An Inversion Recovery NMR Kinetics Experiment.
Ontology highlight
ABSTRACT:
SUBMITTER: Williams TJ
PROVIDER: S-EPMC3088435 | biostudies-literature | 2011 May
REPOSITORIES: biostudies-literature
Publications
An Inversion Recovery NMR Kinetics Experiment.
Williams Travis J TJ Kershaw Allan D AD Li Vincent V Wu Xinping X
Journal of chemical education 20110501 5
A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this article will enable instructors to use inversion recovery as a laboratory activity in applied NMR classes and provide research students with a convenient ...[more]
Similar Datasets
Project description:Background and purposeSynthetic MR imaging (SyMRI) allows the reconstruction of various contrast images, including double inversion recovery (DIR), from a single scan. This study aimed to investigate the advantages of SyMRI by comparing synthetic DIR images with synthetic T2-weighted fluid-attenuated inversion recovery (T2W-FLAIR) and conventional DIR images.Materials and methodsWe retrospectively reviewed the imaging data of 100 consecutive patients who underwent brain MRI between December 2018 and March 2019. Synthetic DIR, T2W-FLAIR, T1-weighted, and phase-sensitive inversion recovery (PSIR) images were generated from SyMRI data. For synthetic DIR, the two inversion times required to suppress white matter and cerebrospinal fluid (CSF) were manually determined by two radiologists. Quantitative analysis was performed by manually tracing the region of interest (ROI) at the sites of the lesion, white matter, and CSF. Synthetic DIR, synthetic T2W-FLAIR, and conventional DIR images were compared on the basis of using the gray matter-to-white matter, lesion-to-white matter, and lesion-to-CSF contrast-to-noise ratios.ResultsThe two radiologists showed no differences in setting inversion time (TI) values, and their evaluations showed excellent interobserver agreement. The mean signal intensities obtained with synthetic DIR were significantly higher than those obtained with synthetic T2W-FLAIR and conventional DIR.ConclusionSynthetic DIR images showed a higher contrast than synthetic T2WFLAIR and conventional DIR images.
| S-EPMC9615305 | biostudies-literature
Project description:NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement.
| S-EPMC4560687 | biostudies-literature
Project description:1H-NMR is a very reproducible spectroscopic method and, therefore, a powerful tool for the metabolomic analysis of biological samples. However, due to the high complexity of natural samples, such as plant extracts, the evaluation of spectra is difficult because of signal overlap. The new NMR "Pure Shift" methods improve spectral resolution by suppressing homonuclear coupling and turning multiplets into singlets. The PSYCHE (Pure Shift yielded by Chirp excitation) and the Zangger-Sterk pulse sequence were tested. The parameters of the more suitable PSYCHE experiment were optimized, and the extracts of 21 Hypericum species were measured. Different evaluation criteria were used to compare the suitability of the PSYCHE experiment with conventional 1H-NMR. The relationship between the integral of a signal and the related bin value established by linear regression demonstrates an equal representation of the integrals in binned PSYCHE spectra compared to conventional 1H-NMR. Using multivariate data analysis based on both techniques reveals comparable results. The obtained data demonstrate that Pure Shift spectra can support the evaluation of conventional 1H-NMR experiments.
| S-EPMC7662903 | biostudies-literature
Project description:At clinical MRI field strengths (1.5 and 3 T), quantitative maps of the longitudinal relaxation time T1 of the myocardium reveal diseased tissue without requiring contrast agents. Cardiac T1 maps can be measured by Look-Locker inversion recovery sequences such as ShMOLLI at 1.5 and 3 T. Cardiovascular MRI at a field strength of 7 T has recently become feasible, but doubts have remained as to whether magnetization inversion is possible in the heart due to subject heating and technical limitations. This work extends the repertoire of 7 T cardiovascular MRI by implementing an adiabatic inversion pulse optimized for use in the heart at 7 T. A "ShMOLLI+IE" adaptation of the ShMOLLI pulse sequence has been introduced together with new postprocessing that accounts for the possibility of incomplete magnetization inversion. These methods were validated in phantoms and then used in a study of six healthy volunteers to determine the degree of magnetization inversion and the T1 of normal myocardium at 7 T within a 22-heartbeat breathhold. Using a scanner with 16 × 1 kW radiofrequency outputs, inversion efficiencies ranging from -0.79 to -0.83 (intrasegment means; perfect 180° would give -1) were attainable across the myocardium. The myocardial T1 was 1925 ± 48 ms (mean ± standard deviation).
| S-EPMC4134266 | biostudies-literature
Project description:An efficient multi-slice inversion-recovery EPI (MS-IR-EPI) sequence for fast, high spatial resolution, quantitative T1 mapping is presented, using a segmented simultaneous multi-slice acquisition, combined with slice order shifting across multiple acquisitions. The segmented acquisition minimises the effective TE and readout duration compared to a single-shot EPI scheme, reducing geometric distortions to provide high quality T1 maps with a narrow point-spread function. The precision and repeatability of MS-IR-EPI T1 measurements are assessed using both T1-calibrated and T2-calibrated ISMRM/NIST phantom spheres at 3 and 7 T and compared with single slice IR and MP2RAGE methods. Magnetization transfer (MT) effects of the spectrally-selective fat-suppression (FS) pulses required for in vivo imaging are shown to shorten the measured in-vivo T1 values. We model the effect of these fat suppression pulses on T1 measurements and show that the model can remove their MT contribution from the measured T1, thus providing accurate T1 quantification. High spatial resolution T1 maps of the human brain generated with MS-IR-EPI at 7 T are compared with those generated with the widely implemented MP2RAGE sequence. Our MS-IR-EPI sequence provides high SNR per unit time and sharper T1 maps than MP2RAGE, demonstrating the potential for ultra-high resolution T1 mapping and the improved discrimination of functionally relevant cortical areas in the human brain.
| S-EPMC8204273 | biostudies-literature
Project description:BackgroundLimited reliability data exist for evaluation of spinal edema changes on magnetic resonance imaging (MRI) with short tau inversion recovery (STIR) sequences.PurposeTo assess the inter-observer reliability for evaluation of STIR signal increase related to Modic changes (MCs) on MRI of the lumbar spine.Material and methodsWe prospectively included 120 patients imaged to confirm their eligibility for the AIM (Antibiotics In Modic changes) trial. Three experienced radiologists independently evaluated MCs on T1-/T2-weighted fast spin-echo images and subsequently MC-related STIR signal increases. Inter-observer reliability was analyzed at four endplates (L4-S1) by calculating kappa values and means of differences with 95% limits of agreement.ResultsOverall agreement (mean Fleiss' kappa for all endplates and observers) was very good for presence of STIR signal increase (0.86), and moderate for its categorized height (0.51), anteroposterior extent (0.48), and volume (0.56). For height of region with STIR signal increase measured in % points of vertebral body height, the largest mean of differences was 6.9 and widest range for limits of agreement was ±22.3 for all endplates combined. The corresponding numbers were 11.2 ± 34.5 for anteroposterior extent of the STIR signal increase measured in % points of anteroposterior endplate diameter and 0.9 ± 7.6 for its maximum measured intensity on a % point scale (0% = normal vertebral marrow intensity, 100% = cerebrospinal fluid intensity).ConclusionInter-observer reliability was very good for the presence and intensity of MC-related STIR signal increases, and moderate for their size.
| S-EPMC6990614 | biostudies-literature
Project description:Experiments detecting low gyromagnetic nuclei have recently been proposed to utilize the relatively slow relaxation properties of these nuclei in comparison to (1)H. Here we present a new type of (15)N direct-detection experiment. Like the previously proposed CaN experiment (Takeuchi et al. in J Biomol NMR 47:271-282, 2010), the hCaN experiment described here sequentially connects amide (15)N resonances, but utilizes the initial high polarization and the faster recovery of the (1)H nucleus to shorten the recycling delay. This allows recording 2D (15)N-detected NMR experiments on proteins within a few hours, while still obtaining superior resolution for (13)C and (15)N, establishing sequential assignments through prolines, and at conditions where amide protons exchange rapidly. The experiments are demonstrated on various biomolecules, including the small globular protein GB1, the 22 kDa HEAT2 domain of eIF4G, and an unstructured polypeptide fragment of NFAT1, which contains many SerPro sequence repeats.
