Chemical Shift Correction Research Articles

Correction to ‘ORYX‐MRSI: A fully‐automated open‐source software for proton magnetic resonance spectroscopic imaging data analysis’

International Journal of Imaging Systems and TechnologyVolume 33, Issue 2 p. 770-770 CORRIGENDUMFree Access Correction to ‘ORYX-MRSI: A fully-automated open-source software for proton magnetic resonance spectroscopic imaging data analysis’ This article corrects the following: ORYX-MRSI: A fully-automated open-source software for proton magnetic resonance spectroscopic imaging data analysis Sevim Cengiz, Muhammed Yildirim, Abdullah Bas, Esin Ozturk-Isik, Volume 32Issue 4International Journal of Imaging Systems and Technology pages: 1068-1083 First Published online: May 17, 2022 First published: 27 January 2023 https://doi.org/10.1002/ima.22857AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat We regret to report a technical error in our manuscript entitled ‘ORYX-MRSI: A fully-automated open-source software for proton magnetic resonance spectroscopic imaging data analysis’. The volume of interest (VOI) for all the MR spectroscopic metabolites, other than the reference metabolite, are shifted in space by their respective chemical shift amounts as calculated by Equation 2 due to the chemical shift error. Even though there is a shift in the VOIs of different metabolites, it was incorrect to shift the metabolite maps along with their corresponding VOIs. This technical error has been corrected in the Oryx-MRSI source code, which has been updated on our laboratory's GitHub page. Currently, if the chemical shift correction is set to ‘on’, the corresponding VOIs for the metabolites are shifted in space by their respective chemical shift amounts, and the metabolite intensities are evaluated at their respective locations. Additionally, the metabolite ratios are evaluated only in the region that is located at the intersection of the corresponding metabolite VOIs. Moreover, the tissue fractions are calculated only once at the reference VOI. As a result, Figure 5 is not accurate after correction and hence should not be considered for further discussion. The authors thank Wolfgang Bogner, Ph.D. and Gilbert Hangel, Ph.D. for their careful reviews of the published manuscript and apologize for this error. REFERENCE 1Cengiz S, Yildirim M, Bas A, Ozturk-Isik E. ORYX-MRSI: a fully-automated open-source software for proton magnetic resonance spectroscopic imaging data analysis. Int J Imaging Syst Technol. 2022; 32: 1068- 1083. doi:10.1002/ima.22748 Volume33, Issue2March 2023Pages 770-770 ReferencesRelatedInformation

Tear metabolomics. An outstanding approach to the molecular diagnosis of glaucoma

AbstractPurpose: The open‐angle glaucoma (OAG) is the first cause of irreversible blindness worldwide, being the main risk factor the elevated intraocular pressure (IOP). The molecular mechanisms of OAG development and progression remains incomplete. Because of this, biomarkers for early diagnosis of OAG are not conclusive. We deal with understanding the metabolomics of OAG by using 1H‐ nuclear magnetic resonance (NMR) spectroscopy in tear samples for searching specific metabolites that improve early molecular diagnosis of OAG.Methods: 1H NMR monodimensional experiments were acquired from tears in 30 tear samples (OAG patients: n = 11 and healthy controls: n = 19). Additionally, 2D (TOCSY and 1H‐13C HSQC) experiments were acquired in a reduced set of samples to assign the resonances. Spectra underwent phase, baseline and chemical shift correction. The signals in the spectra were assigned, integrated and normalized to the total sum of integrals. Finally, data were analysed by multivariate statistics (PLS‐DA) to determine a model to discriminate between the controls and OAG tears. The whole data set was split into calibration (18 samples) to calculate the model and validation set (10 samples) to test the performance and the ability for disease discrimination.Results: The calculated PLS‐DA model showed a sensitivity of 100% and a specificity of 83.3% to discriminate OAG patient's tears versus control tears in the validation set. The set of metabolites participating is this discriminant model were obtained, mainly those involved in specific cellular and molecular pathways regarding the pathologic mechanisms of OAG.Conclusions: Data obtained by 1H‐NMR spectroscopy in tears confirms the validity of metabolomics as a non‐invasive approach to better OAG managing.

ORYX‐MRSI: A fully‐automated open‐source software for proton magnetic resonance spectroscopic imaging data analysis

AbstractProton magnetic resonance spectroscopic imaging (1H‐MRSI) provides a noninvasive, spatially resolved evaluation of brain metabolism. However, there are some limitations of 1H‐MRSI preventing its wider use in the clinics, including the spectral quality issues, partial volume effect and chemical shift artifact. Additionally, it is necessary to create metabolite maps for analyzing spectral data along with other MRI modalities. In this study, a MATLAB‐based open‐source data analysis software for three‐dimensional 1H‐MRSI, called Oryx‐MRSI, which includes modules for visualization of raw 1H‐MRSI data and LCModel outputs, chemical shift correction, tissue fraction calculation, metabolite map production, and registration onto standard MNI152 brain atlas while providing automatic spectral quality control, is presented. Oryx‐MRSI implements region of interest analysis at brain parcellations defined on MNI152 brain atlas. All generated metabolite maps are stored in NIfTI format. Oryx‐MRSI is publicly available at https://github.com/Computational-Imaging-LAB/Oryx-MRSI along with six example datasets.

Creation and Generation Mechanism of Macromolecular Representation for Dongsheng Coal Vitrinite

Insights into macromolecules of coal were critical for improving the understanding of the coal upgrading and coalification process. Here, the creation and generation of macromolecular representation for Dongsheng coal vitrinite was clarified using industry analysis, elemental analysis, and the peak fitting technology of 13C nuclear magnetic resonance (13C NMR), Fourier transform infrared spectrum, and X-ray diffraction. The structural parameters and macromolecular representation (C167H148N2O27) were innovatively calculated and created based on these characterization results and chemical shift correction, finally obtaining the plane macromolecular models whose 13C NMR spectrum was close to the experimental spectrum. The property parameters of basic structural units were La (average lateral sizes) = 19.917 Å, Lc (stacking heights) = 24.776 Å, d002 (interlayer spacing) = 3.488 Å, N (number of stacking layers) = 5.6213, and La/Lc < 1. Suffering from the dynamic metamorphism effects, the length of intermolecular aromatic lamellae for Dongsheng coal vitrinite was 7–8 aromatic rings in size. The aromatic clusters were dominated by benzene, naphthalene, and anthracene, and their numbers were 2, 4, and 2 per vitrinite model, respectively. Hydrogenated aromatic rings, ether bonds, and oxygen-methylene serve as the main bridge bonds to connect the aromatic clusters, where the short aliphatic chains were distributed around the edge of aromatic rings. Oxygen atoms exist in the form of hydroxyl, ether bond, carbonyl, and carboxyl groups, and their numbers were 2, 7, 4, and 8 per vitrinite model, respectively. The nitrogen atoms exist in the form of pyridine and pyrrole. The entropy weighting method was used to estimate the rationality of the macromolecular representation of long frame coal vitrinite, providing a new mathematical evaluation method for molecular simulation. Comparison of various macromolecular models from different geological conditions indicates that tectonic stress can promote the degree of aromatization and ring condensation. The thermal history and tectonic stress have a compensation effect for promoting the aromatization process. Aliphatic carbons were the most unstable units under thermal history and tectonic stress, and they are more easily removed from the aliphatic structure, followed by methyl. This finding of this paper can provide significance for coal liquefaction engineering in Dongsheng coalfield.

Correcting heat-induced chemical shift distortions in proton resonance frequency-shift thermometry.

To reconstruct proton resonance frequency-shift temperature maps free of chemical shift distortions. Tissue heating created by thermal therapies such as focused ultrasound surgery results in a change in proton resonance frequency that causes geometric distortions in the image and calculated temperature maps, in the same manner as other chemical shift and off-resonance distortions if left uncorrected. We propose an online-compatible algorithm to correct these distortions in 2DFT and echo-planar imaging acquisitions, which is based on a k-space signal model that accounts for proton resonance frequency change-induced phase shifts both up to and during the readout. The method was evaluated with simulations, gel phantoms, and in vivo temperature maps from brain, soft tissue tumor, and uterine fibroid focused ultrasound surgery treatments. Without chemical shift correction, peak temperature and thermal dose measurements were spatially offset by approximately 1 mm in vivo. Spatial shifts increased as readout bandwidth decreased, as shown by up to 4-fold greater temperature hot spot asymmetry in uncorrected temperature maps. In most cases, the computation times to correct maps at peak heat were less than 10 ms, without parallelization. Heat-induced proton resonance frequency changes create chemical shift distortions in temperature maps resulting from MR-guided focused ultrasound surgery ablations, but the distortions can be corrected using an online-compatible algorithm. Magn Reson Med 76:172-182, 2016. © 2015 Wiley Periodicals, Inc.

