scholarly journals Sensitivity enhancement of homonuclear multidimensional NMR correlations for labile sites in proteins, polysaccharides, and nucleic acids

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Mihajlo Novakovic ◽  
Ēriks Kupče ◽  
Andreas Oxenfarth ◽  
Marcos D. Battistel ◽  
Darón I. Freedberg ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Spectral Resolution ◽  
A Priori ◽  
Sensitivity Enhancement ◽  
Solvent Exchange ◽  
Relaxation Rates ◽  
Selective Inversion ◽  
Selective Saturation ◽  
Ultrahigh Fields ◽  
Suitable Processing

Abstract Multidimensional TOCSY and NOESY are central experiments in chemical and biophysical NMR. Limited efficiencies are an intrinsic downside of these methods, particularly when targeting labile sites. This study demonstrates that the decoherence imparted on these protons through solvent exchanges can, when suitably manipulated, lead to dramatic sensitivity gains per unit time in the acquisition of these experiments. To achieve this, a priori selected frequencies are encoded according to Hadamard recipes, while concurrently subject to looped selective inversion or selective saturation procedures. Suitable processing then leads to protein, oligosaccharide and nucleic acid cross-peak enhancements of ≈200–1000% per scan, in measurements that are ≈10-fold faster than conventional counterparts. The extent of these gains will depend on the solvent exchange and relaxation rates of the targeted sites; these gains also benefit considerably from the spectral resolution provided by ultrahigh fields, as corroborated by NMR experiments at 600 MHz and 1 GHz. The mechanisms underlying these experiments’ enhanced efficiencies are analyzed on the basis of three-way polarization transfer interplays between the water, labile and non-labile protons, and the experimental results are rationalized using both analytical and numerical derivations. Limitations as well as further extensions of the proposed methods, are also discussed.

scholarly journals Evaluation of ozone profile and tropospheric ozone retrievals from GEMS and OMI spectra

2013 ◽  
Vol 6 (2) ◽  
pp. 239-249 ◽  
Author(s):  
J. Bak ◽  
J. H. Kim ◽  
X. Liu ◽  
K. Chance ◽  
J. Kim
Keyword(s):  
Spectral Resolution ◽  
Tropospheric Ozone ◽  
Stratospheric Ozone ◽  
A Priori ◽  
Ozone Monitoring Instrument ◽  
Satellite Platform ◽  
Ozone Profile ◽  
Retrieval Errors ◽  
Standard Deviations ◽  
Column Ozone

Abstract. South Korea is planning to launch the GEMS (Geostationary Environment Monitoring Spectrometer) instrument into the GeoKOMPSAT (Geostationary Korea Multi-Purpose SATellite) platform in 2018 to monitor tropospheric air pollutants on an hourly basis over East Asia. GEMS will measure backscattered UV radiances covering the 300–500 nm wavelength range with a spectral resolution of 0.6 nm. The main objective of this study is to evaluate ozone profiles and stratospheric column ozone amounts retrieved from simulated GEMS measurements. Ozone Monitoring Instrument (OMI) Level 1B radiances, which have the spectral range 270–500 nm at spectral resolution of 0.42–0.63 nm, are used to simulate the GEMS radiances. An optimal estimation-based ozone profile algorithm is used to retrieve ozone profiles from simulated GEMS radiances. Firstly, we compare the retrieval characteristics (including averaging kernels, degrees of freedom for signal, and retrieval error) derived from the 270–330 nm (OMI) and 300–330 nm (GEMS) wavelength ranges. This comparison shows that the effect of not using measurements below 300 nm on retrieval characteristics in the troposphere is insignificant. However, the stratospheric ozone information in terms of DFS decreases greatly from OMI to GEMS, by a factor of ∼2. The number of the independent pieces of information available from GEMS measurements is estimated to 3 on average in the stratosphere, with associated retrieval errors of ~1% in stratospheric column ozone. The difference between OMI and GEMS retrieval characteristics is apparent for retrieving ozone layers above ~20 km, with a reduction in the sensitivity and an increase in the retrieval errors for GEMS. We further investigate whether GEMS can resolve the stratospheric ozone variation observed from high vertical resolution Earth Observing System (EOS) Microwave Limb Sounder (MLS). The differences in stratospheric ozone profiles between GEMS and MLS are comparable to those between OMI and MLS below ~3 hPa (~40 km), except with slightly larger biases and larger standard deviations by up to 5%. At pressure altitudes above ~3 hPa, GEMS retrievals show strong influence of a priori and large differences with MLS, which, however, can be sufficiently improved by using better a priori information. The GEMS-MLS differences show negative biases of less than 4% for stratospheric column ozone, with standard deviations of 1–3%, while OMI retrievals show similar agreements with MLS except for 1% smaller biases at middle and high latitudes. Based on the comparisons, we conclude that GEMS will measure tropospheric ozone and stratospheric ozone columns with accuracy comparable to that of OMI and ozone profiles with slightly worse performance than that of OMI below ~3 hPa.