| S-EPMC3338130 | biostudies-literature
Project description:ObjectTo develop and evaluate a 2D modified Look-Locker (MOLLI) for high-resolution T1 mapping in mice using a 3T MRI scanner.Materials and methodsTo allow high-resolution T1 mapping in mice at high heart rates a multi-shot ECG-triggered 2D MOLLI sequence was developed. In the proposed T1 mapping sequence the optimal number of sampling points and pause cardiac cycles following an initial adiabatic inversion pulse was investigated in a phantom. Seven native control and eight mice, 3 days post myocardial infarction (MI) after administration of gadolinium were scanned. Two experienced readers graded the visual T1 map quality.ResultsIn T1 phantoms, there were no significant differences (<0.4% error) between 12, 15 and 20 pause cardiac cycles (p = 0.1, 0.2 and 0.6 respectively) for 8 acquisition cardiac cycles for 600bpm in comparison to the conventional inversion recovery spin echo T1 mapping sequence for short T1's (<600 ms). Subsequently, all in-vivo scans were performed with 8 data acquisitions and 12 pause cardiac cycles to minimize scan time. The mean native T1 value of myocardium in control animal was 820.5±52 ms. The post-contrast T1 measured 3 days after MI in scar was 264±59 ms and in healthy myocardium was 512±62 ms. The Bland-Altman analysis revealed mean difference of only -1.06% of infarct size percentage between T1 maps and LGE.ConclusionsA multi-shot 2D MOLLI sequence has been presented that allows reliable measurement of high spatial resolution T1 maps in mice for heart rates up to 600bpm.
| S-EPMC5679534 | biostudies-literature
Project description:PurposeTo develop a new myelin water imaging (MWI) technique using a short-TR adiabatic inversion-recovery (STAIR) sequence on a clinical 3T MR scanner.MethodsMyelin water (MW) in the brain has both a much shorter T1 and a much shorter T2 * than intracellular/extracellular water. A STAIR sequence with a short TR was designed to efficiently suppress long T1 signals from intracellular/extracellular water, and therefore allow selective imaging of MW, which has a much shorter T1 . Numerical simulation and phantom studies were performed to investigate the effectiveness of long T1 signal suppression. TheT2 * in white matter (WM) was measured with STAIR and compared with T2 * measured with a conventional gradient recall echo in in vivo study. Four healthy volunteers and 4 patients with multiple sclerosis were recruited for qualitative and quantitative MWI. Apparent MW fraction was generated to compare MW in normal WM in volunteers to MW in lesions in patients with multiple sclerosis.ResultsBoth simulation and phantom studies showed that when TR was sufficiently short (eg, 250 ms), the STAIR sequence effectively suppressed long T1 signals from tissues with a broad range of T1 s using a single TR/TI combination. The volunteer study showed a short T2 * of 9.5 ± 1.7 ms in WM, which is similar to reported values for MW. Lesions in patients with multiple sclerosis showed a significantly lower apparent MW fraction (4.5% ± 1.0%) compared with that of normal WM (9.2% ± 1.5%) in healthy volunteers (p < 0.05).ConclusionsThe STAIR sequence provides selective MWI in brain and can quantify reductions in MW content in patients with multiple sclerosis.
| S-EPMC9867567 | biostudies-literature
Project description:Efficient acquisition of ultra-wideline solid-state NMR powder patterns is a continuing challenge. In particular, when the breadth of the powder pattern is much larger than the cross-polarization (CP) excitation bandwidth, transfer efficiencies suffer and experimental times are greatly increased. Presented herein is a CP pulse sequence with an excitation bandwidth that is up to ten times greater than that available from a conventional spin-locked CP pulse sequence. The pulse sequence, broadband adiabatic inversion CP (BRAIN-CP), makes use of the broad, uniformly large frequency profiles of chirped inversion pulses, to provide these same characteristics to the polarization transfer process. A detailed theoretical analysis is given, providing insight into the polarization transfer process involved in BRAIN-CP. Experiments on spin-1/2 nuclei including (119)Sn, (199)Hg and (195)Pt nuclei are presented, and the large bandwidth improvements possible with BRAIN-CP are demonstrated. Furthermore, it is shown that BRAIN-CP can be combined with broadband frequency-swept versions of the Carr-Purcell-Meiboom-Gill experiment (for instance with WURST-CPMG, or WCPMG for brevity); the combined BRAIN-CP/WCPMG experiment then provides multiplicative signal enhancements of both CP and multiple-echo acquisition over a broad frequency region.
| S-EPMC5081099 | biostudies-literature