Enhanced Chemical Shift Analysis for Secondary Structure prediction of protein

Predicting secondary structure of protein through assigned backbone chemical shifts has been used widely because of its convenience and flexibility. In spite of its usefulness, chemical shift based analysis has some defects including isotopic shifts and solvent interaction. Here, it is shown that corrected chemical shift analysis for secondary structure of protein. It is included chemical shift correction through consideration of deuterium isotopic effect and calculate chemical shift index using probability-based methods. Enhanced method was applied successfully to one of the proteins from Mycobacterium tuberculosis. It is suggested that correction of chemical shift analysis could increase accuracy of secondary structure prediction of protein and small molecule in solution.

High-throughput, multi-platform metabolomics on very small volumes: 1H NMR metabolite identification in an unadulterated tube-in-tube system

As small animal models of disease become more widely used, there is increasing importance and potential for characterizing their metabolomes. However, as the animal becomes smaller, the amounts of biofluids such as urine and cerebral spinal fluid available for metabolomic studies are more limited. Further, in multi-platform systems biology when the same small sample must be used for several analyses, it is a frequent requirement that no additions are made to the sample (even as simple as D2O or an NMR chemical shift reference) to maintain sample integrity. Herein we describe a method for high-throughput 1H-NMR studies using ~30 µl volumes, suitable for biofluid matrices. The compartmentalization of the sample and NMR standards, however, requires chemical shift corrections due to bulk magnetic susceptibility and ionic strength changes for metabolite profiling using a reference library or data-binning of the chemical shift axis. This set-up minimizes the cost of individual data collection per small animal and is suitable for high-throughput, longitudinal, multimodal metabolomic studies of biofluids available in limited quantities.

Validation of archived chemical shifts through atomic coordinates

The public archives containing protein information in the form of NMR chemical shift data at the BioMagResBank (BMRB) and of 3D structure coordinates at the Protein Data Bank are continuously expanding. The quality of the data contained in these archives, however, varies. The main issue for chemical shift values is that they are determined relative to a reference frequency. When this reference frequency is set incorrectly, all related chemical shift values are systematically offset. Such wrongly referenced chemical shift values, as well as other problems such as chemical shift values that are assigned to the wrong atom, are not easily distinguished from correct values and effectively reduce the usefulness of the archive. We describe a new method to correct and validate protein chemical shift values in relation to their 3D structure coordinates. This method classifies atoms using two parameters: the per-atom solvent accessible surface area (as calculated from the coordinates) and the secondary structure of the parent amino acid. Through the use of Gaussian statistics based on a large database of 3220 BMRB entries, we obtain per-entry chemical shift corrections as well as Z scores for the individual chemical shift values. In addition, information on the error of the correction value itself is available, and the method can retain only dependable correction values. We provide an online resource with chemical shift, atom exposure, and secondary structure information for all relevant BMRB entries (http://www.ebi.ac.uk/pdbe/nmr/vasco) and hope this data will aid the development of new chemical shift-based methods in NMR. Proteins 2010. © 2010 Wiley-Liss, Inc.

Chemical shift imaging without water suppression at 3 T

Proton magnetic resonance spectroscopy without water suppression is possible but is hampered by the presence of sideband artifacts. The aim of this study was to develop a chemical shift imaging method without water suppression for clinical routine with reduced sideband artifacts. Spectra from ten healthy volunteers were acquired using a 3T (TimTrio, Siemens, Erlagen, Germany) scanner with a Point RESolved Spectroscopy sequence for volume selection. Postprocessing was performed in three steps: correcting the water peak position in all spectra (chemical shift correction), subtracting the Gaussian convolution of all free induction decay signals (FIDs) (water signal reduction), and subtracting the FID of a water phantom from the volunteer's FID signal (reduction of sidebands). For the postprocessing customized software was developed with Matlab 2007b. The described technique provides spectra with reduced water signal and sidebands. Quantitative analysis showed that there is a good agreement between spectra obtained with water suppressing radiofrequency pulses and the new method. Moreover, spectra obtained with the new method do not need phase correction. The new method offers sufficient reduction of the water peak and sidebands. Its simplicity allows its use in clinical applications.

Robust Algorithms for Automated Chemical Shift Calibration of 1D 1H NMR Spectra of Blood Serum

In biofluid NMR spectroscopy, the frequency of each resonance is typically calibrated by addition of a reference compound such as 3-(trimethylsilyl)-propionic acid- d 4 (TSP) to the sample. However biofluids such as serum cannot be referenced to TSP, due to shifts resonance caused by binding to macromolecules in solution. In order to overcome this limitation we have developed algorithms, based on analysis of derivative spectra, to locate and calibrate (1)H NMR spectra to the alpha-glucose anomeric doublet. We successfully used these algorithms to calibrate 77 serum (1)H NMR spectra and demonstrate the greater reproducibility of the calculated chemical-shift corrections ( r = 0.97) than those generated by manual alignment ( r = 0.8-0.88). Hence we show that these algorithms provide robust and reproducible methods of calibrating (1)H NMR of serum, plasma, or any biofluid in which glucose is abundant. Precise automated calibration of complex biofluid NMR spectra is an important tool in large-scale metabonomic or metabolomic studies, where hundreds or even thousands of spectra may be analyzed in high-resolution by pattern recognition analysis.

3D interleaved water and fat image acquisition with chemical-shift correction.

A new technique, 3D interleaved water and fat image acquisition with chemical-shift correction (3-DIWFAC), was developed to acquire 3D water and fat images in a single acquisition time and to combine the water and fat images to produce chemical-shift-free images. A 3D gradient-recalled-echo (GRE) sequence was implemented with a 1-3-3-1 binomial Shinnar-Le Roux spatial-spectral excitation, and with interleaved phase-encoding lines that alternate between water and fat excitations separated by half TR. Water-only and fat-only images were then realigned to remove chemical shift artifacts. Results from phantoms and human subjects demonstrated that the image contrast was the same as in the regular GRE sequence. With the chemical shift corrected, the shadow artifacts often seen at water and fat boundaries were removed. Since this sequence simultaneously provides water-only images showing cartilage and bone lesions, and water-fat images that depict soft tissue anatomy, it may be clinically useful in musculoskeletal imaging. Magn Reson Med 44:322-330, 2000.

Production of cams by powder metallurgy: F. Vollertsen and U. Engel, (University of Erlagen-Nuremburg, Erlagen, Germany), Powder Metall Int Vol 24, No 5, 1992, 284–288

Proton magnetic resonance spectroscopy without water suppression is possible but is hampered by the presence of sideband artifacts. The aim of this study was to develop a chemical shift imaging method without water suppression for clinical routine with reduced sideband artifacts.Spectra from ten healthy volunteers were acquired using a 3T (TimTrio, Siemens, Erlagen, Germany) scanner with a Point RESolved Spectroscopy sequence for volume selection. Postprocessing was performed in three steps: correcting the water peak position in all spectra (chemical shift correction), subtracting the Gaussian convolution of all free induction decay signals (FIDs) (water signal reduction), and subtracting the FID of a water phantom from the volunteer's FID signal (reduction of sidebands). For the postprocessing customized software was developed with Matlab 2007b.The described technique provides spectra with reduced water signal and sidebands. Quantitative analysis showed that there is a good agreement between spectra obtained with water suppressing radiofrequency pulses and the new method. Moreover, spectra obtained with the new method do not need phase correction.The new method offers sufficient reduction of the water peak and sidebands. Its simplicity allows its use in clinical applications.

