Dataset Information

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method.

ABSTRACT: The NMR spectra of nucleic acids suffer from severe peak overlap, which complicates resonance assignments. 4D NMR experiments can overcome much of the degeneracy in 2D and 3D spectra; however, the linear increase in acquisition time with each new dimension makes it impractical to acquire high-resolution 4D spectra using standard Fourier transform (FT) techniques. The filter diagonalization method (FDM) is a numerically efficient algorithm that fits the entire multi-dimensional time-domain data to a set of multi-dimensional oscillators. Selective 4D constant-time HCCH-COSY experiments that correlate the H5-C5-C6-H6 base spin systems of pyrimidines or the H1'-C1'-C2'-H2' spin systems of ribose sugars were acquired on the (13)C-labeled iron responsive element (IRE) RNA. FDM-processing of these 4D experiments recorded with only 8 complex points in the indirect dimensions showed superior spectral resolution than FT-processed spectra. Practical aspects of obtaining optimal FDM-processed spectra are discussed. The results here demonstrate that FDM-processing can be used to obtain high-resolution 4D spectra on a medium sized RNA in a fraction of the acquisition time normally required for high-resolution, high-dimensional spectra.

SUBMITTER: Douglas JT

PROVIDER: S-EPMC2865554 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method.

Douglas Justin T JT Latham Michael P MP Armstrong Geoffrey S GS Bendiak Brad B Pardi Arthur A

Journal of biomolecular NMR 20080715 4

The NMR spectra of nucleic acids suffer from severe peak overlap, which complicates resonance assignments. 4D NMR experiments can overcome much of the degeneracy in 2D and 3D spectra; however, the linear increase in acquisition time with each new dimension makes it impractical to acquire high-resolution 4D spectra using standard Fourier transform (FT) techniques. The filter diagonalization method (FDM) is a numerically efficient algorithm that fits the entire multi-dimensional time-domain data t ...[more]

PMID: 18626775

Similar Datasets

Project description:Intraframe motion blurring, as a major challenge in free-breathing dynamic MRI, can be reduced if high temporal resolution can be achieved. To address this challenge, this work proposes a highly accelerated 4D (3D + time) dynamic MRI framework with subsecond temporal resolution that does not require explicit motion compensation. The method combines standard stack-of-stars golden-angle radial sampling and tailored GRASP-Pro (Golden-angle RAdial Sparse Parallel imaging with imProved performance) reconstruction. Specifically, 4D dynamic MRI acquisition is performed continuously without motion gating or sorting. The k-space centers in stack-of-stars radial data are organized to guide estimation of a temporal basis, with which GRASP-Pro reconstruction is employed to enforce joint low-rank subspace and sparsity constraints. This new basis estimation strategy is the new feature proposed for subspace-based reconstruction in this work to achieve high temporal resolution (e.g., subsecond/3D volume). It does not require sequence modification to acquire additional navigation data, it is compatible with commercially available stack-of-stars sequences, and it does not need an intermediate reconstruction step. The proposed 4D dynamic MRI approach was tested in abdominal motion phantom, free-breathing abdominal MRI, and dynamic contrast-enhanced MRI (DCE-MRI). Our results have shown that GRASP-Pro reconstruction with the new basis estimation strategy enables highly-accelerated 4D dynamic imaging at subsecond temporal resolution (with five spokes or less for each dynamic frame per image slice) for both free-breathing non-DCE-MRI and DCE-MRI. In the abdominal phantom, better image quality with lower root mean square error and higher structural similarity index was achieved using GRASP-Pro compared with standard GRASP. With the ability to acquire each 3D image in less than 1 s, intraframe respiratory blurring can be intrinsically reduced for body applications with our approach, which eliminates the need for explicit motion detection and motion compensation.

Project description:Four-dimensional (4D) computed tomography (CT) ventilation imaging is a novel promising technique for lung functional imaging. The current standard 4D CT technique using phase-based sorting frequently results in artifacts, which may deteriorate the accuracy of ventilation imaging. The purpose of this study was to quantify the variability of 4D CT ventilation imaging due to 4D CT sorting.4D CT image sets from nine lung cancer patients were each sorted by the phase-based method and anatomic similarity-based method, designed to reduce artifacts, with corresponding ventilation images created for each method. Artifacts in the resulting 4D CT images were quantified with the artifact score which was defined based on the difference between the normalized cross correlation for CT slices within a CT data segment and that for CT slices bordering the interface between adjacent CT data segments. The ventilation variation was quantified using voxel-based Spearman rank correlation coefficients for all lung voxels, and Dice similarity coefficients (DSC) for the spatial overlap of low-functional lung volumes. Furthermore, the correlations with matching single-photon emission CT (SPECT) ventilation images (assumed ground truth) were evaluated for three patients to investigate which sorting method provides higher physiologic accuracy.Anatomic similarity-based sorting reduced 4D CT artifacts compared to phase-based sorting (artifact score, 0.45 ± 0.14 vs 0.58 ± 0.24, p = 0.10 at peak-exhale; 0.63 ± 0.19 vs 0.71 ± 0.31, p = 0.25 at peak-inhale). The voxel-based correlation between the two ventilation images was 0.69 ± 0.26 on average, ranging from 0.03 to 0.85. The DSC was 0.71 ± 0.13 on average. Anatomic similarity-based sorting yielded significantly fewer lung voxels with paradoxical negative ventilation values than phase-based sorting (5.0 ± 2.6% vs 9.7 ± 8.4%, p = 0.05), and improved the correlation with SPECT ventilation regionally.The variability of 4D CT ventilation imaging due to 4D CT sorting was moderate overall and substantial in some cases, suggesting that 4D CT artifacts are an important source of variations in 4D CT ventilation imaging. Reduction of 4D CT artifacts provided more physiologically convincing and accurate ventilation estimates. Further studies are needed to confirm this result.

Dataset Information

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method.

Publications

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets