Journal of magnetic resonance最新文献

{"title":"A thermally polarized, dissolved-phase 129Xe phantom for quality-control and multisite comparisons of gas-exchange imaging","authors":"Matthew M. Willmering ,&nbsp;Brice J. Albert ,&nbsp;Joseph W. Plummer ,&nbsp;Josh Greer ,&nbsp;Laura L. Walkup ,&nbsp;Diana M. Lindquist ,&nbsp;Zackary I. Cleveland","doi":"10.1016/j.jmr.2025.107829","DOIUrl":"10.1016/j.jmr.2025.107829","url":null,"abstract":"<div><div>Harmonizing and validating ¹²⁹Xe gas exchange imaging across multiple sites is hampered by a lack of a quantitative standard that 1) displays the unique spectral properties of ¹²⁹Xe observed from human subjects <em>in vivo</em> and 2) has short enough <span><math><msub><mi>T</mi><mn>1</mn></msub></math></span> times to enable practical imaging. This work describes and demonstrates the development of two dissolved-phase, thermally polarized phantoms that mimic the <em>in-vivo</em>, red blood cell and membrane resonances of ¹²⁹Xe dissolved in human lungs. Following optimization, combinations of two common organic solvents, acetone and dimethyl sulfoxide, resulted in two <em>in-vivo</em>-like dissolved-phase ¹²⁹Xe phantoms yielding chemical shifts of 212.4 ppm and 193.9 ppm. By doping the solutions with iron(iii) acetylacetonate, the longitudinal relaxation time was reduced <span><math><msub><mi>T</mi><mn>1</mn></msub></math></span> = 1.2 s for both phantoms at 3 T and 7 T. There was minimal change in chemical shift (+1.58 ppm) and <span><math><msub><mi>T</mi><mn>1</mn></msub></math></span> (+1.2 %) over 1 year. In a 2D Dixon-type acquisition with 3 mm² in-plane resolution, ¹²⁹Xe dissolved-phase images yielded signal-to-noise ratios 6 and 12 for the RBC and membrane phantoms, respectively. A simple scaling of these phantoms to clinically relevant volumes of several liters would result in an SNR of 7 for the RBC phantom acquired in less than one minute. These findings demonstrate the ability to fabricate robust, quantitative, thermally polarized dissolved-phase phantoms, which will be needed to validate and harmonize gas exchange imaging in multi-site clinical trials.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"371 ","pages":"Article 107829"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985694","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":"Pseudo-3D HSQC0, a method to create a true 2D HSQC0-plane. Application to softwood extract analysis","authors":"Maarit H. Lahtinen ,&nbsp;Tuomas Niemi-Aro ,&nbsp;Danila Morais de Carvalho ,&nbsp;Kirsi S. Mikkonen ,&nbsp;Ilkka Kilpeläinen ,&nbsp;Sami Heikkinen","doi":"10.1016/j.jmr.2024.107825","DOIUrl":"10.1016/j.jmr.2024.107825","url":null,"abstract":"<div><div>Pseudo-3D HSQC₀ provides an alternative and easy way to record and analyze quantitative HSQC₀-data. In the original time-zero extrapolated ¹H–¹³C HSQC (HSQC₀), three separate 2D constant-time (CT) HSQC-experiments (HSQC_i, <em>i</em> = 1–3) are acquired, where either 1,2 or 3 consecutive CT-HSQC-propagators are repeated in each pulse sequence, and the 2D integral data from the three 2D experiments is analyzed via linear regression. In the presented pseudo-3D HSQC₀, HSQC_i is one of the dimensions and all data is contained within one dataset, which is recorded in interleaved manner by acquiring the same t₁-value for each HSQC_i-point before t₁-incrementation. The 3D-nature of the data allows the utilization of backward linear prediction to calculate an actual time-zero 2D HSQC₀ spectrum, which can be analyzed using normal 2D integration procedures for quantitative results. In all, the pseudo-3D enables straightforward, intuitive and easy analysis of the quantitative 2D HSQC₀ spectrum/plane. As the recorded pseudo 3D data contains the normal HSQC_i planes, also the classic linear regression analysis can be applied.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"371 ","pages":"Article 107825"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904576","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":"Spatially constrained hyperpolarized 13C MRI pharmacokinetic rate constant map estimation using a digital brain phantom and a U-Net","authors":"Sule Sahin ,&nbsp;Anna Bennett Haller ,&nbsp;Jeremy Gordon ,&nbsp;Yaewon Kim ,&nbsp;Jasmine Hu ,&nbsp;Tanner Nickles ,&nbsp;Qing Dai ,&nbsp;Andrew P. Leynes ,&nbsp;Daniel B. Vigneron ,&nbsp;Zhen Jane Wang ,&nbsp;Peder E.Z. Larson","doi":"10.1016/j.jmr.2025.107832","DOIUrl":"10.1016/j.jmr.2025.107832","url":null,"abstract":"<div><div>Fitting rate constants to Hyperpolarized [1-¹³C]Pyruvate (HP C13) MRI data is a promising approach for quantifying metabolism in vivo. Current methods typically fit each voxel of the dataset using a least-squares objective. With these methods, each voxel is considered independently, and the spatial relationships are not considered during fitting.</div><div>In this work, we use a convolutional neural network, a U-Net, with convolutions across the 2D spatial dimensions to estimate pyruvate-to-lactate conversion rate, k_PL, maps from dynamic HP C13 datasets. We designed a framework for creating simulated anatomically accurate brain data that matches typical HP C13 characteristics to provide large amounts of data for training with ground truth results. The U-Net is initially trained with the digital phantom data and then further trained with in vivo datasets for regularization.</div><div>In simulation where ground-truth k_PL maps are available, the U-Net outperforms voxel-wise fitting with and without spatiotemporal denoising, particularly for low SNR data. In vivo data was evaluated qualitatively, as no ground truth is available, and before regularization the U-Net predicted k_PL maps appear oversmoothed. After further training with in vivo data, the resulting k_PL maps appear more realistic.</div><div>This study demonstrates how to use a U-Net to estimate rate constant maps for HP C13 data, including a comprehensive framework for generating a large amount of anatomically realistic simulated data and an approach for regularization. This simulation and architecture provide a foundation that can be built upon in the future for improved performance.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"371 ","pages":"Article 107832"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143019058","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":"Relaxation-optimized correlation spectroscopy ROCSY for assigning 1H or 13C spin systems in large proteins","authors":"M. Rafid Feisal ,&nbsp;Shaista Goel ,&nbsp;Kevin Y.L. Mak ,&nbsp;Albert Wu ,&nbsp;Philip B. Liu ,&nbsp;Peter M. Hwang","doi":"10.1016/j.jmr.2024.107826","DOIUrl":"10.1016/j.jmr.2024.107826","url":null,"abstract":"<div><div>Solution NMR studies of large systems are hampered by rapid signal decay. We hereby introduce ROCSY (relaxation-optimized total correlation spectroscopy), which maximizes transfer efficiency across J-coupling-connected spin networks by minimizing the amount of time magnetization spends in the transverse plane. Hard pulses are substituted into the Clean-CITY TOCSY pulse element first developed by Ernst and co-workers, allowing for longer delays in which magnetization is aligned along the z-axis. This has the following consequences: 1) transverse relaxation is minimized, 2) resonance offset effects are minimized, 3) and through-space nuclear Overhauser enhancement (NOE) adds to J-coupling-mediated magnetization transfer. The major drawbacks of the technique are additional heat generation produced by the hard pulses and complication of analysis by the additional through-space NOE magnetization transfer. We demonstrate H_alpha-to-HN correlations not possible using conventional ¹H-TOCSY in a ¹⁵N-enriched sample of PagP (a 161-residue integral membrane protein) in dodecylphosphocholine detergent micelles. We also demonstrate enhanced signal-to-noise compared to ¹³C-TOCSY in a ¹⁵N,¹³C-enriched sample of cardiac troponin C N-terminal domain. We thus propose that ROCSY can be used to boost signal in any protein NMR experiment that utilizes TOCSY, with greater enhancements seen in higher molecular weight systems.</div></div>","PeriodicalId":16267,"journal":{"name":"Journal of magnetic resonance","volume":"371 ","pages":"Article 107826"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928939","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":"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":"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}