4720679 Magnetic resonance imaging with phase encoded chemical shift correction

RF arrays with a large number of independent coil elements are advantageous for parallel transmission (pTx) and reception at high fields. One of the main challenges in designing RF arrays is to minimize the electromagnetic (EM) coupling between the coil elements. The induced current elimination (ICE) method, which uses additional resonator elements to cancel coils’ mutual EM coupling, has proven to be a simple and efficient solution for decoupling microstrip, L/C loop, monopole and dipole arrays. However, in previous embodiments of conventional ICE decoupling, the decoupling elements acted as “magnetic-walls” with low transmit fields and consequently low MR signal near them. To solve this problem, new resonator geometries including overlapped and perpendicular decoupling loops are proposed. The new geometries were analyzed theoretically and validated in EM simulations, bench tests and MR experiments. The isolation between two closely-placed loops could be improved from about −5 dB to <−45 dB by using the new geometries.

Triethyl phosphate as an internal 31P NMR reference in biological samples

Since the early 1970s 31P NMR has been widely applied to the study of biological systems. Many of the applications have entailed monitoring the variation in chemical shifts that arise as a result of various physical and chemical phenomena. The binding of a number of biological phosphates to macromolecules (e.g., 2,3-bisphosphoglycerate to deoxyhemoglobin) has been shown to cause a variation in the “P NMR chemical shifts of the phosphate groups (I-3). The variation in the “P NMR chemical shifts of titratable phosphorus compounds with pK, values in the physiological pH range has been used to estimate the pH in intact cells (4-8). More recently, the cell volume dependence of the chemical-shift separation between the intraand extracellular 31P NMR resonances of dimethyl methylphosphonate added to a red blood cell suspension has been used to monitor time-dependent changes in cell volume (9). The traditional chemical-shift standard for “P NMR is 85% phosphoric acid; however, it has a number of shortcomings (10, II): (i) it is restricted to use as an external reference; (ii) it gives rise to an inconveniently broad resonance (10); and (in) it has a bulk susceptibility very different from that of aqueous solutions (II). The tetrahydroxyphosphonium ion has been suggested as a variable alternative to phosphoric acid (10) but it too is restricted to use as an external reference. Although the use of an external shift reference eliminates all interactions between components of the sample and the reference compound it often necessitates the introduction of chemical-shift corrections to account for bulk susceptibility differences between the reference and sample (12). Such corrections are particularly important for samples containing hemoglobin, the susceptibility of which has been shown to vary widely with the degree of oxygenation (13, 7). The need for susceptibility difference corrections is obviated by using an internal reference compound, i.e., one added directly to the sample. Any such compound should fulfill a number of criteria (II): (i) it should be water soluble; (ii) it should preferably give rise to a single, narrow resonance, occurring well away from those of the sample; (iii) it should be chemically inert; and (iv), its chemical shift should be independent of the nature of the sample. Triethyl phosphate (TEP, (CH3CH20)3P0, BDH Chemicals, U.K.) has been shown to be suitable for use as an internal reference compound, particularly in the application of “P NMR to the study of red blood cell suspensions and lysates. TEP is an inexpensive, neutral, nontitratable compound which, with proton decoupling, gives rise

Chemical-shift artifact correction scheme using echo-time encoding technique.

An investigation has been undertaken to study the effects of chemical shift on NMR image obtained by the projection reconstruction technique. Mathematical simulation studies indicate that chemical shift causes blurring in NMR images regardless of the image reconstruction technique. A systematic study of such artifacts is presented and possible correction schemes are proposed. Exemplary results with and without correction of the chemical-shift artifact and pulse schemes employed for projection reconstruction are presented. The present chemical-shift correction scheme is basically the same as a spectroscopic imaging technique such as the existing 4-D NMR imaging method except that the encoding steps required can be reduced substantially in the case of modest spectroscopic resolution.

Measurement and correction for magnetic susceptibility with solenoidal magnet NMR spectrometers

A new method of external referencing with NMR spectrometers where the magnetic field is parallel to the sample axis is suggested. It is based on the fact that a gasket made of chemically inert unconducting material being placed in the annular region of a coaxial resonance cell, with a reference material in the capillary tube and an investigated substance in the annular region, causes a shift and a splitting of the reference signal, depending on the volume magnetic susceptibility ( χ v) of the investigated material. With the help of calibration plots obtained for substances with known χ v, unknown χ v of the materials under study can be determined and chemical shift corrections for the spectra measured in the usual manner can be made.

