Journal of magnetic resonance最新文献

{"title":"The use of self-adaptive principal components in PCA-based denoising","authors":"Oleg V. Petrov","doi":"10.1016/j.jmr.2024.107824","DOIUrl":"10.1016/j.jmr.2024.107824","url":null,"abstract":"<div><div>PCA-based denoising usually implies either discarding a number of high-index principal components (PCs) of a data matrix or their attenuation according to a regularization model. This work introduces an alternative, model-free, approach to high-index PC attenuation that seeks to average values of PC vectors as if they were expected from noise perturbation of data. According to the perturbation theory, the average PCs are attenuated versions of the clean PCs of noiseless data – the higher the noise-related content in a PC vector, the lower is its average’s norm. This enables a regularization of the PC expansion of data where the PC terms are self-adapted to their noise content. To approximate the average PC vectors, the data matrix is randomly sampled several times to obtain numerous pseudo-random PC sets. The PCs of same ranks are then used to reconstruct the full-data PCs of that rank. A numerical algorithm of the reconstruction and its implementation in Python are provided. The proposed automatic adaptation to data offers a convenient solution for those who face with a problem of scaling or discarding PCs in PCA-based denoising. Questions of optimal sampling schedule and sampling amount remain issues that future work must address.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"371 ","pages":"Article 107824"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911316","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":"Tribute to Alexander Pines (1945–2024)","authors":"","doi":"10.1016/j.jmr.2025.107839","DOIUrl":"10.1016/j.jmr.2025.107839","url":null,"abstract":"","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"371 ","pages":"Article 107839"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143306609","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":"On the geometric phase effects on time evolution of the density matrix during modulated radiofrequency pulses","authors":"Dennis J. Sorce ,&nbsp;Shalom Michaeli","doi":"10.1016/j.jmr.2025.107840","DOIUrl":"10.1016/j.jmr.2025.107840","url":null,"abstract":"<div><div>In this work the effect of the geometric phase on time evolution of the density matrix was evaluated during nonadiabatic radiofrequency (RF) pulses with <em>Sine</em> amplitude modulation (AM) and <em>Cosine</em> frequency modulation (FM) functions of the RAFF (Relaxations Along a Fictitious Field) family, and the polarization between two energy level ½ spin system coupled by dipolar interaction was evaluated during the application of RF irradiation. The dependencies of the diagonal density matrix elements and the polarization on the rotational correlation times and the time during RF pulses were evaluated. The general treatment of the density matrix elements along with the polarization generated during RF pulses was unavailable thus far, and for the first time was here derived for the nonadiabatic case of the RAFF pulses. The current formalism could be extended to other AM and FM RF waveforms, including the adiabatic RF pulses which are widely used in magnetic resonance (MR). We demonstrate that the sub-geometric phases (SGP) influence the density matrix elements and thus the polarization generated during the application of RF AM and FM pulses. The corrections to describe the SGP influence of the density matrix elements developed in this work could be essential for determination of MR fundamental parameters necessary for evaluation of tissue contrasts <em>in vivo</em> in MRI and for protein dynamics characterization in high resolution NMR, where AM and FM RF pulses are frequently utilized.