? A Case Study: Patchouli Essential Oil.

PubMed

Krause, Andre; Wu, Yu; Tian, Runtao; van Beek, Teris A

2018-04-24

High-field NMR is an expensive and important quality control technique. In recent years, cheaper and simpler low-field NMR has become available as a new quality control technique. In this study, 60 MHz 1 H-NMR was compared with GC-MS and refractometry for the detection of adulteration of essential oils, taking patchouli essential oil as a test case. Patchouli essential oil is frequently adulterated, even today. In total, 75 genuine patchouli essential oils, 10 commercial patchouli essential oils, 10 other essential oils, 17 adulterants, and 1 patchouli essential oil, spiked at 20% with those adulterants, were measured. Visual inspection of the NMR spectra allowed for easy detection of 14 adulterants, while gurjun and copaiba balsams proved difficult and one adulterant could not be detected. NMR spectra of 10 random essential oils differed not only strongly from patchouli essential oil but also from one another, suggesting that fingerprinting by low-field NMR is not limited to patchouli essential oil. Automated chemometric evaluation of NMR spectra was possible by similarity analysis (Mahalanobis distance) based on the integration from 0.1 - 8.1 ppm in 0.01 ppm increments. Good quality patchouli essential oils were recognised as well as 15 of 17 deliberate adulterations. Visual qualitative inspection by GC-MS allowed for the detection of all volatile adulterants. Nonvolatile adulterants, and all but one volatile adulterant, could be detected by semiquantitation. Different chemometric approaches showed satisfactory results. Similarity analyses were difficult with nonvolatile adulterants. Refractive index measurements could detect only 8 of 17 adulterants. Due to advantages such as simplicity, rapidity, reproducibility, and ability to detect nonvolatile adulterants, 60 MHz 1 H-NMR is complimentary to GC-MS for quality control of essential oils. Georg Thieme Verlag KG Stuttgart · New York.

Ceramic vacuum tubes for geothermal well logging

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

Kelly, R.D.

1977-01-12

The results of investigations carried out into the availability and suitability of ceramic vacuum tubes for the development of logging tools for geothermal wells are summarized. Design data acquired in the evaluation of ceramic vacuum tubes for the development of a 500/sup 0/C instrumentation amplifier are presented. The general requirements for ceramic vacuum tubes for application to the development of high temperature well logs are discussed. Commercially available tubes are described and future contract activities that specifically relate to ceramic vacuum tubes are detailed. Supplemental data is presented in the appendix. (MHR)

Multicriteria evaluation of simulated logging scenarios in a tropical rain forest.

PubMed

Huth, Andreas; Drechsler, Martin; Köhler, Peter

2004-07-01

Forest growth models are useful tools for investigating the long-term impacts of logging. In this paper, the results of the rain forest growth model FORMIND were assessed by a multicriteria decision analysis. The main processes covered by FORMIND include tree growth, mortality, regeneration and competition. Tree growth is calculated based on a carbon balance approach. Trees compete for light and space; dying large trees fall down and create gaps in the forest. Sixty-four different logging scenarios for an initially undisturbed forest stand at Deramakot (Malaysia) were simulated. The scenarios differ regarding the logging cycle, logging method, cutting limit and logging intensity. We characterise the impacts with four criteria describing the yield, canopy opening and changes in species composition. Multicriteria decision analysis was used for the first time to evaluate the scenarios and identify the efficient ones. Our results plainly show that reduced-impact logging scenarios are more 'efficient' than the others, since in these scenarios forest damage is minimised without significantly reducing yield. Nevertheless, there is a trade-off between yield and achieving a desired ecological state of logged forest; the ecological state of the logged forests can only be improved by reducing yields and enlarging the logging cycles. Our study also demonstrates that high cutting limits or low logging intensities cannot compensate for the high level of damage caused by conventional logging techniques.

Simultaneous 19F-1H medium resolution NMR spectroscopy for online reaction monitoring

NASA Astrophysics Data System (ADS)

Zientek, Nicolai; Laurain, Clément; Meyer, Klas; Kraume, Matthias; Guthausen, Gisela; Maiwald, Michael

2014-12-01

Medium resolution nuclear magnetic resonance (MR-NMR) spectroscopy is currently a fast developing field, which has an enormous potential to become an important analytical tool for reaction monitoring, in hyphenated techniques, and for systematic investigations of complex mixtures. The recent developments of innovative MR-NMR spectrometers are therefore remarkable due to their possible applications in quality control, education, and process monitoring. MR-NMR spectroscopy can beneficially be applied for fast, non-invasive, and volume integrating analyses under rough environmental conditions. Within this study, a simple 1/16″ fluorinated ethylene propylene (FEP) tube with an ID of 0.04″ (1.02 mm) was used as a flow cell in combination with a 5 mm glass Dewar tube inserted into a benchtop MR-NMR spectrometer with a 1H Larmor frequency of 43.32 MHz and 40.68 MHz for 19F. For the first time, quasi-simultaneous proton and fluorine NMR spectra were recorded with a series of alternating 19F and 1H single scan spectra along the reaction time coordinate of a homogeneously catalysed esterification model reaction containing fluorinated compounds. The results were compared to quantitative NMR spectra from a hyphenated 500 MHz online NMR instrument for validation. Automation of handling, pre-processing, and analysis of NMR data becomes increasingly important for process monitoring applications of online NMR spectroscopy and for its technical and practical acceptance. Thus, NMR spectra were automatically baseline corrected and phased using the minimum entropy method. Data analysis schemes were designed such that they are based on simple direct integration or first principle line fitting, with the aim that the analysis directly revealed molar concentrations from the spectra. Finally, the performance of 1/16″ FEP tube set-up with an ID of 1.02 mm was characterised regarding the limit of detection (LOQ (1H) = 0.335 mol L-1 and LOQ (19F) = 0.130 mol L-1 for trifluoroethanol in D2O (single scan)) and maximum quantitative flow rates up to 0.3 mL min-1. Thus, a series of single scan 19F and 1H NMR spectra acquired with this simple set-up already presents a valuable basis for quantitative reaction monitoring.

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method.

PubMed

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13 C NMR spectrometry (irm- 13 C NMR) provides the complete 13 C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13 C natural abundance values (50‰), irm- 13 C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13 C NMR. Until now, the conventional strategy to determine the position-specific abundance x i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13 C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13 C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1 H NMR pulse sequence (named DWET) with a 13 C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T 1 , which forms a serious limitation for irm- 13 C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T 1 variations. Their performance is evaluated on the determination of the 13 C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm- 13 C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time. Copyright © 2018 Elsevier Inc. All rights reserved.

A discrete Fourier-encoded, diagonal-free experiment to simplify homonuclear 2D NMR correlations.

PubMed

Huang, Zebin; Guan, Quanshuai; Chen, Zhong; Frydman, Lucio; Lin, Yulan

2017-07-21

Nuclear magnetic resonance (NMR) spectroscopy has long served as an irreplaceable, versatile tool in physics, chemistry, biology, and materials sciences, owing to its ability to study molecular structure and dynamics in detail. In particular, the connectivity of chemical sites within molecules, and thereby molecular structure, becomes visible by multi-dimensional NMR. Homonuclear correlation experiments are a powerful tool for identifying coupled spins. Generally, diagonal peaks in these correlation spectra display the strongest intensities and do not offer any new information beyond the standard one-dimensional spectrum, whereas weaker, symmetrically placed cross peaks contain most of the coupling information. The cross peaks near the diagonal are often affected by the tails of strong diagonal peaks or even obscured entirely by the diagonal. In this paper, we demonstrate a homonuclear encoding approach based on imparting a discrete phase modulation of the targeted cross peaks and combine it with a site-selective sculpting scheme, capable of simplifying the patterns arising in these 2D correlation spectra. The theoretical principles of the new methods are laid out, and experimental observations are rationalized on the basis of theoretical analyses. The ensuing techniques provide a new way to retrieve 2D coupling information within homonuclear spin systems, with enhanced sensitivity, speed, and clarity.

A discrete Fourier-encoded, diagonal-free experiment to simplify homonuclear 2D NMR correlations

NASA Astrophysics Data System (ADS)

Huang, Zebin; Guan, Quanshuai; Chen, Zhong; Frydman, Lucio; Lin, Yulan

2017-07-01

Nuclear magnetic resonance (NMR) spectroscopy has long served as an irreplaceable, versatile tool in physics, chemistry, biology, and materials sciences, owing to its ability to study molecular structure and dynamics in detail. In particular, the connectivity of chemical sites within molecules, and thereby molecular structure, becomes visible by multi-dimensional NMR. Homonuclear correlation experiments are a powerful tool for identifying coupled spins. Generally, diagonal peaks in these correlation spectra display the strongest intensities and do not offer any new information beyond the standard one-dimensional spectrum, whereas weaker, symmetrically placed cross peaks contain most of the coupling information. The cross peaks near the diagonal are often affected by the tails of strong diagonal peaks or even obscured entirely by the diagonal. In this paper, we demonstrate a homonuclear encoding approach based on imparting a discrete phase modulation of the targeted cross peaks and combine it with a site-selective sculpting scheme, capable of simplifying the patterns arising in these 2D correlation spectra. The theoretical principles of the new methods are laid out, and experimental observations are rationalized on the basis of theoretical analyses. The ensuing techniques provide a new way to retrieve 2D coupling information within homonuclear spin systems, with enhanced sensitivity, speed, and clarity.

Use of processed resistivity borehole imaging to assess the insoluble content of the massively bedded Preesall Halite NW England

NASA Astrophysics Data System (ADS)

Kingdon, Andrew; Evans, David J.

2013-04-01

With the decline of the UK's remaining conventional reserves of natural gas and associated growth of imports, the lack of adequate storage capacity is a matter of concern for ensuring energy security year-round. In a number of countries, subsurface caverns for gas storage have been created by solution mining of massive halite deposits and similar storage facilities are likely to become an important part of the UK's energy infrastructure. Crucial to the economic viability of such facilities is the percentage of insoluble material within the halite intervals, which influences strongly the relationship between cavern sump and working volumes: successful development of these caverns is dependent upon maximising the efficiency of cavern design and construction. The purity of a massive halite sequence can only be assessed either by direct means (i.e. coring) or indirectly by downhole geophysical logs The use of conventional geophysical logs in subsurface exploration is well established but literature generally relies on a very low resolution tools with a typical vertical logging sample interval of 15 centimetres. This means that such tools provide, at best, a "blurred" view of the sedimentary successions penetrated by the borehole and that discrete narrow bands of insoluble material will not be identifiable or distinguishable from zones of "dirtier" halite with disseminated mud materials. In 2008, Halite-Energy Group (formerly Canatxx Gas Storage Ltd) drilled the Burrows Marsh #1 borehole and acquired resistivity borehole imaging (FMI) logs through the Triassic Preesall Halite in the Preesall Saltfield, NW England. In addition to near full circumferal imaging capability, rather than a single measurement per increment, FMI logs allows millimetre to centimetre scale imaging of sedimentary features, that is one to two orders of magnitude higher vertical resolution. After binary segmentation of the FMI images to achieve a simple halite-insoluble ("mud") separation these were subject to a filtering process to develop a detailed understanding of the halite sequence's insoluble content. The results were then calibrated, post-normalisation, by new laboratory determinations of the insoluble content of laterally equivalent samples of core from the nearby Arm Hill #1 borehole. The FMI logs provide a greater degree of resolution when compared to conventional geophysical logs. With the statistical analysis provided by this process, it further enhances the correlation between the logs and core and ultimately, the assessment of insoluble content. Despite the obvious increase in resolution, precise statistical quantification of the success of the borehole imaging technique is somewhat obfuscated by the absence of both FMI logs and continuous core in a single borehole. The acquisition parameters for these images are at the limits for the tools and therefore more noisy than those acquired in other lithologies or logging environments. The optimum acquisition parameters (in particular gain settings and logging speed), the nature of the filtering required to quantify the insoluble content and the effects of image noise on those calculations are discussed.

Analysis of commercial proanthocyanidins. Part 4: solid state (13)C NMR as a tool for in situ analysis of proanthocyanidin tannins, in heartwood and bark of quebracho and acacia, and related species.

PubMed

Reid, David G; Bonnet, Susan L; Kemp, Gabre; van der Westhuizen, Jan H

2013-10-01

(13)C NMR is an effective method of characterizing proanthocyanidin (PAC) tannins in quebracho (Schinopsis lorentzii) heartwood and black wattle (Acacia mearnsii) bark, before and after commercial extraction. The B-rings of the constituent flavan-3-ols, catechols (quebracho) or pyrogallols (wattle), are recognized in unprocessed source materials by "marker" signals at ca. 118 or 105ppm, respectively. NMR allows the minimum extraction efficiency to be calculated; ca. 30%, and ca. 80%, for quebracho heartwood and black wattle bark, respectively. NMR can also identify PAC tannin (predominantly robinetinidin), and compare tannin content, in bark from other acacia species; tannin content decreases in the order A. mearnsii, Acacia pycnantha (87% of A. mearnsii), Acacia dealbata and Acacia decurrens (each 74%) and Acacia karroo (30%). Heartwood from an underexploited PAC tannin source, Searsia lancea, taxonomically close to quebracho, shows abundant profisetinidin and catechin PACs. NMR offers the advantage of being applicable to source materials in their native state, and has potential applications in optimizing extraction processes, identification of tannin sources, and characterization of tannin content in cultivar yield improvement programmes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.

PubMed

Kobayashi, Masakazu; Retra, Kim; Figaroa, Francis; Hollander, Johan G; Ab, Eiso; Heetebrij, Robert J; Irth, Hubertus; Siegal, Gregg

2010-09-01

Fragment-based drug discovery (FBDD) has become a widely accepted tool that is complementary to high-throughput screening (HTS) in developing small-molecule inhibitors of pharmaceutical targets. Because a fragment campaign can only be as successful as the hit matter found, it is critical that the first stage of the process be optimized. Here the authors compare the 3 most commonly used methods for hit discovery in FBDD: high concentration screening (HCS), solution ligand-observed nuclear magnetic resonance (NMR), and surface plasmon resonance (SPR). They selected the commonly used saturation transfer difference (STD) NMR spectroscopy and the proprietary target immobilized NMR screening (TINS) as representative of the array of possible NMR methods. Using a target typical of FBDD campaigns, the authors find that HCS and TINS are the most sensitive to weak interactions. They also find a good correlation between TINS and STD for tighter binding ligands, but the ability of STD to detect ligands with affinity weaker than 1 mM K(D) is limited. Similarly, they find that SPR detection is most suited to ligands that bind with K(D) better than 1 mM. However, the good correlation between SPR and potency in a bioassay makes this a good method for hit validation and characterization studies.

Tannin fingerprinting in vegetable tanned leather by solid state NMR spectroscopy and comparison with leathers tanned by other processes.

PubMed

Romer, Frederik H; Underwood, Andrew P; Senekal, Nadine D; Bonnet, Susan L; Duer, Melinda J; Reid, David G; van der Westhuizen, Jan H

2011-01-28

Solid state ¹³C-NMR spectra of pure tannin powders from four different sources--mimosa, quebracho, chestnut and tara--are readily distinguishable from each other, both in pure commercial powder form, and in leather which they have been used to tan. Groups of signals indicative of the source, and type (condensed vs. hydrolyzable) of tannin used in the manufacture are well resolved in the spectra of the finished leathers. These fingerprints are compared with those arising from leathers tanned with other common tanning agents. Paramagnetic chromium (III) tanning causes widespread but selective disappearance of signals from the spectrum of leather collagen, including resonances from acidic aspartyl and glutamyl residues, likely bound to Cr (III) structures. Aluminium (III) and glutaraldehyde tanning both cause considerable leather collagen signal sharpening suggesting some increase in molecular structural ordering. The ²⁷Al-NMR signal from the former material is consistent with an octahedral coordination by oxygen ligands. Solid state NMR thus provides easily recognisable reagent specific spectral fingerprints of the products of vegetable and some other common tanning processes. Because spectra are related to molecular properties, NMR is potentially a powerful tool in leather process enhancement and quality or provenance assurance.

1H NMR-Based Metabolomic Analysis of Sub-Lethal Perfluorooctane Sulfonate Exposure to the Earthworm, Eisenia fetida, in Soil

PubMed Central

Lankadurai, Brian P.; Furdui, Vasile I.; Reiner, Eric J.; Simpson, André J.; Simpson, Myrna J.

2013-01-01

1H NMR-based metabolomics was used to measure the response of Eisenia fetida earthworms after exposure to sub-lethal concentrations of perfluorooctane sulfonate (PFOS) in soil. Earthworms were exposed to a range of PFOS concentrations (five, 10, 25, 50, 100 or 150 mg/kg) for two, seven and fourteen days. Earthworm tissues were extracted and analyzed by 1H NMR. Multivariate statistical analysis of the metabolic response of E. fetida to PFOS exposure identified time-dependent responses that were comprised of two separate modes of action: a non-polar narcosis type mechanism after two days of exposure and increased fatty acid oxidation after seven and fourteen days of exposure. Univariate statistical analysis revealed that 2-hexyl-5-ethyl-3-furansulfonate (HEFS), betaine, leucine, arginine, glutamate, maltose and ATP are potential indicators of PFOS exposure, as the concentrations of these metabolites fluctuated significantly. Overall, NMR-based metabolomic analysis suggests elevated fatty acid oxidation, disruption in energy metabolism and biological membrane structure and a possible interruption of ATP synthesis. These conclusions obtained from analysis of the metabolic profile in response to sub-lethal PFOS exposure indicates that NMR-based metabolomics is an excellent discovery tool when the mode of action (MOA) of contaminants is not clearly defined. PMID:24958147

Applications of NMR and computational methodologies to study protein dynamics.

PubMed

Narayanan, Chitra; Bafna, Khushboo; Roux, Louise D; Agarwal, Pratul K; Doucet, Nicolas

2017-08-15

Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes. Copyright © 2017 Elsevier Inc. All rights reserved.

5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy

PubMed Central

Puffer, Barbara; Kreutz, Christoph; Rieder, Ulrike; Ebert, Marc-Olivier; Konrat, Robert; Micura, Ronald

2009-01-01

19F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondary structure equilibria were chosen as model systems and analyzed by 1D 19F and 1H NMR spectroscopy. A comparison with the unmodified analogs revealed that the equilibrium characteristics of the bistable DNA and RNA oligonucleotides were hardly affected upon fluorine substitution at C5 of pyrimidines. This observation was in accordance with UV spectroscopic melting experiments which demonstrated that single 5-fluoro substitutions in double helices lead to comparable thermodynamic stabilities. Thus, 5-fluoro pyrimidine labeling of DNA and RNA can be reliably applied for NMR based nucleic acid secondary structure evaluation. Furthermore, we developed a facile synthetic route towards 5-fluoro cytidine phosphoramidites that enables their convenient site-specific incorporation into oligonucleotides by solid-phase synthesis. PMID:19843610

5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy.

PubMed

Puffer, Barbara; Kreutz, Christoph; Rieder, Ulrike; Ebert, Marc-Olivier; Konrat, Robert; Micura, Ronald

2009-12-01

(19)F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondary structure equilibria were chosen as model systems and analyzed by 1D (19)F and (1)H NMR spectroscopy. A comparison with the unmodified analogs revealed that the equilibrium characteristics of the bistable DNA and RNA oligonucleotides were hardly affected upon fluorine substitution at C5 of pyrimidines. This observation was in accordance with UV spectroscopic melting experiments which demonstrated that single 5-fluoro substitutions in double helices lead to comparable thermodynamic stabilities. Thus, 5-fluoro pyrimidine labeling of DNA and RNA can be reliably applied for NMR based nucleic acid secondary structure evaluation. Furthermore, we developed a facile synthetic route towards 5-fluoro cytidine phosphoramidites that enables their convenient site-specific incorporation into oligonucleotides by solid-phase synthesis.

Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction.

PubMed

Kuhn, Stefan; Egert, Björn; Neumann, Steffen; Steinbeck, Christoph

2008-09-25

Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances and measurements of their concentration. Still, only a fraction of existing metabolites and their spectral fingerprints are known. Computer-Assisted Structure Elucidation (CASE) of biological metabolites will be an important tool to leverage this lack of knowledge. Indispensable for CASE are modules to predict spectra for hypothetical structures. This paper evaluates different statistical and machine learning methods to perform predictions of proton NMR spectra based on data from our open database NMRShiftDB. A mean absolute error of 0.18 ppm was achieved for the prediction of proton NMR shifts ranging from 0 to 11 ppm. Random forest, J48 decision tree and support vector machines achieved similar overall errors. HOSE codes being a notably simple method achieved a comparatively good result of 0.17 ppm mean absolute error. NMR prediction methods applied in the course of this work delivered precise predictions which can serve as a building block for Computer-Assisted Structure Elucidation for biological metabolites.

Solvent signal suppression for high-resolution MAS-DNP

NASA Astrophysics Data System (ADS)

Lee, Daniel; Chaudhari, Sachin R.; De Paëpe, Gaël

2017-05-01

Dynamic nuclear polarization (DNP) has become a powerful tool to substantially increase the sensitivity of high-field magic angle spinning (MAS) solid-state NMR experiments. The addition of dissolved hyperpolarizing agents usually results in the presence of solvent signals that can overlap and obscure those of interest from the analyte. Here, two methods are proposed to suppress DNP solvent signals: a Forced Echo Dephasing experiment (FEDex) and TRAnsfer of Populations in DOuble Resonance Echo Dephasing (TRAPDORED) NMR. These methods reintroduce a heteronuclear dipolar interaction that is specific to the solvent, thereby forcing a dephasing of recoupled solvent spins and leaving acquired NMR spectra free of associated resonance overlap with the analyte. The potency of these methods is demonstrated on sample types common to MAS-DNP experiments, namely a frozen solution (of L-proline) and a powdered solid (progesterone), both containing deuterated glycerol as a DNP solvent. The proposed methods are efficient, simple to implement, compatible with other NMR experiments, and extendable past spectral editing for just DNP solvents. The sensitivity gains from MAS-DNP in conjunction with FEDex or TRAPDORED then permits rapid and uninterrupted sample analysis.

Chemical synthesis and NMR characterization of structured polyunsaturated triacylglycerols.

PubMed

Fauconnot, Laëtitia; Robert, Fabien; Villard, Renaud; Dionisi, Fabiola

2006-02-01

The chemical synthesis of pure triacylglycerol (TAG) regioisomers, that contain long chain polyunsaturated fatty acids, such as arachidonic acid (AA) or docosahexaenoic acid (DHA), and saturated fatty acids, such as lauric acid (La) or palmitic acid (P), at defined positions, is described. A single step methodology using (benzotriazol-1-yloxy)-tripyrrolidinophosphonium hexafluorophosphate (PyBOP), an activator of carboxyl group commonly used in peptide synthesis and occasionally used in carboxylic acid esterification, has been developed for structured TAG synthesis. Identification of the fatty acyl chains for each TAG species was confirmed by atmospheric pressure chemical ionisation mass spectrometry (APCI-MS) and fatty acid positional distribution was determined by (1)H and (13)C NMR spectra. The generic described procedures can be applied to a large variety of substrates and was used for the production of specific triacylglycerols of defined molecular structures, with high regioisomeric purity. Combination of MS and NMR was shown to be an efficient tool for structural analysis of TAG. In particular, some NMR signals were demonstrated to be regioisomer specific, allowing rapid positional analysis of LC-PUFA containing TAG.

Low-field NMR logging sensor for measuring hydraulic parameters of model soils

NASA Astrophysics Data System (ADS)

Sucre, Oscar; Pohlmeier, Andreas; Minière, Adrien; Blümich, Bernhard

2011-08-01

SummaryKnowing the exact hydraulic parameters of soils is very important for improving water management in agriculture and for the refinement of climate models. Up to now, however, the investigation of such parameters has required applying two techniques simultaneously which is time-consuming and invasive. Thus, the objective of this current study is to present only one technique, i.e., a new non-invasive method to measure hydraulic parameters of model soils by using low-field nuclear magnetic resonance (NMR). Hereby, two model clay or sandy soils were respectively filled in a 2 m-long acetate column having an integrated PVC tube. After the soils were completely saturated with water, a low-field NMR sensor was moved up and down in the PVC tube to quantitatively measure along the whole column the initial water content of each soil sample. Thereafter, both columns were allowed to drain. Meanwhile, the NMR sensor was set at a certain depth to measure the water content of that soil slice. Once the hydraulic equilibrium was reached in each of the two columns, a final moisture profile was taken along the whole column. Three curves were subsequently generated accordingly: (1) the initial moisture profile, (2) the evolution curve of the moisture depletion at that particular depth, and (3) the final moisture profile. All three curves were then inverse analyzed using a MATLAB code over numerical data produced with the van Genuchten-Mualem model. Hereby, a set of values ( α, n, θr and θs) was found for the hydraulic parameters for the soils under research. Additionally, the complete decaying NMR signal could be analyzed through Inverse Laplace Transformation and averaged on the 1/ T2 space. Through measurement of the decay in pure water, the effect on the relaxation caused by the sample could be estimated from the obtained spectra. The migration of the sample-related average <1/ T2, Sample> with decreasing saturation speaks for a enhancement of the surface relaxation as the soil dries, in concordance with results found by other authors. In conclusion, this low-field mobile NMR technique has proven itself to be a fast and a non-invasive mean to investigate the hydraulic behavior of soils and to explore microscopical aspect of the water retained in them. In the future, the sensor should allow easy soil moisture measurements on-field.

Structure, equilibrium and ligand exchange dynamics in the binary and ternary dioxouranium(VI)-ethylenediamine-N,N'-diacetic acid-fluoride system: A potentiometric, NMR and X-ray crystallographic study.

PubMed

Palladino, Giuseppe; Szabó, Zoltán; Fischer, Andreas; Grenthe, Ingmar

2006-11-21

The structure, thermodynamics and kinetics of the binary and ternary uranium(VI)-ethylenediamine-N,N'-diacetate (in the following denoted EDDA) fluoride systems have been studied using potentiometry, 1H, 19F NMR spectroscopy and X-ray diffraction. The UO2(2+)-EDDA system could be studied up to -log[H3O+] = 3.4 where the formation of two binary complexes UO2(EDDA)(aq) and UO2(H3EDDA)3+ were identified, with equilibrium constants logbeta(UO2EDDA) = 11.63 +/- 0.02 and logbeta(UO2H3EDDA3+) = 1.77 +/- 0.04, respectively. In the ternary system the complexes UO2(EDDA)F-, UO2(EDDA)(OH)- and (UO2)2(mu-OH)2(HEDDA)2F2(aq) were identified; the latter through 19F NMR. 1H NMR spectra indicate that the EDDA ligand is chelate bonded in UO2(EDDA)(aq), UO2(EDDA)F- and UO2(EDDA)(OH)- while only one carboxylate group is coordinated in UO2(H3EDDA)3+. The rate and mechanism of the fluoride exchange between UO2(EDDA)F- and free fluoride was studied by 19F NMR spectroscopy. Three reactions contribute to the exchange; (i) site exchange between UO2(EDDA)F- and free fluoride without any net chemical exchange, (ii) replacement of the coordinated fluoride with OH- and (iii) the self dissociation of the coordinated fluoride forming UO2(EDDA)(aq); these reactions seem to follow associative mechanisms. (1)H NMR spectra show that the exchange between the free and chelate bonded EDDA is slow and consists of several steps, protonation/deprotonation and chelate ring opening/ring closure, the mechanism cannot be elucidated from the available data. The structure (UO2)2(EDDA)2(mu-H2EDDA) was determined by single crystal X-ray diffraction and contains two UO2(EDDA) units with tetracoordinated EDDA linked by H2EDDA in the "zwitterion" form, coordinated through a single carboxylate oxygen from each end to the two uranium atoms. The geometry of the complexes indicates that there is no geometric constraint for an associative ligand substitution mechanism.

"Ask Ernö": a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra.

PubMed

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

2016-01-01

We present "Ask Ernö", a self-learning system for the automatic analysis of NMR spectra, consisting of integrated chemical shift assignment and prediction tools. The output of the automatic assignment component initializes and improves a database of assigned protons that is used by the chemical shift predictor. In turn, the predictions provided by the latter facilitate improvement of the assignment process. Iteration on these steps allows Ask Ernö to improve its ability to assign and predict spectra without any prior knowledge or assistance from human experts. This concept was tested by training such a system with a dataset of 2341 molecules and their (1)H-NMR spectra, and evaluating the accuracy of chemical shift predictions on a test set of 298 partially assigned molecules (2007 assigned protons). After 10 iterations, Ask Ernö was able to decrease its prediction error by 17 %, reaching an average error of 0.265 ppm. Over 60 % of the test chemical shifts were predicted within 0.2 ppm, while only 5 % still presented a prediction error of more than 1 ppm. Ask Ernö introduces an innovative approach to automatic NMR analysis that constantly learns and improves when provided with new data. Furthermore, it completely avoids the need for manually assigned spectra. This system has the potential to be turned into a fully autonomous tool able to compete with the best alternatives currently available.Graphical abstractSelf-learning loop. Any progress in the prediction (forward problem) will improve the assignment ability (reverse problem) and vice versa.

Repose time and cumulative moment magnitude: A new tool for forecasting eruptions?

USGS Publications Warehouse

Thelen, W.A.; Malone, S.D.; West, M.E.

2010-01-01

During earthquake swarms on active volcanoes, one of the primary challenges facing scientists is determining the likelihood of an eruption. Here we present the relation between repose time and the cumulative moment magnitude (CMM) as a tool to aid in differentiating between an eruption and a period of unrest. In several case studies, the CMM is lower at shorter repose times than it is at longer repose times. The relationship between repose time and CMM may be linear in log-log space, particularly at Mount St. Helens. We suggest that the volume and competence of the plug within the conduit drives the strength of the precursory CMM.

Rapid estimation of aquifer salinity structure from oil and gas geophysical logs

NASA Astrophysics Data System (ADS)

Shimabukuro, D.; Stephens, M.; Ducart, A.; Skinner, S. M.

2016-12-01

We describe a workflow for creating aquifer salinity maps using Archie's equation for areas that have geophysical data from oil and gas wells. We apply this method in California, where geophysical logs are available in raster format from the Division of Oil, Gas, and Geothermal Resource (DOGGR) online archive. This method should be applicable to any region where geophysical logs are readily available. Much of the work is controlled by computer code, allowing salinity estimates for new areas to be rapidly generated. For a region of interest, the DOGGR online database is scraped for wells that were logged with multi-tool suites, such as the Platform Express or Triple Combination Logging Tools. Then, well construction metadata, such as measured depth, spud date, and well orientation, is attached. The resultant local database allows a weighted criteria selection of wells that are most likely to have the shallow resistivity, deep resistivity, and density porosity measurements necessary to calculate salinity over the longest depth interval. The algorithm can be adjusted for geophysical log availability for older well fields and density of sampling. Once priority wells are identified, a student researcher team uses Neuralog software to digitize the raster geophysical logs. Total dissolved solid (TDS) concentration is then calculated in clean, wet sand intervals using the resistivity-porosity method, a modified form of Archie's equation. These sand intervals are automatically selected using a combination of spontaneous potential and the difference in shallow resistivity and deep resistivity measurements. Gamma ray logs are not used because arkosic sands common in California make it difficult to distinguish sand and shale. Computer calculation allows easy adjustment of Archie's parameters. The result is a semi-continuous TDS profile for the wells of interest. These profiles are combined and contoured using standard 3-d visualization software to yield preliminary salinity maps for the region of interest. We present results for select well fields in the Southern San Joaquin Valley, California.

Para-hydrogen induced polarization of Si-29 NMR resonances as a potentially useful tool for analytical applications.

PubMed

Ellena, Silvano; Viale, Alessandra; Gobetto, Roberto; Aime, Silvio

2012-08-01

Para-hydrogen-induced polarization effects have been observed in the (29)Si NMR spectra of trimethylsilyl para-hydrogenated molecules. The high signal enhancements and the long T(1) values observed for the (29)Si hyperpolarized resonances point toward the possibility of using (29)Si for hyperpolarization applications. A method for the discrimination of multiple compounds and/or complex mixtures of hydroxylic compounds (such as steroids), consisting of the silylization of alcoholic functionalities with an unsaturated silylalkyl moiety and subsequent reaction with para-H(2), is proposed. Copyright © 2012 John Wiley & Sons, Ltd.

Detection of low-level PTFE contamination: An application of solid-state NMR to structure elucidation in the pharmaceutical industry.

PubMed

Pham, Tran N; Day, Caroline J; Edwards, Andrew J; Wood, Helen R; Lynch, Ian R; Watson, Simon A; Bretonnet, Anne-Sophie Z; Vogt, Frederick G

2011-01-25

We report a novel use of solid-state ¹⁹F nuclear magnetic resonance to detect and quantify polytetrafluoroethylene contamination from laboratory equipment, which due to low quantity (up to 1% w/w) and insolubility remained undetected by standard analytical techniques. Solid-state ¹⁹F NMR is shown to be highly sensitive to such fluoropolymers (detection limit 0.02% w/w), and is demonstrated as a useful analytical tool for structure elucidation of unknown solid materials. Copyright © 2010 Elsevier B.V. All rights reserved.

Fundamentals of Acoustic Measurements on Trees and Logs and Their Implication to Field Application

Treesearch

Xiping Wang

2011-01-01

Acoustic technologies have been well established as material evaluation tools in the past several decades, and their use has become widely accepted in the forest products industry for on-line quality control and products grading. Recent research developments on acoustic sensing technology offer further opportunities to evaluate standing trees and logs for general wood...

Using Web Logs in the Science Classroom

ERIC Educational Resources Information Center

Duplichan, Staycle C.

2009-01-01

As educators we must ask ourselves if we are meeting the needs of today's students. The science world is adapting to our ever-changing society; are the methodology and philosophy of our educational system keeping up? In this article, you'll learn why web logs (also called blogs) are an important Web 2.0 tool in your science classroom and how they…

Utility of remotely sensed imagery for assessing the impact of salvage logging after forest fires

Treesearch

Sarah A. Lewis; Peter R. Robichaud; Andrew T. Hudak; Brian Austin; Robert J. Liebermann

2012-01-01

Remotely sensed imagery provides a useful tool for land managers to assess the extent and severity of post-wildfire salvage logging disturbance. This investigation uses high resolution QuickBird and National Agricultural Imagery Program (NAIP) imagery to map soil exposure after ground-based salvage operations. Three wildfires with varying post-fire salvage activities...

Bioassessment of silvicultural impacts in streams and wetlands of the eastern United States

Treesearch

John J. Hutchens; Darold P. Batzer; Elizabeth Reese

2003-01-01

Bioassessment is a useful tool to determine the impact of logging practices on the biological integrity of streams and wetlands. Measuring biota directly has an intuitive appeal for impact assessment, and biota can be superior indicators to physical or chemical characteristics because they can reflect cumulative impacts over time. Logging can affect stream and wetland...

Statistics, Structures & Satisfied Customers: Using Web Log Data to Improve Site Performance.

ERIC Educational Resources Information Center

Peacock, Darren

This paper explores some of the ways in which the National Museum of Australia is using Web analysis tools to shape its future directions in the delivery of online services. In particular, it explores the potential of quantitative analysis, based on Web server log data, to convert these ephemeral traces of user experience into a strategic…

Neuromorphic log-domain silicon synapse circuits obey bernoulli dynamics: a unifying tutorial analysis

PubMed Central

Papadimitriou, Konstantinos I.; Liu, Shih-Chii; Indiveri, Giacomo; Drakakis, Emmanuel M.

2014-01-01

The field of neuromorphic silicon synapse circuits is revisited and a parsimonious mathematical framework able to describe the dynamics of this class of log-domain circuits in the aggregate and in a systematic manner is proposed. Starting from the Bernoulli Cell Formalism (BCF), originally formulated for the modular synthesis and analysis of externally linear, time-invariant logarithmic filters, and by means of the identification of new types of Bernoulli Cell (BC) operators presented here, a generalized formalism (GBCF) is established. The expanded formalism covers two new possible and practical combinations of a MOS transistor (MOST) and a linear capacitor. The corresponding mathematical relations codifying each case are presented and discussed through the tutorial treatment of three well-known transistor-level examples of log-domain neuromorphic silicon synapses. The proposed mathematical tool unifies past analysis approaches of the same circuits under a common theoretical framework. The speed advantage of the proposed mathematical framework as an analysis tool is also demonstrated by a compelling comparative circuit analysis example of high order, where the GBCF and another well-known log-domain circuit analysis method are used for the determination of the input-output transfer function of the high (4th) order topology. PMID:25653579

Neuromorphic log-domain silicon synapse circuits obey bernoulli dynamics: a unifying tutorial analysis.

PubMed

Papadimitriou, Konstantinos I; Liu, Shih-Chii; Indiveri, Giacomo; Drakakis, Emmanuel M

2014-01-01

The field of neuromorphic silicon synapse circuits is revisited and a parsimonious mathematical framework able to describe the dynamics of this class of log-domain circuits in the aggregate and in a systematic manner is proposed. Starting from the Bernoulli Cell Formalism (BCF), originally formulated for the modular synthesis and analysis of externally linear, time-invariant logarithmic filters, and by means of the identification of new types of Bernoulli Cell (BC) operators presented here, a generalized formalism (GBCF) is established. The expanded formalism covers two new possible and practical combinations of a MOS transistor (MOST) and a linear capacitor. The corresponding mathematical relations codifying each case are presented and discussed through the tutorial treatment of three well-known transistor-level examples of log-domain neuromorphic silicon synapses. The proposed mathematical tool unifies past analysis approaches of the same circuits under a common theoretical framework. The speed advantage of the proposed mathematical framework as an analysis tool is also demonstrated by a compelling comparative circuit analysis example of high order, where the GBCF and another well-known log-domain circuit analysis method are used for the determination of the input-output transfer function of the high (4(th)) order topology.

NMR-based Metabolomics Applications in Biological and Environmental Science

EPA Science Inventory

As a complimentary tool to other omics platforms, metabolomics is increasingly being used bybiologists to study the dynamic response of biological systems (cells, tissues, or wholeorganisms) under diverse physiological or pathological conditions. Metabolomics deals with the quali...

NMR-based Metabolomics for Cancer Research

EPA Science Inventory

Metabolomics is considered as a complementary tool to other omics platforms to provide a snapshot of the cellular biochemistry and physiology taking place at any instant. Metabolmics approaches have been widely used to provide comprehensive and quantitative analyses of the metabo...

Using nuclear magnetic resonance and transient electromagnetics to characterise water distribution beneath an ice covered volcanic crater: the case of Sherman Crater Mt. Baker Washington.

USGS Publications Warehouse

Irons, Trevor P.; Martin, Kathryn; Finn, Carol A.; Bloss, Benjamin; Horton, Robert J.

2014-01-01

Surface and laboratory Nuclear Magnetic Resonance (NMR) measurements combined with transient electromagnetic (TEM) data are powerful tools for subsurface water detection. Surface NMR (sNMR) and TEM soundings, laboratory NMR, complex resistivity, and X-Ray Diffraction (XRD) analysis were all conducted to characterise the distribution of water within Sherman Crater on Mt. Baker, WA. Clay rich rocks, particularly if water saturated, can weaken volcanoes, thereby increasing the potential for catastrophic sector collapses that can lead to far-travelled, destructive debris flows. Detecting the presence and volume of shallow groundwater is critical for evaluating these landslide hazards. The TEM data identified a low resistivity layer (<10 ohm-m), under 60 m of glacial ice related to water saturated clays. The TEM struggles to resolve the presence or absence of a plausible thin layer of bulk liquid water on top of the clay. The sNMR measurements did not produce any observable signal, indicating the lack of substantial accumulated bulk water below the ice. Laboratory analysis on a sample from the crater wall that likely represented the clays beneath the ice confirmed that the controlling factor for the lack of sNMR signal was the fine-grained nature of the media. The laboratory measurements further indicated that small pores in clays detected by the XRD contain as much as 50% water, establishing an upper bound on the water content in the clay layer. Forward modelling of geologic scenarios revealed that bulk water layers as thin as ½ m between the ice and clay layer would have been detectable using sNMR. The instrumentation conditions which would allow for sNMR detection of the clay layer are investigated. Using current instrumentation the combined analysis of the TEM and sNMR data allow for valuable characterisation of the groundwater system in the crater. The sNMR is able to reduce the uncertainty of the TEM in regards to the presence of a bulk water layer, a valuable piece of information in hazard assessment.

Pattern mining of user interaction logs for a post-deployment usability evaluation of a radiology PACS client.

PubMed

Jorritsma, Wiard; Cnossen, Fokie; Dierckx, Rudi A; Oudkerk, Matthijs; van Ooijen, Peter M A

2016-01-01

To perform a post-deployment usability evaluation of a radiology Picture Archiving and Communication System (PACS) client based on pattern mining of user interaction log data, and to assess the usefulness of this approach compared to a field study. All user actions performed on the PACS client were logged for four months. A data mining technique called closed sequential pattern mining was used to automatically extract frequently occurring interaction patterns from the log data. These patterns were used to identify usability issues with the PACS. The results of this evaluation were compared to the results of a field study based usability evaluation of the same PACS client. The interaction patterns revealed four usability issues: (1) the display protocols do not function properly, (2) the line measurement tool stays active until another tool is selected, rather than being deactivated after one use, (3) the PACS's built-in 3D functionality does not allow users to effectively perform certain 3D-related tasks, (4) users underuse the PACS's customization possibilities. All usability issues identified based on the log data were also found in the field study, which identified 48 issues in total. Post-deployment usability evaluation based on pattern mining of user interaction log data provides useful insights into the way users interact with the radiology PACS client. However, it reveals few usability issues compared to a field study and should therefore not be used as the sole method of usability evaluation. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

New Era of Scientific Ocean Drilling

NASA Astrophysics Data System (ADS)

Eguchi, N.; Toczko, S.; Sanada, Y.; Igarashi, C.; Kubo, Y.; Maeda, L.; Sawada, I.; Takase, K.; Kyo, N.

2014-12-01

The D/V Chikyu, committed to scientific ocean drilling since 2007, has completed thirteen IODP expeditions, and Chikyu's enhanced drilling technology gives us the means to reach deep targets, enhanced well logging, deep water riserless drilling, and state of the art laboratory. Chikyu recovered core samples from 2466 meters below sea floor (mbsf) in IODP Exp. 337, and drilled to 3058.5 mbsf in IODP Exp. 348, but these are still not the limit of Chikyu's capability. As deep as these depths are, they are just halfway to the 5200 mbsf plate boundary target for the NanTroSEIZE deep riser borehole. There are several active IODP proposals in the pipeline. Each has scientific targets requiring several thousand meters of penetration below the sea floor. Riser technology is the only way to collect samples and data from that depth. Well logging has been enhanced with the adoption of riser drilling, especially for logging-while-drilling (LWD). LWD has several advantages over wireline logging, and provides more opportunities for continuous measurements even in unstable boreholes. Because of the larger diameter of riser pipes and enhanced borehole stability, Chikyu can use several state-of-the-art downhole tools, e.g. fracture tester, fluid sampling tool, wider borehole imaging, and the latest sonic tools. These new technologies and tools can potentially expand the envelope of scientific ocean drilling. Chikyu gives us access to ultra-deep water riserless drilling. IODP Exp. 343/343T investigating the March 2011 Tohoku Oki Earthquake, explored the toe of the landward slope of the Japan Trench. This expedition reached the plate boundary fault target at more than 800 mbsf in water depths over 6900 m for logging-while-drilling, coring, and observatory installation. This deep-water drilling capability also expands the scientific ocean drilling envelope and provides access to previously unreachable targets. On top of these operational capabilities, Chikyu's onboard laboratory is equipped with state-of-the-art instruments to analyze all science samples. X-ray CT creates non-destructive 3D images of core samples providing high resolution structural detail. The microbiology laboratory offers clean and contamination-free work environments required for microbiological samples.

A Pipeline Software Architecture for NMR Spectrum Data Translation

PubMed Central

Ellis, Heidi J.C.; Weatherby, Gerard; Nowling, Ronald J.; Vyas, Jay; Fenwick, Matthew; Gryk, Michael R.

2012-01-01

The problem of formatting data so that it conforms to the required input for scientific data processing tools pervades scientific computing. The CONNecticut Joint University Research Group (CONNJUR) has developed a data translation tool based on a pipeline architecture that partially solves this problem. The CONNJUR Spectrum Translator supports data format translation for experiments that use Nuclear Magnetic Resonance to determine the structure of large protein molecules. PMID:24634607

An investigation of the sensitivity of low-field nuclear magnetic resonance to microbial growth and activity

NASA Astrophysics Data System (ADS)

Zhang, C.; Keating, K.

2014-12-01

Microbes and microbial processes play a significant role in shaping subsurface environments and are involved in applications ranging from microbially enhanced oil recovery to soil and groundwater contaminant remediation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface; however, due to the complexity of subsurface systems,it is difficult to monitor the growth of microbes and microbial activity in porous media. The focus of this research is to determine if low-field nuclear magnetic resonance (NMR), a method used in well logging to characterize fluids in hydrocarbon reservoirs or water in aquifers, can be used to directly detect the presence and the growth of microbes in geologic media. In this laboratory study, low-field NMR (2 MHz) relaxation measurements were collected on microbial suspensions with measured densities (i.e. biomasses), microbial pellets (live and dead), and inoculated silica. We focus on the direct contribution of microbes to the NMR signals in the absence of biomineralization. Shewanella oneidensis (MR-1), a facultative metal reducer known to play an important role in subsurface environments, were used as a model organism and were inoculated under aerobic condition. Data were collected using a CPMG pulse sequence, which was to determine the T2-distribution, and using a gradient spin-echo (PGSE) plus CPMG pulse sequence, which was used to encode diffusion properties and determine the effective diffusion-spin-spin relaxation correlation (D-T2) plot. Our data show no obvious change in the T2-distribution as S. oneidensis density varied in suspension, but show a clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets. A decrease in the T2-distribution is observed in the inoculated sand column. These results will provide a basis for understanding the effect of microbes within geologic media on low-field NMR measurements. This research is necessary to determine if NMR measurements can ultimately to be used to monitor microbial growth and activity in oil reservoirs or contaminated aquifers.

Results of investigations at the Zunil geothermal field, Guatemala: Well logging and brine geochemistry

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

Adams, A.; Dennis, B.; Van Eeckhout, E.

1991-07-01

The well logging team from Los Alamos and its counterpart from Central America were tasked to investigate the condition of four producing geothermal wells in the Zunil Geothermal Field. The information obtained would be used to help evaluate the Zunil geothermal reservoir in terms of possible additional drilling and future power plant design. The field activities focused on downhole measurements in four production wells (ZCQ-3, ZCQ-4, ZCQ-5, and ZCQ-6). The teams took measurements of the wells in both static (shut-in) and flowing conditions, using the high-temperature well logging tools developed at Los Alamos National Laboratory. Two well logging missions weremore » conducted in the Zunil field. In October 1988 measurements were made in well ZCQ-3, ZCQ-5, and ZCQ-6. In December 1989 the second field operation logged ZCQ-4 and repeated logs in ZCQ-3. Both field operations included not only well logging but the collecting of numerous fluid samples from both thermal and nonthermal waters. 18 refs., 22 figs., 7 tabs.« less

Thick massive gas hydrate deposits were revealed by LWD in Off-Joetsu area, eastern margin of Japan Sea.

NASA Astrophysics Data System (ADS)

Tanahashi, M.; Morita, S.; Matsumoto, R.

2016-12-01

GR14 and HR15 survey cruises, which were dedicated to the LWD (Logging While Drilling), were carried out in summers of 2014 and 2015, respectively, by Meiji University and Geological Survey of Japan, AIST to explore the "gas chimney" structures in eastern margin of Japan Sea. Shallow (33 to 172m-bsf, average 136m-bsf) 33 LWD drilling were performed in Oki Trough, Off-Joetsu, and Mogami Trough areas along eastern margin of Japan Sea during two cruises. Schlumberger LWD tools, GeoVISION (resistivity), TeleScope, ProVISION (NMR) and SonicVISION were used during GR14. NeoScope (neutron) was added and SonicScope was replaced for SonicVISION during HR14. The data quality was generally good. "Gas chimney" structures with acoustic blanking columns on the high frequency seismic sections with mound and pockmark morphologic features on the sea bottom, are well developed within survey areas. Every LWD records taken from gas chimney structures during the cruises show high resistivity and acoustic velocity anomalies which suggest the development of gas hydrate. Characteristic development of massive gas hydrate was interpreted at the Umitaka CW mound structure, Off-Joetsu. The mound lies at 890-910m in water depth and has very rough bottom surface, regional high resistivity, regional high heat flow, several natural seep sites, 200m x 300m area, and 10-20m height. 8 LWD holes, J18L to J21L and J23L to J26L, were drilled on and around the mound. There are highly anomalous intervals which suggest the development of massive gas hydrate at J24L, with high resistivity, high Vp and Vs, high neutron porosity, low natural gamma ray intensity, low neutron gamma density, low NMR porosity, low NMR permeability, low formation sigma, from 10 to 110m-bsf with intercalating some thin less hydrate layers. It is interpreted that there is several tens of meter thick massive gas hydrate in the gas chimney mound. It is partly confirmed by the later nearby coring result which showed the repetition of the several meter thick massive hydrate recovery (Matsumoto et al., in this conference). Other LWD data at the sites on the mound shows lesser than J24L but still highly concentrated gas hydrate deposits. This study was conducted as a part of the methane hydrate research project funded by METI (the Ministry of Economy, Trade and Industry, Japan).

Validation of an Electronic System for Recording Medical Student Patient Encounters

PubMed Central

Nkoy, Flory L.; Petersen, Sarah; Matheny Antommaria, Armand H.; Maloney, Christopher G.

2008-01-01

The Liaison Committee for Medical Education requires monitoring of the students’ clinical experiences. Student logs, typically used for this purpose, have a number of limitations. We used an electronic system called Patient Tracker to passively generate student encounter data. The data contained in Patient Tracker was compared to the information reported on student logs and data abstracted from the patients’ charts. Patient Tracker identified 30% more encounters than the student logs. Compared to the student logs, Patient Tracker contained a higher average number of diagnoses per encounter (2.28 vs. 1.03, p<0.01). The diagnostic data contained in Patient Tracker was also more accurate under 4 different definitions of accuracy. Only 1.3% (9/677) of diagnoses in Patient Tracker vs. 16.9% (102/601) diagnoses in the logs could not be validated in patients’ charts (p<0.01). Patient Tracker is a more effective and accurate tool for documenting student clinical encounters than the conventional student logs. PMID:18999155

Proton Nuclear Magnetic Resonance-Spectroscopic Discrimination of Wines Reflects Genetic Homology of Several Different Grape (V. vinifera L.) Cultivars.

PubMed

Hu, Boran; Yue, Yaqing; Zhu, Yong; Wen, Wen; Zhang, Fengmin; Hardie, Jim W

2015-01-01

Proton nuclear magnetic resonance spectroscopy coupled multivariate analysis (1H NMR-PCA/PLS-DA) is an important tool for the discrimination of wine products. Although 1H NMR has been shown to discriminate wines of different cultivars, a grape genetic component of the discrimination has been inferred only from discrimination of cultivars of undefined genetic homology and in the presence of many confounding environmental factors. We aimed to confirm the influence of grape genotypes in the absence of those factors. We applied 1H NMR-PCA/PLS-DA and hierarchical cluster analysis (HCA) to wines from five, variously genetically-related grapevine (V. vinifera) cultivars; all grown similarly on the same site and vinified similarly. We also compared the semi-quantitative profiles of the discriminant metabolites of each cultivar with previously reported chemical analyses. The cultivars were clearly distinguishable and there was a general correlation between their grouping and their genetic homology as revealed by recent genomic studies. Between cultivars, the relative amounts of several of the cultivar-related discriminant metabolites conformed closely with reported chemical analyses. Differences in grape-derived metabolites associated with genetic differences alone are a major source of 1H NMR-based discrimination of wines and 1H NMR has the capacity to discriminate between very closely related cultivars. The study confirms that genetic variation among grape cultivars alone can account for the discrimination of wine by 1H NMR-PCA/PLS and indicates that 1H NMR spectra of wine of single grape cultivars may in future be used in tandem with hierarchical cluster analysis to elucidate genetic lineages and metabolomic relations of grapevine cultivars. In the absence of genetic information, for example, where predecessor varieties are no longer extant, this may be a particularly useful approach.

Spreadsheet log analysis in subsurface geology

USGS Publications Warehouse

Doveton, J.H.

2000-01-01

Most of the direct knowledge of the geology of the subsurface is gained from the examination of core and drill-cuttings recovered from boreholes drilled by the petroleum and water industries. Wireline logs run in these same boreholes generally have been restricted to tasks of lithostratigraphic correlation and thee location of hydrocarbon pay zones. However, the range of petrophysical measurements has expanded markedly in recent years, so that log traces now can be transformed to estimates of rock composition. Increasingly, logs are available in a digital format that can be read easily by a desktop computer and processed by simple spreadsheet software methods. Taken together, these developments offer accessible tools for new insights into subsurface geology that complement the traditional, but limited, sources of core and cutting observations.

1H NMR Metabolic Profiling of Earthworm (Eisenia fetida) Coelomic Fluid, Coelomocytes, and Tissue: Identification of a New Metabolite—Malylglutamate

PubMed Central

2017-01-01

Earthworm metabolism is recognized as a useful tool for monitoring environmental insults and measuring ecotoxicity, yet extensive earthworm metabolic profiling using 1H nuclear magnetic resonance (NMR) spectroscopy has been limited in scope. This study aims to expand the embedded metabolic material in earthworm coelomic fluid, coelomocytes, and tissue to aid systems toxicology research. Fifty-nine metabolites within Eisenia fetida were identified, with 47 detected in coelomic fluid, 41 in coelomocytes, and 54 in whole-worm samples and tissue extracts. The newly detected but known metabolites 2-aminobutyrate, nicotinurate, Nδ,Nδ,Nδ-trimethylornithine, and trigonelline are reported along with a novel compound, malylglutamate, elucidated using 2D NMR and high-resolution MS/MS. We postulate that malylglutamate acts as a glutamate/malate store, chelator, and anionic osmolyte and helps to provide electrolyte balance. PMID:28753027

1H NMR Metabolic Profiling of Earthworm (Eisenia fetida) Coelomic Fluid, Coelomocytes, and Tissue: Identification of a New Metabolite-Malylglutamate.

PubMed

Griffith, Corey M; Williams, Preston B; Tinoco, Luzineide W; Dinges, Meredith M; Wang, Yinsheng; Larive, Cynthia K

2017-09-01

Earthworm metabolism is recognized as a useful tool for monitoring environmental insults and measuring ecotoxicity, yet extensive earthworm metabolic profiling using 1 H nuclear magnetic resonance (NMR) spectroscopy has been limited in scope. This study aims to expand the embedded metabolic material in earthworm coelomic fluid, coelomocytes, and tissue to aid systems toxicology research. Fifty-nine metabolites within Eisenia fetida were identified, with 47 detected in coelomic fluid, 41 in coelomocytes, and 54 in whole-worm samples and tissue extracts. The newly detected but known metabolites 2-aminobutyrate, nicotinurate, Nδ,Nδ,Nδ-trimethylornithine, and trigonelline are reported along with a novel compound, malylglutamate, elucidated using 2D NMR and high-resolution MS/MS. We postulate that malylglutamate acts as a glutamate/malate store, chelator, and anionic osmolyte and helps to provide electrolyte balance.

Efficient theory of dipolar recoupling in solid-state nuclear magnetic resonance of rotating solids using Floquet-Magnus expansion: application on BABA and C7 radiofrequency pulse sequences.

PubMed

Mananga, Eugene S; Reid, Alicia E; Charpentier, Thibault

2012-02-01

This article describes the use of an alternative expansion scheme called Floquet-Magnus expansion (FME) to study the dynamics of spin system in solid-state NMR. The main tool used to describe the effect of time-dependent interactions in NMR is the average Hamiltonian theory (AHT). However, some NMR experiments, such as sample rotation and pulse crafting, seem to be more conveniently described using the Floquet theory (FT). Here, we present the first report highlighting the basics of the Floquet-Magnus expansion (FME) scheme and hint at its application on recoupling sequences that excite more efficiently double-quantum coherences, namely BABA and C7 radiofrequency pulse sequences. The use of Λ(n)(t) functions available only in the FME scheme, allows the comparison of the efficiency of BABA and C7 sequences. Copyright © 2011 Elsevier Inc. All rights reserved.

Efficient theory of dipolar recoupling in–solid state nuclear magnetic resonance of rotating solids using Floquet-Magnus expansion: Application on BABA and C7 radiofrequency pulse sequences

PubMed Central

Reid, Alicia E.; Charpentier, Thibault

2013-01-01

This article describes the use of an alternative expansion scheme called Floquet-Magnus expansion (FME) to study the dynamics of spin system in solid-state NMR. The main tool used to describe the effect of time-dependent interactions in NMR is the average Hamiltonian theory (AHT). However, some NMR experiments, such as sample rotation and pulse crafting, seem to be more conveniently described using the Floquet theory (FT). Here, we present the first report highlighting the basics of the Floquet-Magnus expansion (FME) scheme and hint at its application on recoupling sequences that excite more efficiently double-quantum coherences, namely BABA and C7 radiofrequency pulse sequences. The use of Λn(t) functions available only in the FME scheme, allows the comparison of the efficiency of BABA and C7 sequences. PMID:22197191

Chirality and numbering of substituted tropane alkaloids.

PubMed

Humam, Munir; Shoul, Tarik; Jeannerat, Damien; Muñoz, Orlando; Christen, Philippe

2011-08-25

The strict application of IUPAC rules for the numbering of tropane alkaloids is not always applied by authors and there is hence a lot of confusion in the literature. In most cases, the notation of 3, 6/7-disubstituted derivatives has been chosen arbitrarily, based on NMR and MS data, without taking into account the absolute configuration of these two carbons. This paper discusses the problem and the relevance of CD and NMR to determine molecular configurations. We report on the use of (1)H-NMR anisochrony (Δδ) induced by the Mosher's chiral auxiliary reagents (R)-(-)- and (S)-(+)-α-methoxy-α-trifluoromethyl-phenylacetyl chlorides (MTPA-Cl), to determine the absolute configuration of (3R,6R)-3α-hydroxy-6β-senecioyloxytropane, a disubstituted tropane alkaloid isolated from the aerial parts of Schizanthus grahamii (Solanaceae). These analytical tools should help future works in correctly assigning the configuration of additional 3, 6/7 disubstituted tropane derivatives.

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.

Amplification of Dynamic Nuclear Polarization at 200 GHz by Arbitrary Pulse Shaping of the Electron Spin Saturation Profile.

PubMed

Kaminker, Ilia; Han, Songi

2018-06-07

Dynamic nuclear polarization (DNP) takes center stage in nuclear magnetic resonance (NMR) as a tool to amplify its signal by orders of magnitude through the transfer of polarization from electron to nuclear spins. In contrast to modern NMR and electron paramagnetic resonance (EPR) that extensively rely on pulses for spin manipulation in the time domain, the current mainstream DNP technology exclusively relies on monochromatic continuous wave (CW) irradiation. This study introduces arbitrary phase shaped pulses that constitute a train of coherent chirp pulses in the time domain at 200 GHz (7 T) to dramatically enhance the saturation bandwidth and DNP performance compared to CW DNP, yielding up to 500-fold in NMR signal enhancements. The observed improvement is attributed to the recruitment of additional electron spins contributing to DNP via the cross-effect mechanism, as experimentally confirmed by two-frequency pump-probe electron-electron double resonance (ELDOR).

Dipolar filtered magic-sandwich-echoes as a tool for probing molecular motions using time domain NMR

NASA Astrophysics Data System (ADS)

Filgueiras, Jefferson G.; da Silva, Uilson B.; Paro, Giovanni; d'Eurydice, Marcel N.; Cobo, Márcio F.; deAzevedo, Eduardo R.

2017-12-01

We present a simple 1 H NMR approach for characterizing intermediate to fast regime molecular motions using 1 H time-domain NMR at low magnetic field. The method is based on a Goldmann Shen dipolar filter (DF) followed by a Mixed Magic Sandwich Echo (MSE). The dipolar filter suppresses the signals arising from molecular segments presenting sub kHz mobility, so only signals from mobile segments are detected. Thus, the temperature dependence of the signal intensities directly evidences the onset of molecular motions with rates higher than kHz. The DF-MSE signal intensity is described by an analytical function based on the Anderson Weiss theory, from where parameters related to the molecular motion (e.g. correlation times and activation energy) can be estimated when performing experiments as function of the temperature. Furthermore, we propose the use of the Tikhonov regularization for estimating the width of the distribution of correlation times.

Using open hole and cased-hole resistivity logs to monitor gas hydrate dissociation during a thermal test in the mallik 5L-38 research well, Mackenzie Delta, Canada

USGS Publications Warehouse

Anderson, B.I.; Collett, T.S.; Lewis, R.E.; Dubourg, I.

2008-01-01

Gas hydrates, which are naturally occurring ice-like combinations of gas and water, have the potential to provide vast amounts of natural gas from the world's oceans and polar regions. However, producing gas economically from hydrates entails major technical challenges. Proposed recovery methods such as dissociating or melting gas hydrates by heating or depressurization are currently being tested. One such test was conducted in northern Canada by the partners in the Mallik 2002 Gas Hydrate Production Research Well Program. This paper describes how resistivity logs were used to determine the size of the annular region of gas hydrate dissociation that occurred around the wellbore during the thermal test in the Mallik 5L-38 well. An open-hole logging suite, run prior to the thermal test, included array induction, array laterolog, nuclear magnetic resonance and 1.1-GHz electromagnetic propagation logs. The reservoir saturation tool was run both before and after the thermal test to monitor formation changes. A cased-hole formation resistivity log was run after the test.Baseline resistivity values in each formation layer (Rt) were established from the deep laterolog data. The resistivity in the region of gas hydrate dissociation near the wellbore (Rxo) was determined from electromagnetic propagation and reservoir saturation tool measurements. The radius of hydrate dissociation as a function of depth was then determined by means of iterative forward modeling of cased-hole formation resistivity tool response. The solution was obtained by varying the modeled dissociation radius until the modeled log overlaid the field log. Pretest gas hydrate production computer simulations had predicted that dissociation would take place at a uniform radius over the 13-ft test interval. However, the post-test resistivity modeling showed that this was not the case. The resistivity-derived dissociation radius was greatest near the outlet of the pipe that circulated hot water in the wellbore, where the highest temperatures were recorded. The radius was smallest near the center of the test interval, where a conglomerate section with low values of porosity and permeability inhibited dissociation. The free gas volume calculated from the resistivity-derived dissociation radii yielded a value within 20 per cent of surface gauge measurements. These results show that the inversion of resistivity measurements holds promise for use in future gas hydrate monitoring. ?? 2008 Society of Petrophysicists and Well Log Analysts. All rights reserved.

