Journal of magnetic resonance最新文献

{"title":"Chemical shift prediction in 13C NMR spectroscopy using ensembles of message passing neural networks (MPNNs)","authors":"D. Williamson ,&nbsp;S. Ponte ,&nbsp;I. Iglesias ,&nbsp;N. Tonge ,&nbsp;C. Cobas ,&nbsp;E.K. Kemsley","doi":"10.1016/j.jmr.2024.107795","DOIUrl":"10.1016/j.jmr.2024.107795","url":null,"abstract":"<div><div>This study reports a deep learning approach that utilises message passing neural networks (MPNNs) for predicting chemical shifts in ¹³C NMR spectra of small molecules. MPNNs were trained on two distinct datasets: one with approximately 4000 labelled structures and another with over 40,000. To reduce stochastic variation, an ensemble framework was implemented, which is simple to deploy on multiple nodes of a High-Performance Computing facility.</div><div>The results emphasise the critical role of training set size and diversity. While prediction performance was comparable on test sets drawn from each dataset, the ensemble trained on the larger dataset retained its accuracy when these sets were crossed over, and when applied to a further collection of approximately 12,000 previously unseen structures introduced after all development work had been completed. In contrast, the ensemble trained on the smaller dataset showed a notable decline in generalisation ability. This difference is attributed to the greater diversity of atomic environments captured in the larger dataset.</div><div>The larger dataset also enabled more robust modelling of various error properties, providing a quantitative foundation for spectral assignment and verification. This was achieved in two ways. First, a clear relationship was observed between prediction errors and the frequency of different node feature vectors in the training data, allowing error estimates to be associated with individual nodes based on their type. These estimates can be used as weights in a modified cityblock distance metric when assigning observed to predicted shifts. Second, the mean absolute prediction error calculated at the structure level is well-fitted by a Gaussian kernel cumulative distribution. This enabled a probabilistic assessment of whether the predicted shifts and assigned observations are consistent with originating from the same molecular structure.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107795"},"PeriodicalIF":2.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implementing a two-stage, shim field-calibrated superconducting shimming method on a 7 T cryogen-free small animal MRI magnet","authors":"Jinhao Liu ,&nbsp;Yaohui Wang ,&nbsp;Miutian Wang ,&nbsp;Wenchen Wang ,&nbsp;Gang Yang ,&nbsp;Weimin Wang ,&nbsp;Qiuliang Wang ,&nbsp;Feng Liu","doi":"10.1016/j.jmr.2024.107787","DOIUrl":"10.1016/j.jmr.2024.107787","url":null,"abstract":"<div><div>Ultrahigh field systems (<span><math><mo>≥</mo></math></span> 7 T) can increase the signal-to-noise ratio of magnetic resonance imaging (MRI), improving imaging performance compared to systems with lower fields. However, these enhancements heavily rely on a high <span><math><msub><mrow><mi>B</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span> magnetic field homogeneity level, which can be achieved through superconducting shimming. This paper presents a novel two-stage superconducting shimming method designed to achieve precise shimming for a 7 T MRI superconducting magnet. In the initial stage, detailed measurements and fittings were conducted to determine the current polarity and the axial or circumferential positions of the shim fields. Subsequently, an optimization strategy was implemented to determine the optimal shim currents with a flexible target field. The second stage involves an iterative process to fine-tune the current of a specific shim coil, identified as having the most significant impact on field homogeneity. The overall fitness of 99.5% underscores the precision in determining the current polarity and position of the shim fields. Significantly, the calibrated shim system substantially improves the peak-to-peak and Root Mean Square Error (RMSE) field homogeneities from 107.42 ppm and 37.00 ppm to 11.12 ppm and 3.26 ppm, respectively, representing improvements of 89.65% and 91.19%. Furthermore, the simulation results of the fine-tuning stage demonstrate additional enhancements in peak-to-peak field homogeneity, to 9.9 ppm by reducing the current of the Z2 shim coil by 51.3 mA. Additionally, the shimmed magnetic field exhibited high time stability, with a maximum variation of only 27 <span><math><mstyle><mi>µ</mi><mi>T</mi></mstyle></math></span> observed within 48 h. Thus, the proposed two-stage superconducting shimming framework effectively addresses the challenge of imperfect <span><math><msub><mrow><mi>B</mi></mrow><mrow><mn>0</mn></mrow></msub></math></span> magnetic fields, enhancing peak-to-peak and RMSE field homogeneity. The stepwise optimized approach also mitigates deviations caused by shim-to-shim coupling, demonstrating its efficacy in achieving precise shimming in ultrahigh-field MRI systems.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107787"},"PeriodicalIF":2.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neural net analysis of NMR spectra from strongly-coupled spin systems","authors":"James H. Prestegard ,&nbsp;Geert-Jan Boons ,&nbsp;Pradeep Chopra ,&nbsp;John Glushka ,&nbsp;John H. Grimes Jr. ,&nbsp;Bernd Simon","doi":"10.1016/j.jmr.2024.107792","DOIUrl":"10.1016/j.jmr.2024.107792","url":null,"abstract":"<div><div>Extracting parameters such as chemical shifts and coupling constants from proton NMR spectra is often a first step in using spectra for compound identification and structure determination. This can become challenging when scalar couplings between protons are comparable in size to chemical shift differences (strongly coupled), as is often the case with low-field (bench top) spectrometers. Here we explore the potential utility of AI methods, in particular neural networks, for extracting parameters from low-field spectra. Rather than seeking large experimental sets of spectra for training a network, we chose quantum mechanical simulation of sets, something that is possible with modern software packages and computer resources. We show that application of a network trained on 2-D J-resolved spectra and applied to a spectrum of iduronic acid, shows some promise, but also meets with some obstacles. We suggest that these may be overcome with improved pulse sequences and more extensive simulations.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107792"},"PeriodicalIF":2.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142526881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An array of paired folded-end dipoles for whole-brain imaging at 9.4 T","authors":"K.I. Popova ,&nbsp;F. Glang ,&nbsp;D. Bosch ,&nbsp;K. Scheffler ,&nbsp;N.I. Avdievich ,&nbsp;S.B. Glybovski ,&nbsp;G.A. Solomakha","doi":"10.1016/j.jmr.2024.107791","DOIUrl":"10.1016/j.jmr.2024.107791","url":null,"abstract":"<div><h3>Purpose</h3><div>To improve transmit B₁⁺ field homogeneity and longitudinal coverage of a human head RF array, we developed a novel eight-element transceiver (TxRx) array using composite elements based on paired folded-end dipoles.</div></div><div><h3>Methods</h3><div>The developed array consisted of eight pairs of coupled folded-end dipoles. Only one dipole in each pair was driven during transmission, while the other was passively coupled with the active one. The distribution of the transmit B₁⁺ field was numerically optimized by changing the overlap between the dipoles and the value of the reactive lumped element placed in the middle of the passive dipole.</div></div><div><h3>Results</h3><div>The proposed array of paired folded-end dipoles substantially improved the B₁⁺ homogeneity and longitudinal coverage over the entire brain including the brain stem compared to a single-row folded-end dipole array. The improved whole brain coverage was demonstrated both numerically and experimentally.</div></div><div><h3>Conclusion</h3><div>As a proof of concept, we developed and characterized both numerically and experimentally a prototype of a single-row eight-element 9.4 T array for human brain imaging consisting of composite array elements based on paired passively-coupled folded-end dipoles. The array improved the transmit magnetic field distribution due to the laterally elongated field pattern created by one active and one passive dipole per channel. As a result, the provided coverage was substantially better than that of an 8-element dipole array consisting of long folded-end dipoles. For the first time, an image of the entire human brain at 9.4 T, covering the brain stem up to the fourth vertebra, was obtained using a simple single row eight-element array.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107791"},"PeriodicalIF":2.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142526880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"“Nutation” of electron spins in biradicals","authors":"Ruslan Zaripov,&nbsp;Ravil Galeev,&nbsp;Kev Salikhov","doi":"10.1016/j.jmr.2024.107790","DOIUrl":"10.1016/j.jmr.2024.107790","url":null,"abstract":"<div><div>In this work, the nutation of the spins of unpaired electrons in the nitroxide biradical of bis‑methano[60]fullerene was experimentally studied. Nutation frequencies were found in a wide range of microwave field power. To interpret the obtained results, numerical calculations of the nutation of biradicals were carried out for a set of parameters of the spin–spin interaction of a pair of unpaired electrons and for different values of the Rabi frequency of the microwave field. At comparing numerical results with experimental data, we also used the results of analytical calculations of nutation for some model situations. As a result of the analysis of experimental data on nutation, an estimate of the exchange and dipole–dipole interactions for the studied biradical was obtained. They are consistent with the results obtained from analysis of the shape of the EPR spectrum for a given biradical.