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"372 ","pages":"Article 107840"},"PeriodicalIF":2.0,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043801","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":"Observation of NMR signals from samples with flat geometry: Application to in-situ analysis of a direct ethanol fuel cell","authors":"Minchae Kwak ,&nbsp;Minji Kim ,&nbsp;Dong-Hyun Peck ,&nbsp;Seong-Joo Lee ,&nbsp;Jeong Hyun Shim ,&nbsp;Oc Hee Han ,&nbsp;Jung Ho Lee","doi":"10.1016/j.jmr.2025.107831","DOIUrl":"10.1016/j.jmr.2025.107831","url":null,"abstract":"<div><div>Most NMR samples are cylindrical, which is ideal for obtaining high-resolution NMR spectra, especially in superconducting magnets with a vertical bore. However, expanding NMR applicability to samples that are not necessarily cylindrical requires a new approach. In this study, we introduce a method for obtaining solution NMR signals from flat samples, such as flat containers or layered structures like a fuel cell. A flat rectangular NMR coil was developed for RF application and sensitive signal detection, while biplanar shim coils were designed using Bfieldtools and manufactured on multilayered printed circuit boards to improve NMR resolution. Water and ethanol molecules in flat rectangular and flat circular containers, as well as in a direct ethanol fuel cell, were observed with narrow NMR linewidths. We believe that our spectrometer design will enable NMR analysis of samples that need to be contained in flat structures and support <em>in-situ</em> analysis of various devices.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"372 ","pages":"Article 107831"},"PeriodicalIF":2.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143019071","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":"Rela2x: Analytic and automatic NMR relaxation theory","authors":"Perttu Hilla,&nbsp;Juha Vaara","doi":"10.1016/j.jmr.2024.107828","DOIUrl":"10.1016/j.jmr.2024.107828","url":null,"abstract":"<div><div>Spin relaxation is modelled using the so-called relaxation superoperator <span><math><mover><mrow><mover><mrow><mi>Γ</mi></mrow><mrow><mo>ˆ</mo></mrow></mover></mrow><mrow><mo>ˆ</mo></mrow></mover></math></span>. Analytic forms of <span><math><mover><mrow><mover><mrow><mi>Γ</mi></mrow><mrow><mo>ˆ</mo></mrow></mover></mrow><mrow><mo>ˆ</mo></mrow></mover></math></span> have been derived in the literature in the simplest cases of one- or two-spin systems, with <span><math><mrow><mi>S</mi><mo>=</mo><mfrac><mrow><mn>1</mn></mrow><mrow><mn>2</mn></mrow></mfrac></mrow></math></span> nuclei and no more than two different simultaneous relaxation mechanisms involved. Beyond that, for systems of more than two spins, with <span><math><mrow><mi>S</mi><mo>&gt;</mo><mfrac><mrow><mn>1</mn></mrow><mrow><mn>2</mn></mrow></mfrac></mrow></math></span> and/or multiple relaxation mechanisms at play, the derivations become notoriously complicated, which is why analytic relaxation theory has mostly been considered a dead end. Instead, numerical methods of constructing <span><math><mover><mrow><mover><mrow><mi>Γ</mi></mrow><mrow><mo>ˆ</mo></mrow></mover></mrow><mrow><mo>ˆ</mo></mrow></mover></math></span> have been popular. However, they lack some of the physical, chemical and pedagogical insight that can be provided by analytic expressions. To this end, we present a general, interactive and freely available Python programme, named <span>Rela²x</span>, to automatically compute the analytic matrix representation of <span><math><mover><mrow><mover><mrow><mi>Γ</mi></mrow><mrow><mo>ˆ</mo></mrow></mover></mrow><mrow><mo>ˆ</mo></mrow></mover></math></span> for high-field NMR. Tools to analyse, approximate and visualize <span><math><mover><mrow><mover><mrow><mi>Γ</mi></mrow><mrow><mo>ˆ</mo></mrow></mover></mrow><mrow><mo>ˆ</mo></mrow></mover></math></span> are built into <span>Rela²x</span>. As a demonstration of the functionality, <span><math><mover><mrow><mover><mrow><mi>Γ</mi></mrow><mrow><mo>ˆ</mo></mrow></mover></mrow><mrow><mo>ˆ</mo></mrow></mover></math></span> is presented both for the familiar dipole–dipole coupled <span><math><msup><mrow></mrow><mrow><mn>1</mn></mrow></msup></math></span>H-<span><math><msup><mrow></mrow><mrow><mn>1</mn></mrow></msup></math></span>H spin system and for more complicated <span><math><msup><mrow></mrow><mrow><mn>1</mn></mrow></msup></math></span>H-¹⁴N and <span><math><msup><mrow></mrow><mrow><mn>1</mn></mrow></msup></math></span>H-¹³C-¹⁴N systems with dipole–dipole coupling, chemical shift anisotropy and quadrupole interaction. We envision that the code will provide much-needed clarity in the form of a helpful tool for the study of relaxation effects, and constitute a reference source for scientists in the field of NMR.