Applications of NMR-based metabolomics in biological and environmental research

EPA Science Inventory

As a complimentary tool to other omics platforms, metabolomics is increasingly being used by biologists to study the dynamic response of biological systems (cells, tissues, or whole organisms) under diverse physiological or pathological conditions. Metabolomics deals with the qu...

METABOLOMICS FOR DEVELOPING MARKERS OF CHEMICAL EXPOSURE AND DISTINGUISHING TOXICITY PATHWAYS

EPA Science Inventory

Metabolomics involves the application of advanced analytical and statistical tools to profile changes in levels of endogenous metabolites in tissues and biofluids resulting from disease onset, stress, or chemical exposure. Nuclear Magnetic Resonance (NMR) spectroscopy-based meta...

Advances in the Determination of the Speciation of the Carbon Associated with Biogenic Silica Produced by Plants

NASA Astrophysics Data System (ADS)

Masion, A.; Alexandre, A. E.; Ziarelli, F.; Viel, S.; Santos, G.

2016-12-01

Biogenic silica resulting from the precipitation of dissolved Si through biological processes in plants, often contains small amounts of occluded organic carbon. These phases, called phytoliths, have a long persistence in soils, making them tracers of past conditions. In this context, the knowledge of the carbon speciation associated with phytoliths bears significant importance in examining the carbon dynamics in soils. With carbon concentrations as low as the 0.1% range, examining the nature of organic carbon remains very challenging, and available tools (e.g. pyrolysis) are often prone to serious artifacts. Recent improvements of microwave sources enabled the application of the Dynamic Nuclear Polarization (DNP) technique to NMR, thereby establishing a new non-destructive tool for the qualitative and quantitative determination of the carbon speciation. Applied to the analysis of phytoliths, this method showed the presence of carbons from different sources within the sample: About 20% of the signal correspond to carbohydrates, and are assigned to photosynthetic carbon; the marked alkyl, N-alkyl and carbonyl signals indicate a significant proportion of proteins. This is consistent with the hypothesis that parts of the carbon associated with the phytoliths is imported into the host plant via uptake from the soil. Finally, lignins, glomalin-like and/or humic-like compounds are minor species associated with biogenic silica. This speciation was obtained overnight with a DNP-NMR set-up with an excellent sensitivity (few tens of weight ppm); the same spectrum on a standard NMR spectrometer would have required at least 250 days of data acquisition. The considerable gain in sensitivity associated with the use of DNP now makes NMR a relevant technique for the analysis of environmental samples.

Organic solute changes with acidification in Lake Skjervatjern as shown by 1H-NMR spectroscopy

USGS Publications Warehouse

Malcolm, R.L.; Hayes, T.

1994-01-01

1H-NMR spectroscopy has been found to be a useful tool to establish possible real differences and trends between all natural organic solute fractions (fulvic acids, humic acids, and XAD-4 acids) after acid-rain additions to the Lake Skjervatjern watershed. The proton NMR technique used in this study determined the spectral distribution of nonexchangeable protons among four peaks (aliphatic protons; aliphatic protons on carbon ?? or attached to electronegative groups; protons on carbons attached to O or N heteroatoms; and aromatic protons). Differences of 10% or more in the respective peak areas were considered to represent a real difference. After one year of acidification, fulvic acids decreased 13% (relative) in Peak 3 protons on carbon attached to N and O heteratoms and exhibited a decrease in aromatic protons between 27% and 31%. Humic acids also exhibited an 11% relative decrease in aromatic protons as a result of acidification. After one year of acidification, real changes were shown in three of the four proton assignments in XAD-4 acids. Peak 1 aliphatic protons increased by 14% (relative), Peak 3 protons on carbons attached to O and N heteroatoms decreased by 13% (relative), and aromatic protons (Peak 4) decreased by 35% (relative). Upon acidification, there was a trend in all solutes for aromatic protons to decrease and aliphatic protons to increase. The natural variation in organic solutes as shown in the Control Side B of the lake from 1990 to 1991 is perhaps a small limitation to the same data interpretations of acid rain changes at the Lake Skjervatjern site, but the proton NMR technique shows great promise as an independent scientific tool to detect and support other chemical techniques in establishing organic solute changes with different treatments (i.e., additions of acid rain).

MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design

NASA Astrophysics Data System (ADS)

Oberhauser, Nils; Nurisso, Alessandra; Carrupt, Pierre-Alain

2014-05-01

The molecular lipophilicity potential (MLP) is a well-established method to calculate and visualize lipophilicity on molecules. We are here introducing a new computational tool named MLP Tools, written in the programming language Python, and conceived as a free plugin for the popular open source molecular viewer PyMOL. The plugin is divided into several sub-programs which allow the visualization of the MLP on molecular surfaces, as well as in three-dimensional space in order to analyze lipophilic properties of binding pockets. The sub-program Log MLP also implements the virtual log P which allows the prediction of the octanol/water partition coefficients on multiple three-dimensional conformations of the same molecule. An implementation on the recently introduced MLP GOLD procedure, improving the GOLD docking performance in hydrophobic pockets, is also part of the plugin. In this article, all functions of the MLP Tools will be described through a few chosen examples.

EFFECTS OF MANAGEMENT FACTORS ON THE CONCENTRATION OF A HIGH MOLECULAR WEIGHT POLYSACCARIDE FRACTION FROM LOG-GROWN SHIITAKE MUSHROOMS (Lentinula edodes (Berk.) Pegler)

USDA-ARS?s Scientific Manuscript database

Shiitake mushrooms have a reputation as a healthy food. Growers may be able to use the presence of health promoting constituents as a marketing tool to promote sales of their products for premium prices. There are few reports on the effects of management protocols for log-grown shiitakes on the conc...

Electrical Conductive Mechanism of Gas Hydrate-Bearing Reservoirs in the Permafrost Region of Qilian Mountain

NASA Astrophysics Data System (ADS)

Peng, C.; Zou, C.; Tang, Y.; Liu, A.; Hu, X.

2017-12-01

In the Qilian Mountain, gas hydrates not only occur in pore spaces of sandstones, but also fill in fractures of mudstones. This leads to the difficulty in identification and evaluation of gas hydrate reservoir from resistivity and velocity logs. Understanding electrical conductive mechanism is the basis for log interpretation. However, the research is insufficient in this area. We have collected well logs from 30 wells in this area. Well logs and rock samples from DK-9, DK-11 and DK-12 wells were used in this study. The experiments including SEM, thin section, NMR, XRD, synthesis of gas hydrate in consolidated rock cores under low temperature and measurement of their resistivity and others were performed for understanding the effects of pore structure, rock composition, temperature and gas hydrate on conductivity. The results show that the porosity of reservoir of pore filling type is less than 10% and its clay mineral content is high. As good conductive passages, fractures can reduce resistivity of water-saturated rock. If fractures in the mudstone are filled by calcite, resistivity increases significantly. The resistivity of water-saturated rock at 2°C is twice of that at 18°C. The gas hydrate formation process in the sandstone was studied by resistivity recorded in real time. In the early stage of gas hydrate formation, the increase of residual water salinity may lead to the decrease of resistivity. In the late stage of gas hydrate formation, the continuity decrease of water leads to continuity increase of resistivity. In summary, fractures, rock composition, temperature and gas hydrate are important factors influencing resistivity of formation. This study is helpful for more accurate evaluation of gas hydrate from resistivity log. Acknowledgment: We acknowledge the financial support of the National Special Program for Gas Hydrate Exploration and Test-production (GZH201400302).

Accoustic waveform logging--Advances in theory and application

USGS Publications Warehouse

Paillet, F.L.; Cheng, C.H.; Pennington , W.D.

1992-01-01

Full-waveform acoustic logging has made significant advances in both theory and application in recent years, and these advances have greatly increased the capability of log analysts to measure the physical properties of formations. Advances in theory provide the analytical tools required to understand the properties of measured seismic waves, and to relate those properties to such quantities as shear and compressional velocity and attenuation, and primary and fracture porosity and permeability of potential reservoir rocks. The theory demonstrates that all parts of recorded waveforms are related to various modes of propagation, even in the case of dipole and quadrupole source logging. However, the theory also indicates that these mode properties can be used to design velocity and attenuation picking schemes, and shows how source frequency spectra can be selected to optimize results in specific applications. Synthetic microseismogram computations are an effective tool in waveform interpretation theory; they demonstrate how shear arrival picks and mode attenuation can be used to compute shear velocity and intrinsic attenuation, and formation permeability for monopole, dipole and quadrupole sources. Array processing of multi-receiver data offers the opportunity to apply even more sophisticated analysis techniques. Synthetic microseismogram data is used to illustrate the application of the maximum-likelihood method, semblance cross-correlation, and Prony's method analysis techniques to determine seismic velocities and attenuations. The interpretation of acoustic waveform logs is illustrated by reviews of various practical applications, including synthetic seismogram generation, lithology determination, estimation of geomechanical properties in situ, permeability estimation, and design of hydraulic fracture operations.

ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

NASA Astrophysics Data System (ADS)

Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

NMRNet: A deep learning approach to automated peak picking of protein NMR spectra.

PubMed

Klukowski, Piotr; Augoff, Michal; Zieba, Maciej; Drwal, Maciej; Gonczarek, Adam; Walczak, Michal J

2018-03-14

Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy. In particular, deep learning has proven to systematically achieve human-level performance in various recognition tasks, and thus emerges as an ideal tool to address automated identification of NMR signals. We have applied a convolutional neural network for visual analysis of multidimensional NMR spectra. A comprehensive test on 31 manually-annotated spectra has demonstrated top-tier average precision (AP) of 0.9596, 0.9058 and 0.8271 for backbone, side-chain and NOESY spectra, respectively. Furthermore, a combination of extracted peak lists with automated assignment routine, FLYA, outperformed other methods, including the manual one, and led to correct resonance assignment at the levels of 90.40%, 89.90% and 90.20% for three benchmark proteins. The proposed model is a part of a Dumpling software (platform for protein NMR data analysis), and is available at https://dumpling.bio/. michaljerzywalczak@gmail.compiotr.klukowski@pwr.edu.pl. Supplementary data are available at Bioinformatics online.

AQuA: An Automated Quantification Algorithm for High-Throughput NMR-Based Metabolomics and Its Application in Human Plasma.

PubMed

Röhnisch, Hanna E; Eriksson, Jan; Müllner, Elisabeth; Agback, Peter; Sandström, Corine; Moazzami, Ali A

2018-02-06

A key limiting step for high-throughput NMR-based metabolomics is the lack of rapid and accurate tools for absolute quantification of many metabolites. We developed, implemented, and evaluated an algorithm, AQuA (Automated Quantification Algorithm), for targeted metabolite quantification from complex 1 H NMR spectra. AQuA operates based on spectral data extracted from a library consisting of one standard calibration spectrum for each metabolite. It uses one preselected NMR signal per metabolite for determining absolute concentrations and does so by effectively accounting for interferences caused by other metabolites. AQuA was implemented and evaluated using experimental NMR spectra from human plasma. The accuracy of AQuA was tested and confirmed in comparison with a manual spectral fitting approach using the ChenomX software, in which 61 out of 67 metabolites quantified in 30 human plasma spectra showed a goodness-of-fit (r 2 ) close to or exceeding 0.9 between the two approaches. In addition, three quality indicators generated by AQuA, namely, occurrence, interference, and positional deviation, were studied. These quality indicators permit evaluation of the results each time the algorithm is operated. The efficiency was tested and confirmed by implementing AQuA for quantification of 67 metabolites in a large data set comprising 1342 experimental spectra from human plasma, in which the whole computation took less than 1 s.

103Rh NMR spectroscopy and its application to rhodium chemistry.

PubMed

Ernsting, Jan Meine; Gaemers, Sander; Elsevier, Cornelis J

2004-09-01

Rhodium is used for a number of large processes that rely on homogeneous rhodium-catalyzed reactions, for instance rhodium-catalyzed hydroformylation of alkenes, carbonylation of methanol to acetic acid and hydrodesulfurization of thiophene derivatives (in crude oil). Many laboratory applications in organometallic chemistry and catalysis involve organorhodium chemistry and a wealth of rhodium coordination compounds is known. For these and other areas, 103Rh NMR spectroscopy appears to be a very useful analytical tool. In this review, most of the literature concerning 103Rh NMR spectroscopy published from 1989 up to and including 2003 has been covered. After an introduction to several experimental methods for the detection of the insensitive 103Rh nucleus, a discussion of factors affecting the transition metal chemical shift is given. Computational aspects and calculations of chemical shifts are also briefly addressed. Next, the application of 103Rh NMR in coordination and organometallic chemistry is elaborated in more detail by highlighting recent developments in measurement and interpretation of 103Rh NMR data, in relation to rhodium-assisted reactions and homogeneous catalysis. The dependence of the 103Rh chemical shift on the ligands at rhodium in the first coordination sphere, on the complex geometry, oxidation state, temperature, solvent and concentration is treated. Several classes of compounds and special cases such as chiral rhodium compounds are reviewed. Finally, a section on scalar coupling to rhodium is provided. 2004 John Wiley & Sons, Ltd.

Multivariate Analysis of Two-Dimensional 1H, 13C Methyl NMR Spectra of Monoclonal Antibody Therapeutics To Facilitate Assessment of Higher Order Structure.

PubMed

Arbogast, Luke W; Delaglio, Frank; Schiel, John E; Marino, John P

2017-11-07

Two-dimensional (2D) 1 H- 13 C methyl NMR provides a powerful tool to probe the higher order structure (HOS) of monoclonal antibodies (mAbs), since spectra can readily be acquired on intact mAbs at natural isotopic abundance, and small changes in chemical environment and structure give rise to observable changes in corresponding spectra, which can be interpreted at atomic resolution. This makes it possible to apply 2D NMR spectral fingerprinting approaches directly to drug products in order to systematically characterize structure and excipient effects. Systematic collections of NMR spectra are often analyzed in terms of the changes in specifically identified peak positions, as well as changes in peak height and line widths. A complementary approach is to apply principal component analysis (PCA) directly to the matrix of spectral data, correlating spectra according to similarities and differences in their overall shapes, rather than according to parameters of individually identified peaks. This is particularly well-suited for spectra of mAbs, where some of the individual peaks might not be well resolved. Here we demonstrate the performance of the PCA method for discriminating structural variation among systematic sets of 2D NMR fingerprint spectra using the NISTmAb and illustrate how spectral variability identified by PCA may be correlated to structure.

Scale-dependent gas hydrate saturation estimates in sand reservoirs in the Ulleung Basin, East Sea of Korea

USGS Publications Warehouse

Lee, Myung Woong; Collett, Timothy S.

2013-01-01

Through the use of 2-D and 3-D seismic data, several gas hydrate prospects were identified in the Ulleung Basin, East Sea of Korea and thirteen drill sites were established and logging-while-drilling (LWD) data were acquired from each site in 2010. Sites UBGH2–6 and UBGH2–10 were selected to test a series of high amplitude seismic reflections, possibly from sand reservoirs. LWD logs from the UBGH2–6 well indicate that there are three significant sand reservoirs with varying thickness. Two upper sand reservoirs are water saturated and the lower thinly bedded sand reservoir contains gas hydrate with an average saturation of 13%, as estimated from the P-wave velocity. The well logs at the UBGH2–6 well clearly demonstrated the effect of scale-dependency on gas hydrate saturation estimates. Gas hydrate saturations estimated from the high resolution LWD acquired ring resistivity (vertical resolution of about 5–8 cm) reaches about 90% with an average saturation of 28%, whereas gas hydrate saturations estimated from the low resolution A40L resistivity (vertical resolution of about 120 cm) reaches about 25% with an average saturation of 11%. However, in the UBGH2–10 well, gas hydrate occupies a 5-m thick sand reservoir near 135 mbsf with a maximum saturation of about 60%. In the UBGH2–10 well, the average and a maximum saturation estimated from various well logging tools are comparable, because the bed thickness is larger than the vertical resolution of the various logging tools. High resolution wireline log data further document the role of scale-dependency on gas hydrate calculations.

Measuring diffusion-relaxation correlation maps using non-uniform field gradients of single-sided NMR devices.

PubMed

Nogueira d'Eurydice, Marcel; Galvosas, Petrik

2014-11-01

Single-sided NMR systems are becoming a relevant tool in industry and laboratory environments due to their low cost, low maintenance and capacity to evaluate quantity and quality of hydrogen based materials. The performance of such devices has improved significantly over the last decade, providing increased field homogeneity, field strength and even controlled static field gradients. For a class of these devices, the configuration of the permanent magnets provides a linear variation of the magnetic field and can be used in diffusion measurements. However, magnet design depends directly on its application and, according to the purpose, the field homogeneity may significantly be compromised. This may prevent the determination of diffusion properties of fluids based on the natural inhomogeneity of the field using known techniques. This work introduces a new approach that extends the applicability of diffusion-editing CPMG experiments to NMR devices with highly inhomogeneous magnetic fields, which do not vary linearly in space. Herein, we propose a method to determine a custom diffusion kernel based on the gradient distribution, which can be seen as a signature of each NMR device. This new diffusion kernel is then utilised in the 2D inverse Laplace transform (2D ILT) in order to determine diffusion-relaxation correlation maps of homogeneous multi-phasic fluids. The experiments were performed using NMR MObile Lateral Explore (MOLE), which is a single-sided NMR device designed to maximise the volume at the sweet spot with enhanced depth penetration. Copyright © 2014 Elsevier Inc. All rights reserved.

Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.

PubMed

Emwas, Abdul-Hamid; Luchinat, Claudio; Turano, Paola; Tenori, Leonardo; Roy, Raja; Salek, Reza M; Ryan, Danielle; Merzaban, Jasmeen S; Kaddurah-Daouk, Rima; Zeri, Ana Carolina; Nagana Gowda, G A; Raftery, Daniel; Wang, Yulan; Brennan, Lorraine; Wishart, David S

The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.

Chemoselective detection and discrimination of carbonyl-containing compounds in metabolite mixtures by 1H-detected 15N NMR

PubMed Central

Lane, Andrew N.; Arumugam, Sengodagounder; Lorkiewicz, Pawel K.; Higashi, Richard M.; Laulhé, Sébastien; Nantz, Michael H.; Moseley, Hunter N.B.; Fan, Teresa W.-M.

2015-01-01

NMR spectra of mixtures of metabolites extracted from cells or tissues are extremely complex, reflecting the large number of compounds that are present over a wide range of concentrations. Although multidimensional NMR can greatly improve resolution as well as improve reliability of compound assignments, lower abundance metabolites often remain hidden. We have developed a carbonyl selective aminooxy probe that specifically reacts with free keto and aldehyde functions, but not carboxylates. By incorporating 15N in the aminooxy functional group, 15N-edited NMR was used to select exclusively those metabolites that contain a free carbonyl function while all other metabolites are rejected. Here we demonstrate that the chemical shifts of the aminooxy adducts of ketones and aldehydes are very different, which can be used to discriminate between aldoses and ketoses for example. Utilizing the 2 or 3 bond 15N-1H couplings, the 15N-edited NMR analysis was optimized first with authentic standards and then applied to an extract of the lung adenocarcinoma cell line A549. More than 30 carbonyl containing compounds at NMR detectable levels, 6 of which we have assigned by reference to our database. As the aminooxy probe contains a permanently charged quaternary ammonium group, the adducts are also optimized for detection by mass spectrometry. Thus, this sample preparation technique provides a better link between the two structural determination tools, thereby paving the way to faster and more reliable identification of both known and unknown metabolites directly in crude biological extracts. PMID:25616249

NMR Microscopy - Micron-Level Resolution.