scholarly journals Better Baltic Sea wave forecasts: improving resolution or introducing ensembles?

Ocean Science ◽  
2018 ◽  
Vol 14 (6) ◽  
pp. 1435-1447
Author(s):  
Torben Schmith ◽  
Jacob Woge Nielsen ◽  
Till Andreas Soya Rasmussen ◽  
Henrik Feddersen
Keyword(s):  
Baltic Sea ◽  
Wave Height ◽  
Spectral Resolution ◽  
Significant Wave Height ◽  
Initial Conditions ◽  
A Priori ◽  
The Baltic Sea ◽  
Significant Wave ◽  
Operational Forecasts ◽  
The Baltic

Abstract. The performance of short-range operational forecasts of significant wave height (SWH) in the Baltic Sea is evaluated. Forecasts produced by a base configuration are intercompared with forecasts from two improved configurations: one with improved horizontal and spectral resolution and one with ensembles representing uncertainties in the physics of the forcing wind field and the initial conditions of this field. Both of the improved forecast classes represent an almost equal increase in computational costs. Therefore, the intercomparison addresses the question of whether more computer resources would be more favorably spent on enhancing the spatial and spectral resolution or, alternatively, on introducing ensembles. The intercomparison is based on comparisons with hourly observations of significant wave height from seven observation sites in the Baltic Sea during the 3-year period from 2015 to 2017. We conclude that for most wave measurement sites, the introduction of ensembles enhances the overall performance of the forecasts, whereas increasing the horizontal and spectral resolution does not. These sites represent offshore conditions, in that they are well exposed from all directions, are a large distance from the nearest coast and in deep water. Therefore, there is the a priori expectation that a detailed shoreline and bathymetry will not have any impact. Only at one site do we find that increasing the horizontal and spectral resolution significantly improves the forecasts. This site is situated in nearshore conditions, close to land and a nearby island, and is therefore shielded from many directions. Consequently, this study concludes that to improve wave forecasts in offshore areas, ensembles should be introduced. For near shore areas, in comparison, the study suggests that additional computational resources should be used to increase the resolution.

Selective, homonuclear pulse experiments in the Fourier transform mode: a study of 2′,3′-O-isopropylidene uridine

1977 ◽  
Vol 55 (6) ◽  
pp. 1045-1054 ◽  
Author(s):  
Klaus Bock ◽  
Roland Burton ◽  
Laurance D. Hall
Keyword(s):  
Fourier Transform ◽  
Lattice Relaxation ◽  
Spin Lattice Relaxation ◽  
Relaxation Rates ◽  
Simple Modification ◽  
Spin Lattice ◽  
Selective Saturation ◽  
Proton Resonances ◽  
The Fourier Transform ◽  
Mode A

A simple modification of a conventional Fourier transform nmr spectrometer (Varian XL-100) makes it feasible to apply selective, radiofrequency pulses at the resonance frequency of one, or more, proton resonances and to monitor the effects of those perturbations in the usual F.t. fashion. Experiments with 2′,3′-O-isopropylidene uridine are used to illustrate the utility of this technique in measurements of selective spin-lattice relaxation rates, to eliminate unwanted resonances by selective saturation or by selective partial relaxation, and to perform the pulse equivalent of a 1H–1H INDOR experiment.

scholarly journals IMK/IAA MIPAS temperature retrieval version 8: nominal measurements

2020 ◽  
Author(s):  
Michael Kiefer ◽  
Thomas von Clarmann ◽  
Bernd Funke ◽  
Maya García-Comas ◽  
Norbert Glatthor ◽  
...  
Keyword(s):  
Radiative Transfer ◽  
Spectral Resolution ◽  
Spectroscopic Data ◽  
A Priori ◽  
Michelson Interferometer ◽  
High Spectral Resolution ◽  
Transfer Model ◽  
Random Component ◽  
Horizontal Structure ◽  
Total Uncertainty

Abstract. A new global set of atmospheric temperature profiles is retrieved from recalibrated radiance spectra recorded with the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS). Changes with respect to previous data versions include a new radiometric calibration considering the time-dependency of the detector non-linearity, and a more robust frequency calibration scheme. Temperature is retrieved using a smoothing constraint, while tangent altitude pointing information is constrained using optimal estimation. ECMWF ERA-Interim is used as temperature a priori below 43 km. Above, a priori data is based on data from the Whole Atmosphere Community Climate Model Version 4 (WACCM4). Bias-corrected fields from specified dynamics runs, sampled at the MIPAS times and locations, are used, blended with ERA-Interim between 43 and 53 km. Horizontal variability of temperature is considered by scaling an a priori 3D temperature field in the orbit plane in a way that the horizontal structure is provided by the a priori while the vertical structure comes from the measurements. Additional microwindows with better sensitivity at higher altitudes are used. The background continuum is jointly fitted with the target parameters up to 58 km altitude. The radiance offset correction is strongly regularized towards an empirically determined vertical offset profile. In order to avoid the propagation of uncertainties of O3 and H2O a priori assumptions, the abundances of these species are retrieved jointly with temperature. The retrieval is based on HITRAN 2016 spectroscopic data, with a few amendments. Temperature-adjusted climatologies of vibrational populations of CO2 states emitting in the 15 micron region are used in the radiative transfer modelling in order to account for non-local thermodynamic equilibrium. Numerical integration in the radiative transfer model is now performed at higher accuracy. The random component of the temperature uncertainty typically varies between 0.4 and 0.8 K, with occasional excursions up to 1.3 K above 60 km altitude. The leading sources of the random component of the temperature error are measurement noise, gain calibration uncertainty, spectral shift, and uncertain CO2 mixing ratios. The systematic error is caused by uncertainties in spectroscopic data and line shape uncertainties. It ranges from 0.2 K at 24 km altitude for northern midlatitude nighttime conditions to 2.3 K at 12 km for tropical nighttime conditions. The estimated total uncertainty amounts to values between 0.5 K at 24 km and northern polar winter conditions to 2.3 K at 12 km and northern midlatitude day conditions. The vertical resolution varies around 3 km for altitudes below 50 km. The long-term drift encountered in the previous temperature product has been largely reduced. The consistency between high spectral resolution results from 2002–2004 and the reduced spectral resolution results from 2005–2012 has been largely improved. As expected, most pronounced temperature differences between version 8 and previous data versions are found in elevated stratopause situations. The fact that the phase of temperature waves seen by MIPAS is not locked to the wave phase found in ECMWF analyses demonstrates that our retrieval provides independent information and does not merely reproduce the prior information.