Measurement of the magnetic moment of the positive muon by a stroboscopic muon-spin-rotation technique

A new determination of the magnetic moment of the positive muon in units of the magnetic moment of the proton is presented. The Larmor precession of positive muons in liquid bromine was observed by a stroboscopic technique in a field of 0.75 T and combined with concomitant proton NMR measurements in the same chemical environment. The stroboscopic method allows use of the full muon stopping rate available at the Schweizerisches Institut f\"ur Nuklearforschung (SIN) muon channel. Moreover, it permits an intrinsically precise determination of muon Larmor frequency and proton NMR frequency measuring the magnetic field by comparison with the stable reference frequency of the SIN accelerator ($\frac{\ensuremath{\Delta}\ensuremath{\Omega}}{\ensuremath{\Omega}}\ensuremath{\approx}{10}^{\ensuremath{-}8}$). Two different bromine targets were used which allowed an unambiguous determination of the chemical field shift experienced by the muons. One target contained pure and water-free liquid bromine (${\mathrm{Br}}_{2}$), where stopped muons form (${\ensuremath{\mu}}^{+}{e}^{\ensuremath{-}}$)Br molecules. The other target was slightly contaminated with water; there a chemical reaction chain places the muons into (${\ensuremath{\mu}}^{+}{e}^{\ensuremath{-}}$)HO molecules. The diamagnetic shielding of protons in the analogous molecules HBr and ${\mathrm{H}}_{2}$O in liquid bromine was measured by high-resolution NMR. Values for the isotopic shift of the diamagnetic shielding, when protons are replaced by muons, are available from quantum chemical calculations. After application of the chemical-shift corrections, the results from the two different bromine targets are consistent. The final result is $\frac{{\ensuremath{\mu}}_{\ensuremath{\mu}}}{{\ensuremath{\mu}}_{p}}=3.1833441(17)(or \ifmmode\pm\else\textpm\fi{}0.53 \mathrm{ppm})$. This value agrees with other recent precision determinations of $\frac{{\ensuremath{\mu}}_{\ensuremath{\mu}}}{{\ensuremath{\mu}}_{p}}$. For the muon mass the present result implies $\frac{{m}_{\ensuremath{\mu}}}{{m}_{e}}=206.76835(11)(\ifmmode\pm\else\textpm\fi{}0.53 \mathrm{ppm})$.

Magnetic moment of 181Ta

The nuclear magnetic moment of 181Ta is measured by NMR of a tantalum solution. For tantalum dissolved in HF/HNO3 broad lines arising from 181Ta nuclei in TaF6− complexes are observed at room temperature. A study of linewidth vs temperature shows motional narrowing of the quadrupole broadened line with increasing temperature. Applying the quadrupolar correction, we obtain a nuclear gyromagnetic ratio for 181Ta of 2π(0.5098 ± 0.0002) × 103 sec−1 G−1 and an uncorrected nuclear moment of 2.342 ± 0.001 nm. The chemical shift correction gives 2π(0.5097 ± 0.0002) × 103 sec−1 G−1 for the nuclear gyromagnetic ratio. Correcting the nuclear moment for core diamagnetism, we get 2.361 ± 0.010 nm.

Proton chemical shifts and electron densities in aromatic and heteroaromatic molecules. I. Procedure and chemical shift corrections; Applications to azines

In this series, the observed proton chemical shifts of heteroaromatic compounds are used to obtain estimates of the electron distribution in these systems. These estimates are deduced from the measured shifts after applying corrections for the shielding contributions arising from ring currents, magnetic anisotropy of neighbouring atoms, and the electric field from the lone-pair dipoles on heteroatoms, in a manner closely related to that of Gil and Murrell. The corrected chemical shifts are then used to deduce an ?experimental? π-electron distribution via the electric field dependence of the proton shifts on the excess charge at all ring positions. However, in most cases, there are not enough experimental shifts to determine uniquely the excess charge at each ring atom, and it is necessary to assume that some inaccessible charges are close to values obtained from theoretical calculations. With these limitations, a comparison is made between the excess charges deduced in the above fashion from chemical shift data on mono- and poly-cyclic azines and diazines and those obtained by theoretical calculations using the BJ VESCF method. It is emphasized that this interpretation is tentative and that the extent of σ-electron polarization is not well understood at present.