NASA Astrophysics Data System (ADS)

Kwok, Wing-Chi Edmund

1990-01-01

Nuclear Magnetic Resonance Imaging (MRI) has been developed into a powerful and widely used diagnostic tool since the invention of techniques using linear magnetic field gradients in 1973. The variety of imaging contrasts obtainable in MRI, such as spin density, relaxation times and flow rate, gives MRI a significant advantage over other imaging techniques. For common diagnostic applications, image resolutions have been in the order of millimeters with slice thicknesses in centimeters. For many research applications, however, resolutions in the order of tens of microns or smaller are needed. NMR Imaging in these high resolution disciplines is known as NMR microscopy. Compared with conventional microscopy, NMR microscopy has the advantage of being non-invasive and non-destructive. The major obstacles of NMR microscopy are low signal-to-noise ratio and effects due to spin diffusion. To overcome these difficulties, more sensitive RF probes and very high magnetic field gradients have to be used. The most effective way to increase sensitivity is to build smaller probes. Microscope probes of different designs have been built and evaluated. Magnetic field gradient coils that can produce linear field gradients up to 450 Gauss/cm were also assembled. In addition, since microscope probes often employ remote capacitors for RF tuning, the associated signal loss in the transmission line was studied. Imaging experiments have been carried out in a 2.1 Tesla small bore superconducting magnet using the typical two-dimensional spin warp imaging technique. Images have been acquired for both biological and non-biological samples. The highest resolution was obtained in an image of a nerve bundle from the spinal cord of a racoon and has an in-plane resolution of 4 microns. These experiments have demonstrated the potential application of NMR microscopy to pathological research, nervous system study and non -destructive testings of materials. One way to further improve NMR microscopy is to implement a higher static magnetic field which will increase signal strength. In the future, NMR microscopy should prove to be useful in the studies of cell linings, T1 & T2 relaxation mechanisms and NMR contrast agents.

A portable borehole temperature logging system using the four-wire resistance method

NASA Astrophysics Data System (ADS)

Erkan, Kamil; Akkoyunlu, Bülent; Balkan, Elif; Tayanç, Mete

2017-12-01

High-quality temperature-depth information from boreholes with a depth of 100 m or more is used in geothermal studies and in studies of climate change. Electrical wireline tools with thermistor sensors are capable of measuring borehole temperatures with millikelvin resolution. The use of a surface readout mode allows analysis of the thermally conductive state of a borehole, which is especially important for climatic and regional heat flow studies. In this study we describe the design of a portable temperature logging tool that uses the four-wire resistance measurement method. The four-wire method enables the elimination of cable resistance effects, thus allowing millikelvin resolution of temperature data at depth. A preliminary two-wire model of the system is also described. The portability of the tool enables one to collect data from boreholes down to 300 m, even in locations with limited accessibility.

Hazard Management with DOORS: Rail Infrastructure Projects

NASA Astrophysics Data System (ADS)

Hughes, Dave; Saeed, Amer

LOI is a major rail infrastructure project that will contribute to a modernised transport system in time for the 2012 Olympic Games. A review of the procedures and tool infrastructure was conducted in early 2006, coinciding with a planned move to main works. A hazard log support tool was needed to provide: an automatic audit trial, version control and support collaborative working. A DOORS based Hazard Log (DHL) was selected as the Tool Strategy. A systematic approach was followed for the development of DHL, after a series of tests and acceptance gateways, DHL was handed over to the project in autumn 2006. The first few months were used for operational trials and he Hazard Management rocedure was modified to be a hybrid approach that used the strengths of DHL and Excel. The user experience in the deployment of DHL is summarised and directions for future improvement identified.

Quick, sensitive serial NMR experiments with Radon transform.

PubMed

Dass, Rupashree; Kasprzak, Paweł; Kazimierczuk, Krzysztof

2017-09-01

The Radon transform is a potentially powerful tool for processing the data from serial spectroscopic experiments. It makes it possible to decode the rate at which frequencies of spectral peaks shift under the effect of changing conditions, such as temperature, pH, or solvent. In this paper we show how it also improves speed and sensitivity, especially in multidimensional experiments. This is particularly important in the case of low-sensitivity techniques, such as NMR spectroscopy. As an example, we demonstrate how Radon transform processing allows serial measurements of 15 N-HSQC spectra of unlabelled peptides that would otherwise be infeasible. Copyright © 2017 Elsevier Inc. All rights reserved.

Metabolomics as a promising tool for early osteoarthritis diagnosis.

PubMed

de Sousa, E B; Dos Santos, G C; Duarte, M E L; Moura, V; Aguiar, D P

2017-09-21

Osteoarthritis (OA) is the main cause of disability worldwide, due to progressive articular cartilage loss and degeneration. According to recent research, OA is more than just a degenerative disease due to some metabolic components associated to its pathogenesis. However, no biomarker has been identified to detect this disease at early stages or to track its development. Metabolomics is an emerging field and has the potential to detect many metabolites in a single spectrum using high resolution nuclear magnetic resonance (NMR) techniques or mass spectrometry (MS). NMR is a reproducible and reliable non-destructive analytical method. On the other hand, MS has a lower detection limit and is more destructive, but it is more sensitive. NMR and MS are useful for biological fluids, such as urine, blood plasma, serum, or synovial fluid, and have been used for metabolic profiling in dogs, mice, sheep, and humans. Thus, many metabolites have been listed as possibly associated to OA pathogenesis. The goal of this review is to provide an overview of the studies in animal models and humans, regarding the use of metabolomics as a tool for early osteoarthritis diagnosis. The concept of osteoarthritis as a metabolic disease and the importance of detecting a biomarker for its early diagnosis are highlighted. Then, some studies in plasma and synovial tissues are shown, and finally the application of metabolomics in the evaluation of synovial fluid is described.

Study on Ultra-deep Azimuthal Electromagnetic Resistivity LWD Tool by Influence Quantification on Azimuthal Depth of Investigation and Real Signal

NASA Astrophysics Data System (ADS)

Li, Kesai; Gao, Jie; Ju, Xiaodong; Zhu, Jun; Xiong, Yanchun; Liu, Shuai

2018-05-01

This paper proposes a new tool design of ultra-deep azimuthal electromagnetic (EM) resistivity logging while drilling (LWD) for deeper geosteering and formation evaluation, which can benefit hydrocarbon exploration and development. First, a forward numerical simulation of azimuthal EM resistivity LWD is created based on the fast Hankel transform (FHT) method, and its accuracy is confirmed under classic formation conditions. Then, a reasonable range of tool parameters is designed by analyzing the logging response. However, modern technological limitations pose challenges to selecting appropriate tool parameters for ultra-deep azimuthal detection under detectable signal conditions. Therefore, this paper uses grey relational analysis (GRA) to quantify the influence of tool parameters on voltage and azimuthal investigation depth. After analyzing thousands of simulation data under different environmental conditions, the random forest is used to fit data and identify an optimal combination of tool parameters due to its high efficiency and accuracy. Finally, the structure of the ultra-deep azimuthal EM resistivity LWD tool is designed with a theoretical azimuthal investigation depth of 27.42-29.89 m in classic different isotropic and anisotropic formations. This design serves as a reliable theoretical foundation for efficient geosteering and formation evaluation in high-angle and horizontal (HA/HZ) wells in the future.

Molecules to maps: tools for visualization and interaction in support of computational biology.

PubMed

Kraemer, E T; Ferrin, T E

1998-01-01

The volume of data produced by genome projects, X-ray crystallography, NMR spectroscopy, and electron and confocal microscopy present the bioinformatics community with new challenges for analyzing, understanding, and exchanging this data. At the 1998 Pacific Symposium on Biocomputing, a track entitled 'Molecules to Maps: Tools for Visualization and Interaction in Computational Biology' provided tool developers and users with the opportunity to discuss advances in tools and techniques to assist scientists in evaluating, absorbing, navigating, and correlating this sea of information, through visualization and user interaction. In this paper we present these advances and discuss some of the challenges that remain to be solved.

Contributed Review: Nuclear magnetic resonance core analysis at 0.3 T

NASA Astrophysics Data System (ADS)

Mitchell, Jonathan; Fordham, Edmund J.

2014-11-01

Nuclear magnetic resonance (NMR) provides a powerful toolbox for petrophysical characterization of reservoir core plugs and fluids in the laboratory. Previously, there has been considerable focus on low field magnet technology for well log calibration. Now there is renewed interest in the study of reservoir samples using stronger magnets to complement these standard NMR measurements. Here, the capabilities of an imaging magnet with a field strength of 0.3 T (corresponding to 12.9 MHz for proton) are reviewed in the context of reservoir core analysis. Quantitative estimates of porosity (saturation) and pore size distributions are obtained under favorable conditions (e.g., in carbonates), with the added advantage of multidimensional imaging, detection of lower gyromagnetic ratio nuclei, and short probe recovery times that make the system suitable for shale studies. Intermediate field instruments provide quantitative porosity maps of rock plugs that cannot be obtained using high field medical scanners due to the field-dependent susceptibility contrast in the porous medium. Example data are presented that highlight the potential applications of an intermediate field imaging instrument as a complement to low field instruments in core analysis and for materials science studies in general.

Kinetics of cyclopentene isomerization at 1200 K

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

Lewis, D.K.; Baldwin, J.E.; Cianciosi, S.J.

1990-09-20

This study was conducted to determine the rate of intramolecular degenerate rearrangement of cyclopentene (CP), presumably via reversible conversion to vinylcyclopropane (VCP). Cyclopentene-3-{sup 13}C was synthesized and heated to 1,200 K in a single-pulse shock tube and then analyzed by {sup 13}C NMR to ascertain the extent of migration of the {sup 13}C label to the 4-position. The very small amounts of migration observed were consistent with log k(CP {yields} VCP) = 15.7 {minus} (16,000/T). This rate constant for CP {yields} VCP is too small to account for the previously reported evidence of multiple channels for H{sub 2} elimination frommore » CP.« less

Interest of fluorine-19 nuclear magnetic resonance spectroscopy in the detection, identification and quantification of metabolites of anticancer and antifungal fluoropyrimidine drugs in human biofluids.

PubMed

Martino, Robert; Gilard, Véronique; Desmoulin, Franck; Malet-Martino, Myriam

2006-01-01

The metabolism of fluorouracil and fluorocytosine, two 5-fluoropyrimidine drugs in clinical use, was investigated. (19)F nuclear magnetic resonance (NMR) spectroscopy was used as an analytical technique for the detection, identification and quantification of fluorinated metabolites of these drugs in intact human biofluids as well as fluorinated degradation compounds of fluorouracil in commercial vials. (19)F NMR provides a highly specific tool for the detection and absolute quantification, in a single run, of all the fluorinated species, including unexpected substances, present in biofluids of patients treated with fluorouracil or fluorocytosine. Besides the parent drug and the already known fluorinated metabolites, nine new metabolites were identified for the first time with (19)F NMR in human biofluids. Six of them can only be observed with this technique: fluoride ion, N-carboxy-alpha-fluoro-beta-alanine, alpha-fluoro-beta-alanine conjugate with deoxycholic acid, 2-fluoro-3-hydroxypropanoic acid, fluoroacetic acid, O(2)-beta-glucuronide of fluorocytosine. (19)F NMR studies of biological fluids of patients treated with anticancer fluorouracil or antifungal fluorocytosine have furthered the understanding of their catabolic pathways.

Fluorine nuclear magnetic resonance spectroscopy of human biofluids in the field of metabolic studies of anticancer and antifungal fluoropyrimidine drugs.

PubMed

Malet-Martino, Myriam; Gilard, Véronique; Desmoulin, Franck; Martino, Robert

2006-04-01

Fluorine-19 nuclear magnetic resonance (19F NMR) spectroscopy provides a highly specific tool for the detection, identification and quantification of fluorine-containing drugs and their metabolites in biofluids. The value and difficulties encountered in investigations on drug metabolism are first discussed. Then the metabolism of three fluoropyrimidines in clinical use, 5-fluorouracil, 5-fluorocytosine and capecitabine are reported. Besides the parent drug and the already known fluorinated metabolites, 12 new metabolites were identified for the first time with 19F NMR in human biofluids. Nine of them can only be observed with this technique: fluoride ion, N-carboxy-alpha-fluoro-beta-alanine, alpha-fluoro-beta-alanine conjugate with deoxycholic acid, 2-fluoro-3-hydroxypropanoic acid, fluoroacetic acid, O2-beta-glucuronide of fluorocytosine, fluoroacetaldehyde hydrate and its adduct with urea, fluoromalonic acid semi-aldehyde adducts with urea. This emphasizes the high analytical potential of 19F NMR for the furtherance in the understanding of fluoropyrimidine catabolic pathways. 19F NMR should also play a role in the therapeutic monitoring of FU and its prodrugs in specific groups of patients, e.g. hemodialyzed patients or patients with deficiency in FU catabolic enzymes.

Physicochemical properties of liposomes as potential anticancer drugs carriers. Interaction of etoposide and cytarabine with the membrane: Spectroscopic studies

NASA Astrophysics Data System (ADS)

Pentak, Danuta

2014-03-01

The interactions between etoposide, cytarabine and 1,2-dihexadecanoyl-sn-glycerol-3-phosphocholine bilayers were studied using differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance (NMR). These techniques have proven to be a very powerful tool in studying the structure and dynamics of phospholipid bilayers. In particular, DSC can provide information on the phase transition temperature and cooperativity of the lipid molecules in the absence and presence of the drug. Vibrational spectroscopy is well suited to the study of drug-lipid interactions, since it allows for an investigation of the conformation of phospholipid molecules at different levels in lipid bilayers and follows structural changes that occur during the gel to liquid-crystalline phase transition. NMR supported the determination of the main phase transition temperatures (TC) of 1,2-dihexadecanoyl-sn-glycerol-3-phosphocholine (DPPC). The main phase transition temperature (TC) determined by 1H NMR is comparable with values obtained by DSC for all studied liposomes. The location of cytarabine and etoposide in liposomes was also determined by NMR. Atomic force microscopy (AFM) images, acquired immediately after sample deposition on a mica surface, revealed the spherical shape of lipid vesicles.

Fluorine-19 nuclear magnetic resonance of chimeric antigen receptor T cell biodistribution in murine cancer model.

PubMed

Chapelin, Fanny; Gao, Shang; Okada, Hideho; Weber, Thomas G; Messer, Karen; Ahrens, Eric T

2017-12-18

Discovery of effective cell therapies against cancer can be accelerated by the adaptation of tools to rapidly quantitate cell biodistribution and survival after delivery. Here, we describe the use of nuclear magnetic resonance (NMR) 'cytometry' to quantify the biodistribution of immunotherapeutic T cells in intact tissue samples. In this study, chimeric antigen receptor (CAR) T cells expressing EGFRvIII targeting transgene were labeled with a perfluorocarbon (PFC) emulsion ex vivo and infused into immunocompromised mice bearing subcutaneous human U87 glioblastomas expressing EGFRvIII and luciferase. Intact organs were harvested at day 2, 7 and 14 for whole-sample fluorine-19 ( 19 F) NMR to quantitatively measure the presence of PFC-labeled CAR T cells, followed by histological validation. NMR measurements showed greater CAR T cell homing and persistence in the tumors and spleen compared to untransduced T cells. Tumor growth was monitored with bioluminescence imaging, showing that CAR T cell treatment resulted in significant tumor regression compared to untransduced T cells. Overall, 19 F NMR cytometry is a rapid and quantitative method to evaluate cell biodistribution, tumor homing, and fate in preclinical studies.

Natural Abundance 43Ca NMR as a Tool for Exploring Calcium Biomineralization: Renal Stone Formation and Growth

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

Bowers, Geoffrey M.; Kirkpatrick, Robert J.

2011-12-07

Renal stone diseases are a global health issue with little effective therapeutic recourse aside from surgery and shock-wave lithotripsy, primarily because the fundamental chemical mechanisms behind calcium biomineralization are poorly understood. In this work, we show that natural abundance 43Ca NMR at 21.1 T is an effective means to probe the molecular-level Ca2+ structure in oxalate-based kidney stones. We find that the 43Ca NMR resonance of an authentic oxalate-based kidney stone cannot be explained by a single pure phase of any common Ca2+-bearing stone mineral. Combined with XRD results, our findings suggest an altered calcium oxalate monohydrate-like Ca2+ coordination environmentmore » for some fraction of Ca2+ in our sample. The evidence is consistent with existing literature hypothesizing that nonoxalate organic material interacts directly with Ca2+ at stone surfaces and is the primary driver of renal stone aggregation and growth. Our findings show that 43Ca NMR spectroscopy may provide unique and crucial insight into the fundamental chemistry of kidney stone formation, growth, and the role organic molecules play in these processes.« less

Quantitative determination and validation of octreotide acetate using 1 H-NMR spectroscopy with internal standard method.

PubMed

Yu, Chen; Zhang, Qian; Xu, Peng-Yao; Bai, Yin; Shen, Wen-Bin; Di, Bin; Su, Meng-Xiang

2018-01-01

Quantitative nuclear magnetic resonance (qNMR) is a well-established technique in quantitative analysis. We presented a validated 1 H-qNMR method for assay of octreotide acetate, a kind of cyclic octopeptide. Deuterium oxide was used to remove the undesired exchangeable peaks, which was referred to as proton exchange, in order to make the quantitative signals isolated in the crowded spectrum of the peptide and ensure precise quantitative analysis. Gemcitabine hydrochloride was chosen as the suitable internal standard. Experimental conditions, including relaxation delay time, the numbers of scans, and pulse angle, were optimized first. Then method validation was carried out in terms of selectivity, stability, linearity, precision, and robustness. The assay result was compared with that by means of high performance liquid chromatography, which is provided by Chinese Pharmacopoeia. The statistical F test, Student's t test, and nonparametric test at 95% confidence level indicate that there was no significant difference between these two methods. qNMR is a simple and accurate quantitative tool with no need for specific corresponding reference standards. It has the potential of the quantitative analysis of other peptide drugs and standardization of the corresponding reference standards. Copyright © 2017 John Wiley & Sons, Ltd.

IN SITU MAGIC ANGLE SPINNING NMR FOR STUDYING GEOLOGICAL CO(2) SEQUESTRATION

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

Hoyt, David W.; Turcu, Romulus VF; Sears, Jesse A.

2011-03-27

Geological carbon sequestration (GCS) is one of the most promising ways of mitigating atmospheric greenhouse gases (1-3). Mineral carbonation reactions are potentially important to the long-term sealing effectiveness of caprock but remain poorly predictable, particularly in low-water supercritical CO2 (scCO2)-dominated environments where the chemistry has not been adequately explored. In situ probes that provide molecular-level information is desirable for investigating mechanisms and rates of GCS mineral carbonation reactions. MAS-NMR is a powerful tool for obtaining detailed molecular structure and dynamics information of a system regardless whether the system is in a solid, a liquid, a gaseous, or a supercritical state,more » or a mixture thereof (4,5). However, MAS NMR under scCO2 conditions has never been realized due to the tremendous technical difficulties of achieving and maintaining high pressure within a fast spinning MAS rotor (6,7), where non-metal materials must be used. In this work, we report development of a unique high pressure MAS NMR capability, and its application to mineral carbonation chemistry in scCO2 under geologically relevant temperatures and pressures.« less

Rheo-NMR Measurements of Cocoa Butter Crystallized Under

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

Mudge, E.; Mazzanti, G

2009-01-01

Modifications of a benchtop NMR instrument were made to apply temperature control to a shearing NMR cell. This has enabled the determination in situ of the solid fat content (SFC) of cocoa butter under shearing conditions. The cocoa butter was cooled at 3 C/min to three final temperatures of 17.5, 20.0, and 22.5 C with applied shear rates between 45 and 720 s-1. Polymorphic transitions of the cocoa butter were determined using synchrotron X-ray diffraction with an identical shearing system constructed of Lexan. Sheared samples were shown to have accelerated phase transitions compared to static experiments. In experiments where formmore » V was confirmed to be the dominant polymorph, the final SFC averaged around 50%. However, when other polymorphic forms were formed, a lower SFC was measured because the final temperature was within the melting range of that polymorph and only partial crystallization happened. A shear rate of 720 s-1 delayed phase transitions, likely due to viscous heating of the sample. Pulsed NMR is an invaluable tool for determining the crystalline fraction in hydrogen containing materials, yet its use for fundamental and industrial research on fat or alkanes crystallization under shear has only recently been developed.« less

Sweep visually evoked potentials and visual findings in children with West syndrome.