ACES: A co-evolution simulator generates co-varying protein and nucleic acid sequences

2020 ◽  
Vol 18 (06) ◽  
pp. 2050039
Author(s):  
Devin Camenares
Keyword(s):  
Nucleic Acid ◽  
In Silico ◽  
A Priori ◽  
Software Tool ◽  
Real Data ◽  
Biological Data ◽  
Evolutionary Constraints ◽  
Wide Range ◽  
Nucleic Acid Sequences

Sequence-specific and consequential interactions within or between proteins and/or RNAs can be predicted by identifying co-evolution of residues in these molecules. Different algorithms have been used to detect co-evolution, often using biological data to benchmark a methods ability to discriminate against indirect co-evolution. Such a benchmark is problematic, because not all the interactions and evolutionary constraints underlying real data can be known a priori. Instead, sequences generated in silico to simulate co-evolution would be preferable, and can be obtained using aCES, the software tool presented here. Conservation and co-evolution constraints can be specified for any residue across a number of molecules, allowing the user to capture a complex, realistic set of interactions. Resulting alignments were used to benchmark several co-evolution detection tools for their ability to separate signal from background as well as discriminating direct from indirect signals. This approach can aid in refinement of these algorithms. In addition, systematic tuning of these constraints sheds new light on how they drive co-evolution between residues. Better understanding how to detect co-evolution and the residue interactions they predict can lead to a wide range of insights important for synthetic biologists interested in engineering new, orthogonal interactions between two macromolecules.

On the surface apparent reflectance exploitation: Entangled Solar Induced Fluorescence emission and aerosol scattering effects at oxygen absorption regions

2020 ◽  
Author(s):  
Neus Sabater ◽  
Pekka Kolmonen ◽  
Luis Alonso ◽  
Jorge Vicent ◽  
José Moreno ◽  
...  
Keyword(s):  
Spectral Resolution ◽  
A Priori ◽  
European Space Agency ◽  
High Spectral Resolution ◽  
Oxygen Absorption ◽  
Aerosol Scattering ◽  
Scattering Effects ◽  
Spectrally Resolved ◽  
Absorption Features ◽  
Aerosol Characterization

<p>Monitoring vegetation photosynthetic activity and its link with the carbon cycle at a global scale is a leading breakthrough that the scientific community has been seeking in recent years. Pursuing this goal, one of the most important advances in the last decade has been the measurement of the Solar Induced Fluorescence (SIF) at a satellite scale. Current satellite-derived SIF estimations provide SIF measured at certain specific wavelengths depending on the retrieval strategy and the instrument capabilities. However, for the time being, no global observations of the total spectrally resolved and integrated SIF signal have been yet achieved. In a near-future context, spectrally resolved SIF estimations will be provided by missions such as the FLuorescence EXplorer (FLEX) from the European Space Agency.</p><p>When disentangling the total SIF contribution, emitted between 650-800 nm, from the acquired satellite signal, molecular and aerosol absorption and scattering effects must be carefully accounted for.  Particularly, within the oxygen absorption features, the characterization of the aerosol scattering effects represents the most critical step prior to the SIF estimation.</p><p>In the context of the FLEX/Sentinel-3 tandem mission concept, this work presents a novel technique that refines any a priori aerosol characterization process through the exploitation of the high spectral resolution surface apparent reflectance signal at the oxygen absorption regions. Within the absorption features, SIF contribution on satellite-derived surface apparent reflectance generates a characteristic peaky spectrum. However, the shape of these peaks can be simultaneously distorted through the atmospheric correction process due to inaccuracies in the aerosol characterization among other secondary sources. Inaccuracies in the estimation of aerosol optical thickness, Angstrom exponent, asymmetry of the scattering or single scattering albedo translate into characteristic distortions in the shape of the peaks in the apparent reflectance. This particular behaviour allows inferring the magnitude of the errors and correcting them. The presented technique improves the accuracy of any a priori aerosol retrieval.</p><p>Authors expect this study to be also of interest to other hyperspectral missions when exploiting, at high spectral resolution, information from oxygen absorption regions.</p>