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"372 ","pages":"Article 107828"},"PeriodicalIF":2.0,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143019074","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":"Cryogenic sample eject system for electron paramagnetic resonance spectrometers","authors":"Karl Rieger,&nbsp;Joshua Hoy,&nbsp;Timothy J. Keller,&nbsp;Thorsten Maly","doi":"10.1016/j.jmr.2024.107823","DOIUrl":"10.1016/j.jmr.2024.107823","url":null,"abstract":"<div><div>We present a fully automated cryogenic sample insertion and ejection system for use with low-temperature EPR probes. We show how the system can be implemented on a conventional EPR spectrometer and that ejection and insertion is reliably possible at temperatures down to 10 K. Furthermore, we investigate the glass properties of a 0.1 mM sample of TEMPO in d₈-glycerol/D₂O (25/75, v/v) by measuring the electron phase memory time T_m in addition to determining the effective spin concentration from a PELDOR/DEER background trace. These experiments were done either using the sample eject system or samples that were manually flash frozen. We show that using the ejection system we can consistently obtain a better glass matrix as indicated by the longer T_m times and the lower effective concentrations.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"370 ","pages":"Article 107823"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873696","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":"Homonuclear decoupled INADEQUATE NMR methods with improved sensitivity and resolution in solid-state NMR","authors":"Yury G. Kolyagin ,&nbsp;Julien Trébosc ,&nbsp;Koffi Jean Baptiste Alloko ,&nbsp;Olivier Lafon ,&nbsp;Jean-Paul Amoureux","doi":"10.1016/j.jmr.2024.107822","DOIUrl":"10.1016/j.jmr.2024.107822","url":null,"abstract":"<div><div>The two-dimensional (2D) refocused INADEQUATE NMR experiment, which correlates double-quantum (DQ) and single-quantum (SQ) coherences, is widely used to probe the chemical connectivities in solids. Nevertheless, the multiplets along the <em>F</em>₂ dimension reduce the resolution and sensitivity of this experiment. The Composite-Refocusing (CR) technique with two excitation pulses has been proposed to suppress these multiplets in 2D INADEQUATE spectra of liquids. Recently (Kolyagin et al., <em>J. Phys. Chem. Lett</em>., 13 (<strong>2022</strong>) 10793), we showed that this technique can also be applied to suppress doublets in 2D ²⁹Si INADEQUATE spectra of ²⁹Si-enriched zeolites, which resulted in improved sensitivity and resolution. We investigate here how this INADEQUATE-CR scheme can also be applied for two other spin-1/2 isotopes: ¹³C and ³¹P. We also demonstrate the possibility to accelerate the acquisition of these 2D INADEQUATE-CR spectra with a very simple bi-exponential non-uniform sampling (NUS). For instance, in the case of ³¹P nuclei in SnP₂O₇, the use of the INADEQUATE-CR method with NUS yields a 7.5-fold reduction in experimental time with a simultaneous 1.4–1.5 gain in resolution with respect to a conventional INADEQUATE acquisition. Furthermore, we analyze the origins of the possible artifacts in these 2D spectra, including mismatching between <em>J</em>-coupling constants and refocusing delays, differences in relaxation times, coupling with a proton bath, and spin systems containing multiple identical nuclei. Based on this analysis, we introduce a new z-filtered INADEQUATE-CR version, which produces artifact-free 2D spectra, even in the presence of several distinct <em>J</em>-couplings and relaxation times or for multi-spin systems, and notably samples with high proton density.