PubMed

de Freitas Dotto, Patrícia; Cavascan, Nívea Nunes; Berezovsky, Adriana; Sacai, Paula Yuri; Rocha, Daniel Martins; Pereira, Josenilson Martins; Salomão, Solange Rios

2014-03-01

West syndrome (WS) is a type of early childhood epilepsy characterized by progressive neurological development deterioration that includes vision. To demonstrate the clinical importance of grating visual acuity thresholds (GVA) measurement by sweep visually evoked potentials technique (sweep-VEP) as a reliable tool for evaluation of the visual cortex status in WS children. This is a retrospective study of the best-corrected binocular GVA and ophthalmological features of WS children referred for the Laboratory of Clinical Electrophysiology of Vision of UNIFESP from 1998 to 2012 (Committee on Ethics in Research of UNIFESP n° 0349/08). The GVA deficit was calculated by subtracting binocular GVA score (logMAR units) of each patient from the median values of age norms from our own lab and classified as mild (0.1-0.39 logMAR), moderate (0.40-0.80 logMAR) or severe (>0.81 logMAR). Associated ophthalmological features were also described. Data from 30 WS children (age from 6 to 108 months, median = 14.5 months, mean ± SD = 22.0 ± 22.1 months; 19 male) were analyzed. The majority presented severe GVA deficit (0.15-1.44 logMAR; mean ± SD = 0.82 ± 0.32 logMAR; median = 0.82 logMAR), poor visual behavior, high prevalence of strabismus and great variability in ocular positioning. The GVA deficit did not vary according to gender (P = .8022), WS type (P = .908), birth age (P = .2881), perinatal oxygenation (P = .7692), visual behavior (P = .8789), ocular motility (P = .1821), nystagmus (P = .2868), risk of drug-induced retinopathy (P = .4632) and participation in early visual stimulation therapy (P = .9010). The sweep-VEP technique is a reliable tool to classify visual system impairment in WS children, in agreement with the poor visual behavior exhibited by them. Copyright © 2013 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved.

Wood-inhabiting beetles in low stumps, high stumps and logs on boreal clear-cuts: implications for dead wood management.

PubMed

Andersson, Jon; Hjältén, Joakim; Dynesius, Mats

2015-01-01

The increasing demand for biofuels from logging residues require serious attention on the importance of dead wood substrates on clear-cuts for the many forestry-intolerant saproxylic (wood-inhabiting) species. In particular, the emerging harvest of low stumps motivates further study of these substrates. On ten clear-cuts we compared the species richness, abundance and species composition of saproxylic beetles hatching from four to nine year old low stumps, high stumps and logs of Norway spruce. By using emergence traps we collected a total of 2,670 saproxylic beetles among 195 species during the summers of 2006, 2007 and 2009. We found that the species assemblages differed significantly between high stumps and logs all three years. The species assemblages of low stumps, on the other hand, were intermediate to those found in logs and high stumps. There were also significant difference in species richness between the three examined years, and we found significant effect of substrate type on richness of predators and fungivores. As shown in previous studies of low stumps on clear-cuts they can sustain large numbers of different saproxylic beetles, including red-listed species. Our study does, in addition to this fact, highlight a possible problem in creating just one type of substrate as a tool for conservation in forestry. Species assemblages in high stumps did not differ significantly from those found in low stumps. Instead logs, which constitute a scarcer substrate type on clear-cuts, provided habitat for a more distinct assemblage of saproxylic species than high stumps. It can therefore be questioned whether high stumps are an optimal tool for nature conservation in clear-cutting forestry. Our results also indicate that low stumps constitute an equally important substrate as high stumps and logs, and we therefore suggest that stump harvesting is done after carefully evaluating measures to provide habitat for saproxylic organisms.

Diagnostic Tools for Performance Evaluation of Innovative In-Situ Remediation Technologies at Chlorinated Solvent-Contaminated Sites

DTIC Science & Technology

2011-07-01

fluid resistivity , temperature logging, and flow metering at other sites that typically indicated only two or three active fractures in each hole...was consistent with results of conventional borehole fluid resistivity , temperature logging, and flow metering at other sites that typically indicated...following tests were performed in each boundary monitoring well: ■ Gamma Ray; ■ Spontaneous Potential (SP); ■ Single Point Resistance (SPR

Novel 1H low field nuclear magnetic resonance applications for the field of biodiesel

PubMed Central

2013-01-01

Background Biodiesel production has increased dramatically over the last decade, raising the need for new rapid and non-destructive analytical tools and technologies. 1H Low Field Nuclear Magnetic Resonance (LF-NMR) applications, which offer great potential to the field of biodiesel, have been developed by the Phyto Lipid Biotechnology Lab research team in the last few years. Results Supervised and un-supervised chemometric tools are suggested for screening new alternative biodiesel feedstocks according to oil content and viscosity. The tools allowed assignment into viscosity groups of biodiesel-petrodiesel samples whose viscosity is unknown, and uncovered biodiesel samples that have residues of unreacted acylglycerol and/or methanol, and poorly separated and cleaned glycerol and water. In the case of composite materials, relaxation time distribution, and cross-correlation methods were successfully applied to differentiate components. Continuous distributed methods were also applied to calculate the yield of the transesterification reaction, and thus monitor the progress of the common and in-situ transesterification reactions, offering a tool for optimization of reaction parameters. Conclusions Comprehensive applied tools are detailed for the characterization of new alternative biodiesel resources in their whole conformation, monitoring of the biodiesel transesterification reaction, and quality evaluation of the final product, using a non-invasive and non-destructive technology that is new to the biodiesel research area. A new integrated computational-experimental approach for analysis of 1H LF-NMR relaxometry data is also presented, suggesting improved solution stability and peak resolution. PMID:23590829

TU-CD-304-11: Veritas 2.0: A Cloud-Based Tool to Facilitate Research and Innovation

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

Mishra, P; Patankar, A; Etmektzoglou, A

Purpose: We introduce Veritas 2.0, a cloud-based, non-clinical research portal, to facilitate translation of radiotherapy research ideas to new delivery techniques. The ecosystem of research tools includes web apps for a research beam builder for TrueBeam Developer Mode, an image reader for compressed and uncompressed XIM files, and a trajectory log file based QA/beam delivery analyzer. Methods: The research beam builder can generate TrueBeam readable XML file either from scratch or from pre-existing DICOM-RT plans. DICOM-RT plan is first converted to XML format and then researcher can interactively modify or add control points to them. Delivered beam can be verifiedmore » via reading generated images and analyzing trajectory log files. Image reader can read both uncompressed and HND-compressed XIM images. The trajectory log analyzer lets researchers plot expected vs. actual values and deviations among 30 mechanical axes. The analyzer gives an animated view of MLC patterns for the beam delivery. Veritas 2.0 is freely available and its advantages versus standalone software are i) No software installation or maintenance needed, ii) easy accessibility across all devices iii) seamless upgrades and iv) OS independence. Veritas is written using open-source tools like twitter bootstrap, jQuery, flask, and Python-based modules. Results: In the first experiment, an anonymized 7-beam DICOM-RT IMRT plan was converted to XML beam containing 1400 control points. kV and MV imaging points were inserted into this XML beam. In another experiment, a binary log file was analyzed to compare actual vs expected values and deviations among axes. Conclusions: Veritas 2.0 is a public cloud-based web app that hosts a pool of research tools for facilitating research from conceptualization to verification. It is aimed at providing a platform for facilitating research and collaboration. I am full time employee at Varian Medical systems, Palo Alto.« less

Direct push driven in situ color logging tool (CLT): technique, analysis routines, and application

NASA Astrophysics Data System (ADS)

Werban, U.; Hausmann, J.; Dietrich, P.; Vienken, T.

2014-12-01

Direct push technologies have recently seen a broad development providing several tools for in situ parameterization of unconsolidated sediments. One of these techniques is the measurement of soil colors - a proxy information that reveals to soil/sediment properties. We introduce the direct push driven color logging tool (CLT) for real-time and depth-resolved investigation of soil colors within the visible spectrum. Until now, no routines exist on how to handle high-resolved (mm-scale) soil color data. To develop such a routine, we transform raw data (CIEXYZ) into soil color surrogates of selected color spaces (CIExyY, CIEL*a*b*, CIEL*c*h*, sRGB) and denoise small-scale natural variability by Haar and Daublet4 wavelet transformation, gathering interpretable color logs over depth. However, interpreting color log data as a single application remains challenging. Additional information, such as site-specific knowledge of the geological setting, is required to correlate soil color data to specific layers properties. Hence, we exemplary provide results from a joint interpretation of in situ-obtained soil color data and 'state-of-the-art' direct push based profiling tool data and discuss the benefit of additional data. The developed routine is capable of transferring the provided information obtained as colorimetric data into interpretable color surrogates. Soil color data proved to correlate with small-scale lithological/chemical changes (e.g., grain size, oxidative and reductive conditions), especially when combined with additional direct push vertical high resolution data (e.g., cone penetration testing and soil sampling). Thus, the technique allows enhanced profiling by means of providing another reproducible high-resolution parameter for analysis subsurface conditions. This opens potential new areas of application and new outputs for such data in site investigation. It is our intention to improve color measurements by means method of application and data interpretation, useful to characterize vadose layer/soil/sediment characteristics.

Novel synthesis and structural characterization of a high-affinity paramagnetic kinase probe for the identification of non-ATP site binders by nuclear magnetic resonance.

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

Moy, Franklin J.; Lee, Arthur; Gavrin, Lori Krim

2010-07-23

To aid in the pursuit of selective kinase inhibitors, we have developed a unique ATP site binder tool for the detection of binders outside the ATP site by nuclear magnetic resonance (NMR). We report here the novel synthesis that led to this paramagnetic spin-labeled pyrazolopyrimidine probe (1), which exhibits nanomolar inhibitory activity against multiple kinases. We demonstrate the application of this probe by performing NMR binding experiments with Lck and Src kinases and utilize it to detect the binding of two compounds proximal to the ATP site. The complex structure of the probe with Lck is also presented, revealing howmore » the probe fits in the ATP site and the specific interactions it has with the protein. We believe that this spin-labeled probe is a valuable tool that holds broad applicability in a screen for non-ATP site binders.« less

Generating porosity spectrum of carbonate reservoirs using ultrasonic imaging log

NASA Astrophysics Data System (ADS)

Zhang, Jie; Nie, Xin; Xiao, Suyun; Zhang, Chong; Zhang, Chaomo; Zhang, Zhansong

2018-03-01

Imaging logging tools can provide us the borehole wall image. The micro-resistivity imaging logging has been used to obtain borehole porosity spectrum. However, the resistivity imaging logging cannot cover the whole borehole wall. In this paper, we propose a method to calculate the porosity spectrum using ultrasonic imaging logging data. Based on the amplitude attenuation equation, we analyze the factors affecting the propagation of wave in drilling fluid and formation and based on the bulk-volume rock model, Wyllie equation and Raymer equation, we establish various conversion models between the reflection coefficient β and porosity ϕ. Then we use the ultrasonic imaging logging and conventional wireline logging data to calculate the near-borehole formation porosity distribution spectrum. The porosity spectrum result obtained from ultrasonic imaging data is compared with the one from the micro-resistivity imaging data, and they turn out to be similar, but with discrepancy, which is caused by the borehole coverage and data input difference. We separate the porosity types by performing threshold value segmentation and generate porosity-depth distribution curves by counting with equal depth spacing on the porosity image. The practice result is good and reveals the efficiency of our method.

Quantitative analysis of protein-ligand interactions by NMR.

PubMed

Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

2016-08-01

Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used to analyze population-averaged NMR quantities. Essentially, to apply NMR successfully, both the type of experiment and equation to fit the data must be carefully and specifically chosen for the protein-ligand interaction under analysis. In this review, we first explain the exchange regimes and kinetic models of protein-ligand interactions, and then describe the NMR methods that quantitatively analyze these specific interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Cement bond evaluation method in horizontal wells using segmented bond tool

NASA Astrophysics Data System (ADS)

Song, Ruolong; He, Li

2018-06-01

Most of the existing cement evaluation technologies suffer from tool eccentralization due to gravity in highly deviated wells and horizontal wells. This paper proposes a correction method to lessen the effects of tool eccentralization on evaluation results of cement bond using segmented bond tool, which has an omnidirectional sonic transmitter and eight segmented receivers evenly arranged around the tool 2 ft from the transmitter. Using 3-D finite difference parallel numerical simulation method, we investigate the logging responses of centred and eccentred segmented bond tool in a variety of bond conditions. From the numerical results, we find that the tool eccentricity and channel azimuth can be estimated from measured sector amplitude. The average of the sector amplitude when the tool is eccentred can be corrected to the one when the tool is centred. Then the corrected amplitude will be used to calculate the channel size. The proposed method is applied to both synthetic and field data. For synthetic data, it turns out that this method can estimate the tool eccentricity with small error and the bond map is improved after correction. For field data, the tool eccentricity has a good agreement with the measured well deviation angle. Though this method still suffers from the low accuracy of calculating channel azimuth, the credibility of corrected bond map is improved especially in horizontal wells. It gives us a choice to evaluate the bond condition for horizontal wells using existing logging tool. The numerical results in this paper can provide aids for understanding measurements of segmented tool in both vertical and horizontal wells.

Genome-Wide Association of the Laboratory-Based Nicotine Metabolite Ratio in Three Ancestries.

PubMed

Baurley, James W; Edlund, Christopher K; Pardamean, Carissa I; Conti, David V; Krasnow, Ruth; Javitz, Harold S; Hops, Hyman; Swan, Gary E; Benowitz, Neal L; Bergen, Andrew W

2016-09-01

Metabolic enzyme variation and other patient and environmental characteristics influence smoking behaviors, treatment success, and risk of related disease. Population-specific variation in metabolic genes contributes to challenges in developing and optimizing pharmacogenetic interventions. We applied a custom genome-wide genotyping array for addiction research (Smokescreen), to three laboratory-based studies of nicotine metabolism with oral or venous administration of labeled nicotine and cotinine, to model nicotine metabolism in multiple populations. The trans-3'-hydroxycotinine/cotinine ratio, the nicotine metabolite ratio (NMR), was the nicotine metabolism measure analyzed. Three hundred twelve individuals of self-identified European, African, and Asian American ancestry were genotyped and included in ancestry-specific genome-wide association scans (GWAS) and a meta-GWAS analysis of the NMR. We modeled natural-log transformed NMR with covariates: principal components of genetic ancestry, age, sex, body mass index, and smoking status. African and Asian American NMRs were statistically significantly (P values ≤ 5E-5) lower than European American NMRs. Meta-GWAS analysis identified 36 genome-wide significant variants over a 43 kilobase pair region at CYP2A6 with minimum P = 2.46E-18 at rs12459249, proximal to CYP2A6. Additional minima were located in intron 4 (rs56113850, P = 6.61E-18) and in the CYP2A6-CYP2A7 intergenic region (rs34226463, P = 1.45E-12). Most (34/36) genome-wide significant variants suggested reduced CYP2A6 activity; functional mechanisms were identified and tested in knowledge-bases. Conditional analysis resulted in intergenic variants of possible interest (P values < 5E-5). This meta-GWAS of the NMR identifies CYP2A6 variants, replicates the top-ranked single nucleotide polymorphism from a recent Finnish meta-GWAS of the NMR, identifies functional mechanisms, and provides pan-continental population biomarkers for nicotine metabolism. This multiple ancestry meta-GWAS of the laboratory study-based NMR provides novel evidence and replication for genome-wide association of CYP2A6 single nucleotide and insertion-deletion polymorphisms. We identify three regions of genome-wide significance: proximal, intronic, and distal to CYP2A6. We replicate the top-ranking single nucleotide polymorphism from a recent GWAS of the NMR in Finnish smokers, identify a functional mechanism for this intronic variant from in silico analyses of RNA-seq data that is consistent with CYP2A6 expression measured in postmortem lung and liver, and provide additional support for the intergenic region between CYP2A6 and CYP2A7. © The Author 2016. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco.

Genome-Wide Association of the Laboratory-Based Nicotine Metabolite Ratio in Three Ancestries

PubMed Central

Baurley, James W.; Edlund, Christopher K.; Pardamean, Carissa I.; Conti, David V.; Krasnow, Ruth; Javitz, Harold S.; Hops, Hyman; Swan, Gary E.; Benowitz, Neal L.

2016-01-01

Introduction: Metabolic enzyme variation and other patient and environmental characteristics influence smoking behaviors, treatment success, and risk of related disease. Population-specific variation in metabolic genes contributes to challenges in developing and optimizing pharmacogenetic interventions. We applied a custom genome-wide genotyping array for addiction research (Smokescreen), to three laboratory-based studies of nicotine metabolism with oral or venous administration of labeled nicotine and cotinine, to model nicotine metabolism in multiple populations. The trans-3′-hydroxycotinine/cotinine ratio, the nicotine metabolite ratio (NMR), was the nicotine metabolism measure analyzed. Methods: Three hundred twelve individuals of self-identified European, African, and Asian American ancestry were genotyped and included in ancestry-specific genome-wide association scans (GWAS) and a meta-GWAS analysis of the NMR. We modeled natural-log transformed NMR with covariates: principal components of genetic ancestry, age, sex, body mass index, and smoking status. Results: African and Asian American NMRs were statistically significantly (P values ≤ 5E-5) lower than European American NMRs. Meta-GWAS analysis identified 36 genome-wide significant variants over a 43 kilobase pair region at CYP2A6 with minimum P = 2.46E-18 at rs12459249, proximal to CYP2A6. Additional minima were located in intron 4 (rs56113850, P = 6.61E-18) and in the CYP2A6-CYP2A7 intergenic region (rs34226463, P = 1.45E-12). Most (34/36) genome-wide significant variants suggested reduced CYP2A6 activity; functional mechanisms were identified and tested in knowledge-bases. Conditional analysis resulted in intergenic variants of possible interest (P values < 5E-5). Conclusions: This meta-GWAS of the NMR identifies CYP2A6 variants, replicates the top-ranked single nucleotide polymorphism from a recent Finnish meta-GWAS of the NMR, identifies functional mechanisms, and provides pan-continental population biomarkers for nicotine metabolism. Implications: This multiple ancestry meta-GWAS of the laboratory study-based NMR provides novel evidence and replication for genome-wide association of CYP2A6 single nucleotide and insertion–deletion polymorphisms. We identify three regions of genome-wide significance: proximal, intronic, and distal to CYP2A6. We replicate the top-ranking single nucleotide polymorphism from a recent GWAS of the NMR in Finnish smokers, identify a functional mechanism for this intronic variant from in silico analyses of RNA-seq data that is consistent with CYP2A6 expression measured in postmortem lung and liver, and provide additional support for the intergenic region between CYP2A6 and CYP2A7. PMID:27113016

Two-dimensional NMR spectroscopy as a tool to link soil organic matter composition to ecosystem processes

NASA Astrophysics Data System (ADS)

Soucemarianadin, Laure; Erhagen, Björn; Öquist, Mats; Nilsson, Mats; Schleucher, Jürgen

2014-05-01

Environmental factors (e.g. temperature and moisture) and the size and composition of soil microbial populations are often considered the main drivers of soil organic matter (SOM) mineralization. Less consideration is given to the role of SOM as a substrate for microbial metabolism and the importance of the organo-chemical composition of SOM on decomposition. In addition, a fraction of the SOM is often considered as recalcitrant to mineralization leading to accumulation of SOM. However, recently the concept of intrinsic recalcitrance of SOM to mineralization has been questioned. The challenge in investigating the role of SOM composition on its mineralization to a large extent stems from the difficulties in obtaining high resolution characterization of a very complex matrix. 13C nuclear magnetic resonance (NMR) spectroscopy is a widely used tool to characterize SOM. However, SOM is a very complex mixture and in the resulting 13C NMR spectra, the identified functional groups may represent different molecular fragments that appear in the same spectral region leading to broad peaks. These overlaps defy attempts to identify molecular moieties, and this makes it impossible to derive information at a resolution needed for evaluating e.g. recalcitrance of SOM. Here we applied a method, developed in wood science for the pulp paper industry, to achieve a better characterization of SOM. We directly dissolved finely ground organic layers of boreal forest floors-litters, fibric and humic horizons of both coniferous and broadleaved stands-in dimethyl sulfoxide and analyzed the resulting solution with a two-dimensional (2D) 1H-13C NMR experiment. We will discuss methodological aspects related to the ability to identify and quantify individual molecular moieties in SOM. We will demonstrate how the spectra resolve signals of CH groups in a 2D plane determined by the 13C and 1H chemical shifts, thereby vastly increasing the resolving power and information content of NMR spectra. The obtained 2D spectra resolve overlaps observed in 1D 13C spectra, so that hundreds of distinct CH moieties can be observed and many individual molecular fragments can be identified. For instance, in the aromatic spectral region, signals originating from various lignin monomers and unsaturated compounds can be resolved. This yields a detailed chemical fingerprint of the SOM samples, and valuable insights on molecular structures. We observed differences in the respective aromatic region of the 2D spectra of the litter layers and the fibric and humic horizons, in relation with humification processes. We were also able to relate the cross-peak complexity and abundance patterns of identifiable molecular moieties to variability in the temperature response of organic matter degradation, as assessed by Q10. To conclude, solution-state 2D NMR spectroscopy is a highly promising new tool to characterize SOM composition at the molecular level, which opens completely new possibilities to link SOM molecular composition to ecosystem processes, and their responses to environmental changes.