A selective inversion recovery method for the improvement of23Na NMR spectral resolution in isolated perfused rat hearts

1993 ◽  
Vol 6 (3) ◽  
pp. 201-208 ◽  
Author(s):  
Tamás Simor ◽  
Sung K. Kim ◽  
Wen-Jang Chu ◽  
Gerald M. Pohost ◽  
Gabriel A. Elgavish
Keyword(s):  
Spectral Resolution ◽  
Inversion Recovery ◽  
Recovery Method ◽  
Selective Inversion ◽  
Rat Hearts ◽  
Perfused Rat Hearts ◽  
Isolated Perfused Rat Hearts

scholarly journals Evaluation of ozone profile and tropospheric ozone retrievals from GEMS and OMI spectra

2012 ◽  
Vol 5 (5) ◽  
pp. 6733-6762 ◽  
Author(s):  
J. Bak ◽  
J. H. Kim ◽  
X. Liu ◽  
K. Chance ◽  
J. Kim
Keyword(s):  
Spectral Resolution ◽  
Tropospheric Ozone ◽  
Degrees Of Freedom ◽  
Stratospheric Ozone ◽  
A Priori ◽  
Ozone Monitoring Instrument ◽  
Ozone Profile ◽  
Retrieval Errors ◽  
Standard Deviations ◽  
Column Ozone

Abstract. Korea is planning to launch the GEMS (Geostationary Environment Monitoring Spectrometer) instrument into a Geostationary (GEO) platform in 2018 to monitor tropospheric air pollutants on an hourly basis over East Asia. GEMS will measure backscattered UV radiances covering the 300–500 nm wavelength range with a spectral resolution of 0.6 nm. The main objective of this study is to evaluate ozone profiles and stratospheric column ozone amounts retrieved from simulated GEMS measurements. Ozone Monitoring Instrument (OMI) Level 1B radiances, which have the spectral range 270–500 nm at spectral resolution of 0.42–0.63 nm, are used to simulate the GEMS radiances. An optimal estimation-based ozone profile algorithm is used to retrieve ozone profiles from simulated GEMS radiances. Firstly, we compare the retrieval characteristics (including averaging kernels, degrees of freedom for signal, and retrieval error) derived from the 270–330 nm (OMI) and 300–330 nm (GEMS) wavelength ranges. This comparison shows that the effect of not using measurements below 300 nm on tropospheric ozone retrievals is insignificant. However, the stratospheric ozone information decreases greatly from OMI to GEMS, by a factor of ∼2. The number of the independent pieces of information available from GEMS measurements is estimated to 3 on average in the stratosphere, with associated retrieval errors of ∼1% in stratospheric column ozone. The difference between OMI and GEMS retrieval characteristics is apparent for retrieving ozone layers above ∼20 km, with a reduction in the sensitivity and an increase in the retrieval errors for GEMS. We further investigate whether GEMS can resolve the stratospheric ozone variation observed from high vertical resolution EOS Microwave Limb Sounder (MLS). The differences in stratospheric ozone profiles between GEMS and MLS are comparable to those between OMI and MLS above ∼3 hPa (∼40 km) except with slightly larger biases and larger standard deviations by up to 5%. At pressure altitudes above ∼3 hPa, GEMS retrievals show strong influence of a priori and large differences with MLS, which, however, can be sufficiently improved by using better a priori information. The GEMS-MLS differences show negative biases of less than 4% for stratospheric column ozone, with standard deviations of 1–3%, while OMI retrievals show similar agreements with MLS except for 1% smaller biases at mid and high latitudes. Based on the comparisons, we conclude that GEMS will measure tropospheric ozone and stratospheric ozone columns with accuracy comparable to that of OMI and ozone profiles with slightly worse performance than that of OMI below ∼3 hPa.

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