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107790"},"PeriodicalIF":2.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rationalising spin relaxation during slice-selective refocusing pulses","authors":"Howard M. Foster ,&nbsp;Runchao Li ,&nbsp;Yushi Wang ,&nbsp;Laura Castañar ,&nbsp;Mathias Nilsson ,&nbsp;Ralph W. Adams ,&nbsp;Gareth A. Morris","doi":"10.1016/j.jmr.2024.107789","DOIUrl":"10.1016/j.jmr.2024.107789","url":null,"abstract":"<div><div>Slice-selective refocusing pulses are powerful building blocks in contemporary magnetic resonance experiments, but their use in quantitative applications is complicated by the site-dependent signal loss they introduce. One source of this attenuation is the spin relaxation that occurs during such pulses, which causes losses that depend on the specific longitudinal and transverse relaxation time constants for a given resonance. This dependence is complicated both by any amplitude shaping of the radiofrequency pulse, and by the presence of the spatial encoding pulsed field gradient. The latter causes the net signal measured to be the weighted sum of signal contributions from a continuous range of offsets from resonance. In general, each offset will make a different contribution to the overall signal, and will be attenuated by a different mixture of longitudinal and transverse relaxation that is dictated by the different trajectories that the nuclear magnetisations take during experiments. Despite this complex behaviour, we present evidence from experiments and numerical simulations showing that in practical experimental applications a relatively simple empirical function can be used to accurately predict relaxational attenuation during slice-selective refocusing pulses. This approach may be of practical use in correcting for relaxational losses in quantitative applications of slice-selective pulse methods such as Zangger–Sterk pure shift NMR.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107789"},"PeriodicalIF":2.0,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A high-volume resonator for L-band DNP-NMR","authors":"Adam R. Altenhof ,&nbsp;Qing Yang ,&nbsp;Michal Kern ,&nbsp;Shaun G. Newman ,&nbsp;Jens Anders ,&nbsp;Michael W. Malone","doi":"10.1016/j.jmr.2024.107788","DOIUrl":"10.1016/j.jmr.2024.107788","url":null,"abstract":"<div><div>DNP-NMR and EPR experiments that operate at or greater than L-band (<em>i.e.,</em> ν₀(e⁻) = 1–2 GHz) are typically limited to maximum sample volumes of several hundred µL. These experiments rely on well-known resonator designs for DNP/EPR irradiation such as the loop-gap resonator and Alderman-Grant coil, where their maximum volumes limit further application to imaging experiments and high-throughput screening beyond L-band. Herein, we demonstrate a birdcage (BC) resonator design that can accommodate several mL of sample while operating around 1.5 GHz. The sample volume is maximized by using two identical BC resonators in a stacked configuration. Simulations are used to optimize the BC design and the performance is validated experimentally with liquid-state Overhauser-DNP-NMR experiments. This BC design exploits just the parasitic capacitance of conductive rings and features no fixed tuning capacitors. An enhancement of −77 is achieved on a 10 mM 4-Amino-TEMPO in H₂O sample for a 5 mL sample volume. The associated sample heating is minimal due to the low-<em>E</em>-fields generated and the large sample mass with +3.4 K when driving 100 W for several seconds.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107788"},"PeriodicalIF":2.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Frequency-independent dual-tuned cable traps for multi-nuclear MRI and MRS","authors":"Yijin Yang ,&nbsp;Ming Lu ,&nbsp;Xinqiang Yan","doi":"10.1016/j.jmr.2024.107786","DOIUrl":"10.1016/j.jmr.2024.107786","url":null,"abstract":"<div><div>Magnetic Resonance Imaging (MRI) and Magnetic Resonance Spectroscopy (MRS) of non-proton nuclei (X-nuclei) typically require additional proton imaging for anatomical reference and B₀ shimming. Therefore, two RF systems exist, necessitating cable traps to block the unwanted common-mode current at both Larmor frequencies of ¹H and X-nuclei. This study introduces a frequency-independent dual-tuned cable trap that combines a standard solenoid cable trap with a float solenoid trap to independently tune high and low frequencies without compromising performance. The methods involved theoretical analysis, electromagnetic simulations, and bench tests. Two design approaches were evaluated: a float cable trap for ¹H, a non-float cable trap for X-nuclei, and vice versa. Results showed that the design with the float trap for X-nuclei and non-float for ¹H had superior performance, with high common-mode current suppression ability at both frequencies. Bench tests confirmed these findings, demonstrating effectiveness across various static fields and X-nuclei. The proposed frequency-independent dual-tuned cable trap provides a compact and efficient solution for multinuclear MRI and MRS, enhancing safety, image quality, and flexibility.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107786"},"PeriodicalIF":2.0,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142432878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Homonuclear J-couplings and heteronuclear structural constraints","authors":"Edward P. Saliba ,&nbsp;Ravi Shankar Palani,&nbsp;Robert G. Griffin","doi":"10.1016/j.jmr.2024.107785","DOIUrl":"10.1016/j.jmr.2024.107785","url":null,"abstract":"<div><div>In magic angle spinning (MAS) experiments involving uniformly ¹³C/¹⁵N labeled proteins, ¹³C–¹³C and ¹³C–¹⁵N dipolar recoupling experiments are now routinely used to measure direct dipole–dipole couplings that constrain distances and torsion angles and determine molecular structures. When the distances are short (&lt;4 Å), the direct couplings dominate the evolution of the spin system, and the ¹³C–¹³C and ¹³C–¹⁵N J-couplings (scalar couplings) are ignored. However, for structurally interesting &gt;4 Å distances, the dipolar and J-couplings are generally of comparable magnitude, and the variation in J must be included in order to optimize the precision of the experiment. This problem is circumvented in cases with well resolved spectra by using frequency-selective dipolar recoupling methods where the effects of J-couplings are refocused. However, for larger molecules with more spectral crowding, the requisite pulse length to achieve selectivity becomes long and leads to unacceptable sensitivity losses during the pulse or the spectral overlap precludes selective excitation. In this paper, we address this problem with two approaches aimed at facilitating higher precision internuclear distance measurements in systems that are not fully resolved. Namely, (1) we describe an approach for high precision measurements of specific J-couplings using the in-phase anti-phase (IPAP) sequence which is integrated into a non-selective dipolar recoupling technique and (2) we utilize the measured J-couplings to implement a double quantum filter experiment capable of providing the resolution necessary for frequency selective dipolar recoupling techniques without resorting to multidimensional spectroscopy. We illustrate these methods using a 7-peptide segment from the amyloidogenic Sup-35p protein, U-¹³C/¹⁵N-GNNQQNY, where we have measured 25 of the 27 possible one bond ¹³C–¹³C J-couplings.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107785"},"PeriodicalIF":2.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simultaneous multinuclear MRI via a single RF channel","authors":"Mohammad Rasool Vaezi K.,&nbsp;Jan G. Korvink,&nbsp;Mazin Jouda","doi":"10.1016/j.jmr.2024.107782","DOIUrl":"10.1016/j.jmr.2024.107782","url":null,"abstract":"<div><div>Magnetic resonance imaging (MRI) stands as one of the most powerful noninvasive and non-destructive imaging techniques, finding extensive utility in medical and industrial applications. Its ability to acquire signals from multiple nuclei grants it additional levels of strength by providing multi-dimensional datasets of the object under test. However, this typically requires dedicated hardware to detect each nucleus. In this paper, we report on the use of a digital lock-in amplifier to perform simultaneous multi-nuclear MRI with a single physical radio frequency (RF) channel. While we showcase this concept by demonstrating the results of fully parallel (TX and RX) ¹H and ¹⁹F MRI images, we emphasize that it is not limited to two nuclei but can accommodate more nuclei with no extra cost on the hardware or scan time. The scalability is virtually unlimited, constrained only by the processing speed of the digital unit. Furthermore, we demonstrate that the quality of parallel imaging with SNR of 54 is comparable to the commercial single channel with SNR of 43. Thus with no reduction in imaging quality, the proposed concept promises a tremendous reduction in scan time, system complexity, and hardware costs.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"368 ","pages":"Article 107782"},"PeriodicalIF":2.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142442903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}