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations

PubMed Central

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, PK

2009-01-01

Background Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. Results We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (α-phase) and the facial (δ-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the α-phase and the δ-phase, although the fluorescence emission shows no substantial difference between the α-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the α-phase. Conclusion The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the α-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation. PMID:19900275

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations.

PubMed

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, P K

2009-11-09

Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (alpha-phase) and the facial (delta-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the alpha-phase and the delta-phase, although the fluorescence emission shows no substantial difference between the alpha-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the alpha-phase. The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the alpha-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation.

3D Extended Logging for Geothermal Resources: Field Trials with the Geo-Bilt System

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

Mallan, R; Wilt, M; Kirkendall, B

2002-05-29

Geo-BILT (Geothermal Borehole Induction Logging Tool) is an extended induction logging tool designed for 3D resistivity imaging around a single borehole. The tool was developed for deployment in high temperature geothermal wells under a joint program funded by the California Energy Commission, Electromagnetic Instruments (EMI) and the U.S. Department of Energy. EM1 was responsible for tool design and manufacture, and numerical modeling efforts were being addressed at Lawrence Livermore Laboratory (LLNL) and other contractors. The field deployment was done by EM1 and LLNL. The tool operates at frequencies from 2 to 42 kHz, and its design features a series ofmore » three-component magnetic sensors offset at 2 and 5 meters from a three-component magnetic source. The combined package makes it possible to do 3D resistivity imaging, deep into the formation, from a single well. The manufacture and testing of the tool was completed in spring of 2001, and the initial deployment of Geo-BILT occurred in May 2001 at the Lost Hills oil field in southern California at leases operated by Chevron USA. This site was chosen for the initial field test because of the favorable geological conditions and the availability of a number of wells suitable for tool deployment. The second deployment occurred in April 2002 at the Dixie Valley geothermal field, operated by Caithness Power LLC, in central Nevada. This constituted the first test in a high temperature environment. The Chevron site features a fiberglass-cased observation well in the vicinity of a water injector. The injected water, which is used for pressure maintenance and for secondary sweep of the heavy oil formation, has a much lower resistivity than the oil bearing formation. This, in addition to the non-uniform flow of this water, creates a 3D resistivity structure, which is analogous to conditions produced from flowing fractures adjacent to geothermal boreholes. Therefore, it is an excellent site for testing the 3D capability of the tool in a low risk environment. The Dixie Valley site offered an environment where the tool could locate near-well fractures associated with steam development. The Lost Hills field measurements yielded a data set suitable for 3D imaging. The Geo-BLT data corresponded to existing conventional logging data and showed clear indications, in several depth intervals, of near-well 3D structure. Subsequent 3D inversion of these data produced a model consistent with non-planar water flow in specific layers. The Dixie Valley measurements identified structures associated with dike intrusions and water inflow at particular depths. Preliminary analysis suggests these structures are steeply dipping, which is consistent with the geology.« less

Towards a geospatial wikipedia

NASA Astrophysics Data System (ADS)

Fritz, S.; McCallum, I.; Schill, C.; Perger, C.; Kraxner, F.; Obersteiner, M.

2009-04-01

Based on the Google Earth (http://earth.google.com) platform we have developed a geospatial Wikipedia (geo-wiki.org). The tool allows everybody in the world to contribute to spatial validation and is made available to the internet community interested in that task. We illustrate how this tool can be used for different applications. In our first application we combine uncertainty hotspot information from three global land cover datasets (GLC, MODIS, GlobCover). With an ever increasing amount of high resolution images available on Google Earth, it is becoming increasingly possible to distinguish land cover features with a high degree of accuracy. We first direct the land cover validation community to certain hotspots of land cover uncertainty and then ask them to fill in a small popup menu on type of land cover, possibly a picture at that location with the different cardinal points as well as date and what type of validation was chosen (google earth imagery/panoramio or if the person has ground truth data). We have implemented the tool via a land cover validation community at FACEBOOK which is based on a snowball system which allows the tracking of individuals and the possibility to ignore users which misuse the system. In a second application we illustrate how the tool could possibly be used for mapping malaria occurrence and small water bodies as well as overall malaria risk. For this application we have implemented a polygon as well as attribute function using Google maps as along with virtual earth using openlayers. The third application deals with illegal logging and how an alert system for illegal logging detection within a certain land tenure system could be implemented. Here we show how the tool can be used to document illegal logging via a YouTube video.

Well Monitoring System For EGS

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

Normann, Randy; Glowka, Dave; Normann, Charles

This grant is a collection of projects designed to move aircraft high temperature electronics technology into the geothermal industry. Randy Normann is the lead. He licensed the HT83SNL00 chip from Sandia National Labs. This chip enables aircraft developed electronics for work within a geothermal well logging tool. However, additional elements are needed to achieve commercially successful logging tools. These elements are offered by a strong list of industrial partners on this grant as: Electrochemical Systems Inc. for HT Rechargeable Batteries, Frequency Management Systems for 300C digital clock, Sandia National Labs for experts in high temperature solder, Honeywell Solid-State Electronics Centermore » for reprogrammable high temperature memory. During the course of this project MagiQ Technologies for high temperature fiber optics.« less

Electronic neutron sources for compensated porosity well logging

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

Chen, A. X.; Antolak, A. J.; Leung, K. -N.

2012-08-01

The viability of replacing Americium–Beryllium (Am–Be) radiological neutron sources in compensated porosity nuclear well logging tools with D–T or D–D accelerator-driven neutron sources is explored. The analysis consisted of developing a model for a typical well-logging borehole configuration and computing the helium-3 detector response to varying formation porosities using three different neutron sources (Am–Be, D–D, and D–T). The results indicate that, when normalized to the same source intensity, the use of a D–D neutron source has greater sensitivity for measuring the formation porosity than either an Am–Be or D–T source. The results of the study provide operational requirements that enablemore » compensated porosity well logging with a compact, low power D–D neutron generator, which the current state-of-the-art indicates is technically achievable.« less

Digital Photography as an Educational Food Logging Tool in Obese Patients with Type 2 Diabetes: Lessons Learned from A Randomized, Crossover Pilot Trial

PubMed Central

Ehrmann, Brett J.; Anderson, Robert M.; Piatt, Gretchen A.; Funnell, Martha M.; Rashid, Hira; Shedden, Kerby; Douyon, Liselle

2014-01-01

Purpose The purpose of this pilot study is to investigate the utility of, and areas of refinement for, digital photography as an educational tool for food logging in obese patients with type 2 diabetes (T2DM). Methods Thirty-three patients aged 18-70 with T2DM, BMI at least 30 kg/m2, and A1C 7.5-9% were recruited from an endocrinology clinic and randomized to a week of food logging using a digital camera (DC) or paper diary (PD), crossing over for week two. Patients then viewed a presentation about dietary effects on blood glucose, using patient DC and blood glucose entries. Outcomes of adherence (based on number of weekly entries), changes in mean blood glucose and frequency of blood glucose checks, and patient satisfaction were compared between methods. Patient feedback on the DC intervention and presentation was also analyzed. Results Thirty patients completed the study. Adherence was identical across methods. The mean difference in number of entries was not significant between methods. This difference increased and neared statistical significance (favoring DC) among patients who were adherent for at least one week (21 entries, with 2 entries per day for 5 of 7 days, n=25). Mean blood glucose did not significantly decrease in either method. Patient satisfaction was similar between interventions. Feedback indicated concerns over photograph accuracy, forgetting to use the cameras, and embarrassment using them in public. Conclusion Though comparable to PD in adherence, blood glucose changes, and patient satisfaction in this pilot trial, patient feedback suggested specific areas of refinement to maximize utility of DC-based food logging as an educational tool in T2DM. PMID:24168836

Relation of short-range and long-range lithium ion dynamics in glass-ceramics: Insights from 7Li NMR field-cycling and field-gradient studies

NASA Astrophysics Data System (ADS)

Haaks, Michael; Martin, Steve W.; Vogel, Michael

2017-09-01

We use various 7Li NMR methods to investigate lithium ion dynamics in 70Li 2S-30 P 2S5 glass and glass-ceramic obtained from this glass after heat treatment. We employ 7Li spin-lattice relaxometry, including field-cycling measurements, and line-shape analysis to investigate short-range ion jumps as well as 7Li field-gradient approaches to characterize long-range ion diffusion. The results show that ceramization substantially enhances the lithium ion mobility on all length scales. For the 70Li 2S-30 P 2S5 glass-ceramic, no evidence is found that bimodal dynamics result from different ion mobilities in glassy and crystalline regions of this sample. Rather, 7Li field-cycling relaxometry shows that dynamic susceptibilities in broad frequency and temperature ranges can be described by thermally activated jumps governed by a Gaussian distribution of activation energies g (Ea) with temperature-independent mean value Em=0.43 eV and standard deviation σ =0.07 eV . Moreover, use of this distribution allows us to rationalize 7Li line-shape results for the local ion jumps. In addition, this information about short-range ion dynamics further explains 7Li field-gradient results for long-range ion diffusion. In particular, we quantitatively show that, consistent with our experimental results, the temperature dependence of the self-diffusion coefficient D is not described by the mean activation energy Em of the local ion jumps, but by a significantly smaller apparent value whenever the distribution of correlation times G (logτ ) of the jump motion derives from an invariant distribution of activation energies and, hence, continuously broadens upon cooling. This effect occurs because the harmonic mean, which determines the results of diffusivity or also conductivity studies, continuously separates from the peak position of G (logτ ) when the width of this distribution increases.

Using pulse field gradient NMR diffusion measurements to define molecular size distributions in glycan preparations.

PubMed

Miller, Michelle C; Klyosov, Anatole; Platt, David; Mayo, Kevin H

2009-07-06

Glycans comprise perhaps the largest biomass in nature, and more and more glycans are used in a number of applications, including those as pharmaceutical agents in the clinic. However, defining glycan molecular weight distributions during and after their preparation is not always straightforward. Here, we use pulse field gradient (PFG) (1)H NMR self-diffusion measurements to assess molecular weight distributions in various glycan preparations. Initially, we derived diffusion coefficients, D, on a series of dextrans with reported weight-average molecular weights from about 5 kDa to 150 kDa. For each dextran sample, we analyzed 15 diffusion decay curves, one from each of the 15 major (1)H resonance envelopes, to provide diffusion coefficients. By measuring D as a function of dextran concentration, we determined D at infinite dilution, D(inf), which allowed estimation of the hydrodynamic radius, R(h), using the Stokes-Einstein relationship. A plot of log D(inf) versus log R(h) was linear and provided a standard calibration curve from which R(h) is estimated for other glycans. We then applied this methodology to investigate two other glycans, an alpha-(1-->2)-L-rhamnosyl-alpha-(1-->4)-D-galacturonosyl with quasi-randomly distributed, mostly terminal beta(1-->4)-linked galactose side-chains (GRG) and an alpha(1-->6)-D-galacto-beta(1-->4)-D-mannan (Davanat), which is presently being tested against cancer in the clinic. Using the dextran-derived calibration curve, we find that average R(h) values for GRG and Davanat are 76+/-6 x 10(-10) m and 56+/-3 x 10(-10) m, with GRG being more polydispersed than Davanat. Results from this study will be useful to investigators requiring knowledge of polysaccharide dispersity, needing to study polysaccharides under various solution conditions, or wanting to follow degradation of polysaccharides during production.

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

Eportfolio Adoption's Mediating Influence on Faculty Perspectives: An Activity Theory View

ERIC Educational Resources Information Center

Thomas, Jonathan M.

2017-01-01

A case-comparative mixed methods approach was used to discover how faculty members' teaching perspectives changed as they adopted an eportfolio tool (Pathbrite). Ten faculty members took the Teaching Perspectives Inventory (TPI) before and after using the tool during Fall semester 2015. Also, systems logs were collected and interviews were…

Predicting Knowledge Workers' Participation in Voluntary Learning with Employee Characteristics and Online Learning Tools

ERIC Educational Resources Information Center

Hicks, Catherine

2018-01-01

Purpose: This paper aims to explore predicting employee learning activity via employee characteristics and usage for two online learning tools. Design/methodology/approach: Statistical analysis focused on observational data collected from user logs. Data are analyzed via regression models. Findings: Findings are presented for over 40,000…

Capricorn-A Web-Based Automatic Case Log and Volume Analytics for Diagnostic Radiology Residents.

PubMed

Chen, Po-Hao; Chen, Yin Jie; Cook, Tessa S

2015-10-01

On-service clinical learning is a mainstay of radiology education. However, an accurate and timely case log is difficult to keep, especially in the absence of software tools tailored to resident education. Furthermore, volume-related feedback from the residency program sometimes occurs months after a rotation ends, limiting the opportunity for meaningful intervention. We surveyed the residents of a single academic institution to evaluate the current state of and the existing need for tracking interpretation volume. Using the results of the survey, we created an open-source automated case log software. Finally, we evaluated the effect of the software tool on the residency in a 1-month, postimplementation survey. Before implementation of the system, 89% of respondents stated that volume is an important component of training, but 71% stated that volume data was inconvenient to obtain. Although the residency program provides semiannual reviews, 90% preferred reviewing interpretation volumes at least once monthly. After implementation, 95% of the respondents stated that the software is convenient to access, 75% found it useful, and 88% stated they would use the software at least once a month. The included analytics module, which benchmarks the user using historical aggregate average volumes, is the most often used feature of the software. Server log demonstrates that, on average, residents use the system approximately twice a week. An automated case log software system may fulfill a previously unmet need in diagnostic radiology training, making accurate and timely review of volume-related performance analytics a convenient process. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

NMR imaging of density distributions in tablets.

PubMed

Djemai, A; Sinka, I C

2006-08-17

This paper describes the use of (1)H nuclear magnetic resonance (NMR) for 3D mapping of the relative density distribution in pharmaceutical tablets manufactured under controlled conditions. The tablets are impregnated with a compatible liquid. The technique involves imaging of the presence of liquid which occupies the open pore space. The method does not require special calibration as the signal is directly proportional to the porosity for the imaging conditions used. The NMR imaging method is validated using uniform density flat faced tablets and also by direct comparison with X-ray computed tomography. The results illustrate (1) the effect of die wall friction on density distribution by compressing round, curved faced tablets using clean and pre-lubricated tooling, (2) the evolution of density distribution during compaction for both clean and pre-lubricated die wall conditions, by imaging tablets compressed to different compaction forces, and (3) the effect of tablet image on density distribution by compressing two complex shape tablets in identical dies to the same average density using punches with different geometries.

Solid-State NMR Study of the Cicada Wing.

PubMed

Gullion, John D; Gullion, Terry

2017-08-17

Wings of flying insects are part of the cuticle which forms the exoskeleton. The primary molecular components of cuticle are protein, chitin, and lipid. How these components interact with one another to form the exoskeleton is not completely understood. The difficulty in characterizing the cuticle arises because it is insoluble and noncrystalline. These properties severely limit the experimental tools that can be used for molecular characterization. Solid-state nuclear magnetic resonance experiments have been used in the past to characterize the exoskeleton of beetles and have found that chitin and protein make comparable contributions to the molecular matrix. However, little work has been done to characterize the components of the wing, which includes vein and membrane. In this work, solid-state NMR was used to characterize the wing of the 17-year cycle cicada (Magicicada cassini) that appeared in northern West Virginia during the summer of 2016. The NMR results show noticeable differences between the molecular components of the vein and membrane.

PGI chicory (Cichorium intybus L.) traceability by means of HRMAS-NMR spectroscopy: a preliminary study.

PubMed

Ritota, Mena; Casciani, Lorena; Valentini, Massimiliano

2013-05-01

Analytical traceability of PGI and PDO foods (Protected Geographical Indication and Protected Denomination Origin respectively) is one of the most challenging tasks of current applied research. Here we proposed a metabolomic approach based on the combination of (1)H high-resolution magic angle spinning-nuclear magnetic resonance (HRMAS-NMR) spectroscopy with multivariate analysis, i.e. PLS-DA, as a reliable tool for the traceability of Italian PGI chicories (Cichorium intybus L.), i.e. Radicchio Rosso di Treviso and Radicchio Variegato di Castelfranco, also known as red and red-spotted, respectively. The metabolic profile was gained by means of HRMAS-NMR, and multivariate data analysis allowed us to build statistical models capable of providing clear discrimination among the two varieties and classification according to the geographical origin. Based on Variable Importance in Projection values, the molecular markers for classifying the different types of red chicories analysed were found accounting for both the cultivar and the place of origin. © 2012 Society of Chemical Industry.

A LEAN approach toward automated analysis and data processing of polymers using proton NMR spectroscopy.

PubMed

de Brouwer, Hans; Stegeman, Gerrit

2011-02-01

To maximize utilization of expensive laboratory instruments and to make most effective use of skilled human resources, the entire chain of data processing, calculation, and reporting that is needed to transform raw NMR data into meaningful results was automated. The LEAN process improvement tools were used to identify non-value-added steps in the existing process. These steps were eliminated using an in-house developed software package, which allowed us to meet the key requirement of improving quality and reliability compared with the existing process while freeing up valuable human resources and increasing productivity. Reliability and quality were improved by the consistent data treatment as performed by the software and the uniform administration of results. Automating a single NMR spectrophotometer led to a reduction in operator time of 35%, doubling of the annual sample throughput from 1400 to 2800, and reducing the turn around time from 6 days to less than 2. Copyright © 2011 Society for Laboratory Automation and Screening. Published by Elsevier Inc. All rights reserved.

Rapid approach to identify the presence of Arabica and Robusta species in coffee using 1H NMR spectroscopy.

PubMed

Monakhova, Yulia B; Ruge, Winfried; Kuballa, Thomas; Ilse, Maren; Winkelmann, Ole; Diehl, Bernd; Thomas, Freddy; Lachenmeier, Dirk W

2015-09-01

NMR spectroscopy was used to verify the presence of Arabica and Robusta species in coffee. Lipophilic extracts of authentic roasted and green coffees showed the presence of established markers for Robusta (16-O-methylcafestol (16-OMC)) and for Arabica (kahweol). The integration of the 16-OMC signal (δ 3.165 ppm) was used to estimate the amount of Robusta in coffee blends with an approximate limit of detection of 1-3%. The method was successfully applied for the analysis of 77 commercial coffee samples (coffee pods, coffee capsules, and coffee beans). Furthermore, principal component analysis (PCA) was applied to the spectra of lipophilic and aqueous extracts of 20 monovarietal authentic samples. Clusters of the two species were observed. NMR spectroscopy can be used as a rapid prescreening tool to discriminate Arabica and Robusta coffee species before the confirmation applying the official method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Direct study of minor extra-virgin olive oil components without any sample modification. 1H NMR multisupression experiment: A powerful tool.

PubMed

Ruiz-Aracama, Ainhoa; Goicoechea, Encarnación; Guillén, María D

2017-08-01

Proton Nuclear Magnetic Resonance ( 1 H NMR) was employed to study monovarietal commercial Spanish extra-virgin olive oils (EVOO) (Arbequina, Arroniz, Cornicabra, Hojiblanca and Picual). Each sample was analyzed by a standard pulse and by an experiment suppressing the main lipid signals, enabling the detection of signals of minor components. The aim was to determine the possibilities of both 1 H NMR approaches to characterize EVOO composition, focusing on acyl groups, squalene, sterols, triterpene acids/esters, fatty alcohols, wax esters and phenols (lignans, tyrosol, hydroxytyrosol, oleocanthal, oleacein, oleokoronal, oleomissional, ligstrodials and oleuropeindials), and to determine hydrolysis and oxidation levels. The signal assignments (in deuterated chloroform) are thoroughly described, identifying for the first time those of the protons of esters of phytol and of geranylgeraniol. Correct signal assignment is fundamental for obtaining sound results when interpreting statistical data from metabolomic studies of EVOO composition and adulteration, making it possible to differentiate and classify oils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fishing tool retrieves MWD nuclear source from deep well

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

Not Available

A new wire line tool has successfully retrieved the nuclear sources and formation data from a measurement-while-drilling (MWD) tool stuck in a deep, highly deviated well in the Gulf of Mexico. On Nov. 8, 1993, Schlumberger Wireline and Testing and Anadrill ran a logging-while-drilling inductive coupling (LINC) tool on conventional wire line to fish the gamma ray and neutron sources from a compensated density neutron (CDN) tool stuck in a well at 19,855 ft with an inclination greater than 80[degree]. The paper briefly describes the operation and equipment.

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

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

Liu, Qing; Shi, Chaowei; Yu, Lu

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in amore » defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.« less

(1)H nuclear magnetic resonance (NMR) as a tool to measure dehydration in mice.