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"370 ","pages":"Article 107822"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901471","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":"Physics-guided multi-dimensional scan optimization and quasi-steady-state reconstruction to enhance CEST MRI sensitivity efficiency and quantification accuracy","authors":"Phillip Zhe Sun","doi":"10.1016/j.jmr.2024.107821","DOIUrl":"10.1016/j.jmr.2024.107821","url":null,"abstract":"<div><div>Chemical exchange saturation transfer (CEST) MRI has become increasingly utilized for detecting dilute labile protons and characterizing microenvironment properties. However, the CEST MRI effect is only a few percent, and there is a need for a systematic approach to optimize scan parameters for sensitive and accurate CEST quantification. We propose multi-dimensional adjustments of key parameters such as the repetition time (TR) and RF duty cycle to optimize CEST MRI sensitivity per unit of time and utilization of quasi-steady-state (QUASS) reconstruction to recover the full CEST effect during postprocessing. Our work herein derived the CEST effect based on the generalized spin-lock CEST model and determined the interdependency of the optimal RF duty cycle and TR, showing the optimal TR decreases with the RF duty cycle but plateaus beyond 60–80 %. The accuracy of the solution was validated with both numerical simulations and CEST MRI experiments on a dual pH creatine gel phantom. The desired equilibrium CEST effect was further reconstructed with the QUASS algorithm from the optimized CEST MRI scan. In summary, our study establishes a workflow for CEST MRI scan optimization and postprocessing analysis, providing a framework to boost both the sensitivity of CEST MRI scans and the accuracy of CEST quantification. This approach holds promise for future in vivo validation and translation.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"370 ","pages":"Article 107821"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848664","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":"Denoising low-field MR images with a deep learning algorithm based on simulated data from easily accessible open-source software","authors":"Aram Salehi ,&nbsp;Mathieu Mach ,&nbsp;Chloe Najac ,&nbsp;Beatrice Lena ,&nbsp;Thomas O’Reilly ,&nbsp;Yiming Dong ,&nbsp;Peter Börnert ,&nbsp;Hieab Adams ,&nbsp;Tavia Evans ,&nbsp;Andrew Webb","doi":"10.1016/j.jmr.2024.107812","DOIUrl":"10.1016/j.jmr.2024.107812","url":null,"abstract":"<div><div>In this study, we introduce a denoising method aimed at improving the contrast ratio in low-field MRI (LFMRI) using an advanced 3D deep convolutional residual network model. Our approach employs synthetic brain imaging datasets that closely mimic the contrast and noise characteristics of LFMRI scans, addressing the limitation of available in-vivo LFMRI datasets for training deep learning models. In the simulation data, the Relative Contrast Ratio (RCR) increased, and similar improvements were observed in the in-vivo data across different imaging conditions. Comparative evaluations demonstrate that our model performs better than the widely used non-deep learning method, BM4D, in enhancing RCR and maintaining high spatial frequency components in in-vivo data.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"370 ","pages":"Article 107812"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796632","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":"Using machine learning to improve the hard modeling of NMR time series","authors":"Jan Hellwig ,&nbsp;Tobias Strauß ,&nbsp;Erik von Harbou ,&nbsp;Klaus Neymeyr","doi":"10.1016/j.jmr.2024.107813","DOIUrl":"10.1016/j.jmr.2024.107813","url":null,"abstract":"<div><div>Modeling time series of NMR spectra is a useful method to accurately extract information such as temporal concentration profiles from complex processes, e.g. reactions. Modeling these time series by using nonlinear optimization often suffers from high runtimes. On the other hand, using deep learning solves the modeling problem quickly, especially for single spectra with separated peaks. However, the accuracy decreases significantly when peaks overlap or cross. We propose a hybrid approach combining the strengths of both methods while mitigating their drawbacks. This hybrid methods improves on a previous work (Meinhardt et al., 2022) and employs neural networks to predict initial parameters for the optimization algorithm, which only needs to fine-tune the parameters afterwards. We present results for both constructed and experimental data sets and achieve improvements in both runtime and accuracy.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"370 ","pages":"Article 107813"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866467","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}