PubMed

Li, Matthew; Vassiliou, Christophoros C; Colucci, Lina A; Cima, Michael J

2015-08-01

Dehydration is a prevalent pathology, where loss of bodily water can result in variable symptoms. Symptoms can range from simple thirst to dire scenarios involving loss of consciousness. Clinical methods exist that assess dehydration from qualitative weight changes to more quantitative osmolality measurements. These methods are imprecise, invasive, and/or easily confounded, despite being practiced clinically. We investigate a non-invasive, non-imaging (1)H NMR method of assessing dehydration that attempts to address issues with existing clinical methods. Dehydration was achieved by exposing mice (n = 16) to a thermally elevated environment (37 °C) for up to 7.5 h (0.11-13% weight loss). Whole body NMR measurements were made using a Bruker LF50 BCA-Analyzer before and after dehydration. Physical lean tissue, adipose, and free water compartment approximations had NMR values extracted from relaxation data through a multi-exponential fitting method. Changes in before/after NMR values were compared with clinically practiced metrics of weight loss (percent dehydration) as well as blood and urine osmolality. A linear correlation between tissue relaxometry and both animal percent dehydration and urine osmolality was observed in lean tissue, but not adipose or free fluids. Calculated R(2) values for percent dehydration were 0.8619 (lean, P < 0.0001), 0.5609 (adipose, P = 0.0008), and 0.0644 (free fluids, P = 0.3445). R(2) values for urine osmolality were 0.7760 (lean, P < 0.0001), 0.5005 (adipose, P = 0.0022), and 0.0568 (free fluids, P = 0.3739). These results suggest that non-imaging (1)H NMR methods are capable of non-invasively assessing dehydration in live animals. Copyright © 2015 John Wiley & Sons, Ltd.

Chemometric Methods to Quantify 1D and 2D NMR Spectral Differences Among Similar Protein Therapeutics.

PubMed

Chen, Kang; Park, Junyong; Li, Feng; Patil, Sharadrao M; Keire, David A

2018-04-01

NMR spectroscopy is an emerging analytical tool for measuring complex drug product qualities, e.g., protein higher order structure (HOS) or heparin chemical composition. Most drug NMR spectra have been visually analyzed; however, NMR spectra are inherently quantitative and multivariate and thus suitable for chemometric analysis. Therefore, quantitative measurements derived from chemometric comparisons between spectra could be a key step in establishing acceptance criteria for a new generic drug or a new batch after manufacture change. To measure the capability of chemometric methods to differentiate comparator NMR spectra, we calculated inter-spectra difference metrics on 1D/2D spectra of two insulin drugs, Humulin R® and Novolin R®, from different manufacturers. Both insulin drugs have an identical drug substance but differ in formulation. Chemometric methods (i.e., principal component analysis (PCA), 3-way Tucker3 or graph invariant (GI)) were performed to calculate Mahalanobis distance (D M ) between the two brands (inter-brand) and distance ratio (D R ) among the different lots (intra-brand). The PCA on 1D inter-brand spectral comparison yielded a D M value of 213. In comparing 2D spectra, the Tucker3 analysis yielded the highest differentiability value (D M  = 305) in the comparisons made followed by PCA (D M  = 255) then the GI method (D M  = 40). In conclusion, drug quality comparisons among different lots might benefit from PCA on 1D spectra for rapidly comparing many samples, while higher resolution but more time-consuming 2D-NMR-data-based comparisons using Tucker3 analysis or PCA provide a greater level of assurance for drug structural similarity evaluation between drug brands.

A Modular Implementation for the Simulation of 1D and 2D Solid-State NMR Spectra of Quadrupolar Nuclei in the Virtual Multifrequency Spectrometer-Draw Graphical Interface.

PubMed

Presti, Davide; Pedone, Alfonso; Licari, Daniele; Barone, Vincenzo

2017-05-09

We present the implementation of the solid state (SoS)NMR module for the simulation of several 1D and 2D NMR spectra of all the elements in the periodic table in the virtual multifrequency spectrometer (VMS). This module is fully integrated with the graphical user interface of VMS (VMS-Draw) [Licari et al., J. Comput. Chem. 36, 2015, 321-334], a freeware tool which allows a user-friendly handling of structures and analyses of advanced spectroscopical properties of chemical compounds-from model systems to real-world applications. Besides the numerous modules already available in VMS for the study of electronic, optical, vibrational, vibronic, and EPR properties, here the simulation of NMR spectra is presented with a particular emphasis on those techniques usually employed to investigate solid state systems. The SoSNMR module benefits from its ability to work under both periodic and nonperiodic conditions, such that small molecules/molecular clusters can be treated, as well as extended three-dimensional systems enforcing (or not) translational periodicity. These features allow VMS to simulate spectra resulting from NMR calculations by some popular quantum chemistry codes, namely Gaussian09/16, Castep, and Quantum Espresso. The effectiveness of the SoSNMR module of VMS is examined throughout the manuscript, and applied to simulate 1D static, MAS, and VAS NMR spectra as well as 2D correlation (90°, MAS) and MQMAS spectra of active NMR nuclei embedded in different amorphous and crystalline systems of actual interest in chemistry and material science. Finally, the program is able to simulate the spectra of both the total ensemble of spin-active nuclei present in the system and of subensembles differentiated depending on the chemical environment of the first and second coordination sphere in a very general way applicable to any kind of systems.

A combined solid-state NMR and X-ray crystallography study of the bromide ion environments in triphenylphosphonium bromides.

PubMed

Burgess, Kevin M N; Korobkov, Ilia; Bryce, David L

2012-04-27

Multinuclear ((31)P and (79/81)Br), multifield (9.4, 11.75, and 21.1 T) solid-state nuclear magnetic resonance experiments are performed for seven phosphonium bromides bearing the triphenylphosphonium cation, a molecular scaffold found in many applications in chemistry. This is undertaken to fully characterise their bromine electric field gradient (EFG) tensors, as well as the chemical shift (CS) tensors of both the halogen and the phosphorus nuclei, providing a rare and novel insight into the local electronic environments surrounding them. New crystal structures, obtained from single-crystal X-ray diffraction, are reported for six compounds to aid in the interpretation of the NMR data. Among them is a new structure of BrPPh(4), because the previously reported one was inconsistent with our magnetic resonance data, thereby demonstrating how NMR data of non-standard nuclei can correct or improve X-ray diffraction data. Our results indicate that, despite sizable quadrupolar interactions, (79/81)Br magnetic resonance spectroscopy is a powerful characterisation tool that allows for the differentiation between chemically similar bromine sites, as shown through the range in the characteristic NMR parameters. (35/37)Cl solid-state NMR data, obtained for an analogous phosphonium chloride sample, provide insight into the relationship between unit cell volume, nuclear quadrupolar coupling constants, and Sternheimer antishielding factors. The experimental findings are complemented by gauge-including projector-augmented wave (GIPAW) DFT calculations, which substantiate our experimentally determined strong dependence of the largest component of the bromine CS tensor, δ(11), on the shortest Br-P distance in the crystal structure, a finding that has possible application in the field of NMR crystallography. This trend is explained in terms of Ramsey's theory on paramagnetic shielding. Overall, this work demonstrates how careful NMR studies of underexploited exotic nuclides, such as (79/81)Br, can afford insights into structure and bonding environments in the solid state. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proton Nuclear Magnetic Resonance-Spectroscopic Discrimination of Wines Reflects Genetic Homology of Several Different Grape (V. vinifera L.) Cultivars

PubMed Central

Zhu, Yong; Wen, Wen; Zhang, Fengmin; Hardie, Jim W.

2015-01-01

Background and Aims Proton nuclear magnetic resonance spectroscopy coupled multivariate analysis (1H NMR-PCA/PLS-DA) is an important tool for the discrimination of wine products. Although 1H NMR has been shown to discriminate wines of different cultivars, a grape genetic component of the discrimination has been inferred only from discrimination of cultivars of undefined genetic homology and in the presence of many confounding environmental factors. We aimed to confirm the influence of grape genotypes in the absence of those factors. Methods and Results We applied 1H NMR-PCA/PLS-DA and hierarchical cluster analysis (HCA) to wines from five, variously genetically-related grapevine (V. vinifera) cultivars; all grown similarly on the same site and vinified similarly. We also compared the semi-quantitative profiles of the discriminant metabolites of each cultivar with previously reported chemical analyses. The cultivars were clearly distinguishable and there was a general correlation between their grouping and their genetic homology as revealed by recent genomic studies. Between cultivars, the relative amounts of several of the cultivar-related discriminant metabolites conformed closely with reported chemical analyses. Conclusions Differences in grape-derived metabolites associated with genetic differences alone are a major source of 1H NMR-based discrimination of wines and 1H NMR has the capacity to discriminate between very closely related cultivars. Significance of the Study The study confirms that genetic variation among grape cultivars alone can account for the discrimination of wine by 1H NMR-PCA/PLS and indicates that 1H NMR spectra of wine of single grape cultivars may in future be used in tandem with hierarchical cluster analysis to elucidate genetic lineages and metabolomic relations of grapevine cultivars. In the absence of genetic information, for example, where predecessor varieties are no longer extant, this may be a particularly useful approach. PMID:26658757

NMR doesn't lie or how solid-state NMR spectroscopy contributed to a better understanding of the nature and function of soil organic matter (Philippe Duchaufour Medal Lecture)

NASA Astrophysics Data System (ADS)

Knicker, Heike

2016-04-01

"Nuclear magnetic resonance (NMR) does not lie". More than anything else, this statement of a former colleague and friend has shaped my relation to solid-state NMR spectroscopy. Indeed, if this technique leads to results which contradict the expectations, it is because i) some parts of the instrument are broken, ii) maladjustment of the acquisition parameters or iii) wrong preparation or confusion of samples. However, it may be even simpler, namely that the expectations were wrong. Of course, for researchers, the latter is the most interesting possibility since it forces to reassess accepted views and to search for new explanations. As my major analytical tool, NMR spectroscopy has confronted me with this challenge often enough to turn this issue into the main subject of my talk and to share with the audience how it formed my understanding of function and nature of soil organic matter (SOM). Already shortly after its introduction into soil science in the 1980's, the data obtained with solid-state 13C NMR spectroscopy opened the stage for ongoing discussions, since they showed that in humified SOM aromatic carbon is considerably less important than previously thought. This finding had major implications regarding the understanding of the origin of SOM and the mechanisms by which it is formed. Certainly, the discrepancy between the new results and previous paradigms contributed to mistrust in the reliability of solid-state NMR techniques. The respective discussion has survived up to our days, although already in the 1980's and 1990's fundamental studies could demonstrate that quantitative solid-state NMR data can be obtained if i) correct acquisition parameters are chosen, ii) the impact of paramagnetic compounds is reduced and iii) the presence of soot in soils can be excluded. On the other hand, this mistrust led to a detailed analysis of the impact of paramagnetics on the NMR behavior of C groups which then improved our understanding of the role of carbohydrates for organo-mineral interactions. Since decent solid-state NMR spectra cannot be obtained from graphenic components, the successful acquisition of solid-state 13C and 15N NMR spectra of charcoals challenged the well accepted model of their chemical nature. Application of advanced 2D NMR approaches confirmed the new view of charcoal as a heterogeneous material, the composition of which depends upon the feedstock and charring condition. The respective consequences of this alternative for the understanding of C sequestration are still matter of ongoing debates. Although the sensitivity of 15N for NMR spectroscopy is 50 times lower than that of 13C, first solid-state 15N NMR spectra of soils with natural 15N abundance were already published in the 1990's. They clearly identified peptide-like structures as the main organic N form in unburnt soils. However, in spite of their high contribution to SOM, the role of peptides in soils is far from understood. Considering the new technological developments in the field of NMR spectroscopy, this technique will certainly not stop to contribute to unexpected results.

Metabonomics by proton nuclear magnetic resonance in human pleural effusions: A route to discriminate between benign and malignant pleural effusions and to target small molecules as potential cancer biomarkers.

PubMed

Zennaro, Lucio; Vanzani, Paola; Nicolè, Lorenzo; Cappellesso, Rocco; Fassina, Ambrogio

2017-05-01

Cytopathology is a noninvasive and cost-effective method for detecting cancer cells in pleural effusions (PEs), although in many cases, the diagnostic performance is hindered by the paucity of significant cells or the lack of clear morphological criteria. This study presents the results of an omics approach to improving the diagnostic performance of PE cytology. Metabolic profiling with proton nuclear magnetic resonance ( 1 H-NMR) was performed for 92 PEs (44 malignant cases of 8 different cancers and 48 benign cases of 7 nonneoplastic conditions). Light's criteria were used to further classify PEs as transudates or exudates, and 1 H-NMR spectroscopy was used to differentiate malignant pleural effusions (mPEs) from benign pleural effusions (bPEs). 1 H-NMR metabolic analysis showed clearly different spectra for mPEs and bPEs in the regions of the signals due to lipids, branched amino acids, and lactate, which were increased in mPEs. Transudates and exudates in bPEs were differentiated as well on the basis of the 1 H-NMR signals from lipids and lipoproteins, which were increased in exudates. Subject to validation in further larger studies, 1 H-NMR metabonomics could be an effective and reliable ancillary tool for PE investigations and diagnoses. Cancer Cytopathol 2017;125:341-348. © 2017 American Cancer Society. © 2017 American Cancer Society.

ImatraNMR: novel software for batch integration and analysis of quantitative NMR spectra.

PubMed

Mäkelä, A V; Heikkilä, O; Kilpeläinen, I; Heikkinen, S

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D (1)H and (13)C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request. Copyright © 2011 Elsevier Inc. All rights reserved.

Theoretical DFT, vibrational and NMR studies of benzimidazole and alkyl derivatives

NASA Astrophysics Data System (ADS)

Infante-Castillo, Ricardo; Rivera-Montalvo, Luis A.; Hernández-Rivera, Samuel P.

2008-04-01

Benzimidazoles are heterocyclic compounds that have awaked great interest during the last few years because of their proven biological activity as antiviral, antimicrobial, and antitumoral agents. For this reason, the development of a systematic FT-IR, FT-Raman and NMR study of 1-substituted compounds in 2-methylbenzimidazole constitutes a significant tool in understanding the molecular dynamics and the structural parameters that govern their behavior. Two new 1-alkyl-2-methylbenzimidazoles compounds were synthesized from reaction of 2-methylbenzimidazole with primary and secondary alkyl halides using a strong base as a catalyst. These compounds were purified and characterized by elemental analysis and different spectroscopic methods. The comparative analysis of vibrational modes of benzimidazole and its alkyl derivatives show that regions of absorption are very similar in all of them. However, changes are produced at low frequencies specifically in the C-H out of plane deformations, ring breathing and ring skeletal vibrations. The ring out-of plane bending modes shift by 10-15 cm -1 in some cases as results of alkyl substitution. The theoretical calculated spectra, using Density Functional Theory (DFT) approximation, and experimental results were consistent with each other. The GIAO method was used to calculate absolute shieldings, which agree consistently with those measured by 1H and 13C NMR. The consistency and efficiency of the GIAO 13C and 1H NMR calculations were thoroughly checked by the analysis of statistical parameters concerning computed and experimental 13C and 1H NMR chemical shift values of the studied compounds.

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data

PubMed Central

Larralde, Martin; Lawson, Thomas N.; Weber, Ralf J. M.; Moreno, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; Viant, Mark R.; Steinbeck, Christoph; Salek, Reza M.

2017-01-01

Abstract Summary Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. Availability and Implementation mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools. Documentation is available from http://2isa.readthedocs.io/en/latest/. Contact reza.salek@ebi.ac.uk or isatools@googlegroups.com Supplementary information Supplementary data are available at Bioinformatics online. PMID:28402395

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

PubMed

Larralde, Martin; Lawson, Thomas N; Weber, Ralf J M; Moreno, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; Viant, Mark R; Steinbeck, Christoph; Salek, Reza M

2017-08-15

Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools. Documentation is available from http://2isa.readthedocs.io/en/latest/. reza.salek@ebi.ac.uk or isatools@googlegroups.com. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

NMR metabolomics of thrips (Frankliniella occidentalis) resistance in Senecio hybrids.

PubMed

Leiss, Kirsten A; Choi, Young H; Abdel-Farid, Ibrahim B; Verpoorte, Robert; Klinkhamer, Peter G L

2009-02-01

Western flower thrips (Frankliniella occidentalis) has become a key insect pest of agricultural and horticultural crops worldwide. Little is known about host plant resistance to thrips. In this study, we investigated thrips resistance in F (2) hybrids of Senecio jacobaea and Senecio aquaticus. We identified thrips-resistant hybrids applying three different bioassays. Subsequently, we compared the metabolomic profiles of these hybrids applying nuclear magnetic resonance spectroscopy (NMR). The new developments of NMR facilitate a wide range coverage of the metabolome. This makes NMR especially suitable if there is no a priori knowledge of the compounds related to herbivore resistance and allows a holistic approach analyzing different chemical compounds simultaneously. We show that the metabolomes of thrips-resistant and -susceptible hybrids differed considerably. Thrips-resistant hybrids contained higher amounts of the pyrrolizidine alkaloids (PA), jacobine, and jaconine, especially in younger leaves. Also, a flavanoid, kaempferol glucoside, accumulated in the resistant plants. Both PAs and kaempferol are known for their inhibitory effect on herbivores. In resistant and susceptible F (2) hybrids, young leaves showed less thrips damage than old leaves. Consistent with the optimal plant defense theory, young leaves contained increased levels of primary metabolites such as sucrose, raffinose, and stachyose, but also accumulated jacaranone as a secondary plant defense compound. Our results prove NMR as a promising tool to identify different metabolites involved in herbivore resistance. It constitutes a significant advance in the study of plant-insect relationships, providing key information on the implementation of herbivore resistance breeding strategies in plants.

PepsNMR for 1H NMR metabolomic data pre-processing.

PubMed

Martin, Manon; Legat, Benoît; Leenders, Justine; Vanwinsberghe, Julien; Rousseau, Réjane; Boulanger, Bruno; Eilers, Paul H C; De Tullio, Pascal; Govaerts, Bernadette

2018-08-17

In the analysis of biological samples, control over experimental design and data acquisition procedures alone cannot ensure well-conditioned 1 H NMR spectra with maximal information recovery for data analysis. A third major element affects the accuracy and robustness of results: the data pre-processing/pre-treatment for which not enough attention is usually devoted, in particular in metabolomic studies. The usual approach is to use proprietary software provided by the analytical instruments' manufacturers to conduct the entire pre-processing strategy. This widespread practice has a number of advantages such as a user-friendly interface with graphical facilities, but it involves non-negligible drawbacks: a lack of methodological information and automation, a dependency of subjective human choices, only standard processing possibilities and an absence of objective quality criteria to evaluate pre-processing quality. This paper introduces PepsNMR to meet these needs, an R package dedicated to the whole processing chain prior to multivariate data analysis, including, among other tools, solvent signal suppression, internal calibration, phase, baseline and misalignment corrections, bucketing and normalisation. Methodological aspects are discussed and the package is compared to the gold standard procedure with two metabolomic case studies. The use of PepsNMR on these data shows better information recovery and predictive power based on objective and quantitative quality criteria. Other key assets of the package are workflow processing speed, reproducibility, reporting and flexibility, graphical outputs and documented routines. Copyright © 2018 Elsevier B.V. All rights reserved.

1H NMR study of inclusion compounds of phenylurea derivatives in β-cyclodextrin

NASA Astrophysics Data System (ADS)

Dupuy, N.; Barbry, D.; Bria, M.; Marquis, S.; Vrielynck, L.; Kister, J.

2005-04-01

Proton nuclear magnetic resonance spectroscopy ( 1H NMR), which has become an important tool for the study "in situ" of β-cyclodextrin (β-CD) complexes, was used to study and structurally characterize the inclusion complexes formed between β-CD and isoproturon, fenuron, monuron and diuron. The high variation of the chemical shifts from the proton located inside the cavity (H-3, H-5 and H-6) coupled with the non variation of the one located outer sphere of the β-CD (H-1, H-2 and H-4) provided clear evidence of the inclusion phenomena. Two-dimensional rotating frame Overhauser effect spectroscopy (ROESY) experiments were carried out to further support the proposed inclusion mode.

A novel series of N-acyl substituted indole-linked benzimidazoles and naphthoimidazoles as potential anti inflammatory, anti biofilm and anti microbial agents.

PubMed

Abraham, Rajan; Prakash, Periakaruppan; Mahendran, Karthikeyan; Ramanathan, Murugappan

2018-01-01

A novel N-acyl substituted indole-linked benzimidazoles and naphthoimidazoles were synthesized. Their chemical structures were confirmed using spectroscopic tools including 1 H NMR, 13 C NMR and CHN-elemental analyses. Anti inflammatory activity for all target compounds was evaluated in-vitro. The synthesized compounds hinder the biofilm formation and control the growth of the pathogen, Staphylococcus epidermis. Anti microbial activity of the compounds was evaluated against both Gram negative and Gram positive bacteria such as Staphylococcus aureus (MTCC 2940), Pseudomonas aeruginosa (MTCC424), Escherchia coli (MTCC 443) and Enterococcus fecalis. Copyright © 2017 Elsevier Ltd. All rights reserved.