High-sensitivity CEST mapping using a spatiotemporal correlation-enhanced method.
Ontology highlight
ABSTRACT: Purpose
To obtain high-sensitivity CEST maps by exploiting the spatiotemporal correlation between CEST images.Methods
A postprocessing method accomplished by multilinear singular value decomposition (MLSVD) was used to enhance the CEST SNR by exploiting the correlation between the Z-spectrum for each voxel and the low-rank property of the overall CEST data. The performance of this method was evaluated using CrCEST in ischemic mouse brain at 11.7 tesla. Then, MLSVD CEST was applied to obtain Cr, amide, and amine CEST maps of the ischemic mouse brain to demonstrate its general applications.Results
Complex-valued Gaussian noise was added to CEST k-space data to mimic a low SNR situation. MLSVD CEST analysis was able to suppress the noise, recover the degraded CEST peak, and provide better CrCEST quality compared to the smoothing and singular value decomposition (SVD)-based denoising methods. High-resolution Cr, amide, and amine CEST maps of an ischemic stroke using MLSVD CEST suggest that CrCEST is also a sensitive pH mapping method, and a wide range of pH changes can be detected by combing CrCEST with amine CEST at high magnetic fields.Conclusion
MLSVD CEST provides a simple and efficient way to improve the SNR of CEST images.
SUBMITTER: Chen L
PROVIDER: S-EPMC7722217 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Deoxycytidine kinase (DCK) is a key enzyme for the activation of a broad spectrum of nucleoside-based chemotherapy drugs (e.g., gemcitabine); low DCK activity is one of the most important causes of cancer drug-resistance. Noninvasive imaging methods that can quantify DCK activity are invaluable for assessing tumor resistance and predicting treatment efficacy. Here we developed a "natural" MRI approach to detect DCK activity using its natural substrate deoxycytidine (dC) as the imaging probe, which can be detected directly by chemical exchange saturation transfer (CEST) MRI without any synthetic labeling. CEST MRI contrast of dC and its phosphorylated form, dCTP, successfully discriminated DCK activity in two mouse leukemia cell lines with different DCK expression. This dC-enhanced CEST MRI in xenograft leukemic cancer mouse models demonstrated that DCK(+) tumors have a distinctive dynamic CEST contrast enhancement and a significantly higher CEST contrast than DCK(-) tumors (AUC0-60 min = 0.47 ± 0.25 and 0.20 ± 0.13, respectively; P = 0.026, paired Student t test, n = 4) at 1 hour after the injection of dC. dC-enhanced CEST contrast also correlated well with tumor responses to gemcitabine treatment. This study demonstrates a novel MR molecular imaging approach for predicting cancer resistance using natural, nonradioactive, nonmetallic, and clinically available agents. This method has great potential for pursuing personalized chemotherapy by stratifying patients with different DCK activity. SIGNIFICANCE: A new molecular MRI method that detects deoxycytidine kinase activity using its natural substrate deoxycytidine has great translational potential for clinical assessment of tumor resistance and prediction of treatment efficacy.
| S-EPMC6522309 | biostudies-literature
Project description:Chemical exchange saturation transfer MRI is a promising new technique for cellular and molecular imaging. This contrast allows the detection of tumors and ischemia without the use of gadolinium as well as the design of microenvironment-sensitive probes that can be discriminated based on their exchange contrast properties and saturation frequency. Current acquisition schemes to detect and analyze this contrast suffer from sensitivity to spatial B0 inhomogeneity and low contrast-to-noise-ratio, which is an obstacle to widespread adoption of the technology. A new method to detect chemical exchange saturation transfer contrast is proposed here, termed "length and offset varied saturation" which acquires a set of images with the saturation parameters varied so as to modulate the exchange contrast. Either fast fourier transform or the general linear model can be employed to decompose the modulation patterns into separate sources of water signal loss. After transformation, a length and offset varied saturation phase map is generated, which is insensitive to B0 inhomogeneity. When collected on live mice bearing 9L gliosarcomas, and compared to the conventional asymmetry in the magnetization transfer ratio map using offset increment correction, the results show that length and offset varied saturation phase mapping obtains about three to four times contrast-to-noise-ratio and exhibits less B0 artifacts.
| S-EPMC3336046 | biostudies-literature
Project description:Biomolecules undergo motions on the micro-to-millisecond timescale to adopt low-populated transient states that play important roles in folding, recognition, and catalysis. NMR techniques, such as Carr-Purcell-Meiboom-Gill (CPMG), chemical exchange saturation transfer (CEST), and R1ρ are the most commonly used methods for characterizing such transitions at atomic resolution under solution conditions. CPMG and CEST are most effective at characterizing motions on the millisecond timescale. While some implementations of the R1ρ experiment are more broadly sensitive to motions on the micro-to-millisecond timescale, they entail the use of selective irradiation schemes and inefficient 1D data acquisition methods. Herein, we show that high-power radio-frequency fields can be used in CEST experiments to extend the sensitivity to faster motions on the micro-to-millisecond timescale. Given the ease of implementing high-power fields in CEST, this should make it easier to characterize micro-to-millisecond dynamics in biomolecules.
| S-EPMC7857695 | biostudies-literature
Project description:Transcatheter aortic valve replacement (TAVR) is a safe and effective treatment option for patients deemed at high and intermediate risk for surgical aortic valve replacement. Similar to surgical aortic valves (SAVs), transcatheter aortic valves (TAVs) undergo calcification and mechanical wear over time. However, to date, there have been limited publications on the long-term durability of TAV devices. To assess longevity and mechanical strength of TAVs in comparison to surgical bioprosthetic valves, three-dimensional deformation analysis and strain measurement of the leaflets become an inevitable part of the evaluation. The goal of this study was to measure and compare leaflet displacement and strain of two commonly used TAVs in a side-by-side comparison with a commonly used SAV using a high-resolution digital image correlation (DIC) system. 26-mm Edwards SAPIEN 3, 26-mm Medtronic CoreValve, and 25-mm Carpentier-Edwards PERIMOUNT Magna surgical bioprosthesis were examined in a custom-made valve testing apparatus. A time-varying, spatially uniform pressure was applied to the leaflets at different loading rates. GOM ARAMIS® software was used to map leaflet displacement and strain fields during loading and unloading. High displacement regions were found to be at the leaflet belly region of the three bioprosthetic valves. In addition, the frame of the surgical bioprosthesis was found to be remarkably flexible, in contrary to CoreValve and SAPIEN 3 in which the stent was nearly rigid under a similar loading condition. The experimental DIC measurements can be used to characterize the anisotropic materiel behavior of the bioprosthetic heart valve leaflets and validate heart valve computational simulations.
| S-EPMC9910203 | biostudies-literature
Project description:Despite major advances in next-generation sequencing, assembly of sequencing data, especially data from novel microorganisms or re-emerging pathogens, remains constrained by the lack of suitable reference sequences. De novo assembly is the best approach to achieve an accurate finished sequence, but multiple sequencing platforms or paired-end libraries are often required to achieve full genome coverage. In this study, we demonstrated a method to assemble complete bacterial genome sequences by integrating shotgun Roche 454 pyrosequencing with optical whole genome mapping (WGM). The whole genome restriction map (WGRM) was used as the reference to scaffold de novo assembled sequence contigs through a stepwise process. Large de novo contigs were placed in the correct order and orientation through alignment to the WGRM. De novo contigs that were not aligned to WGRM were merged into scaffolds using contig branching structure information. These extended scaffolds were then aligned to the WGRM to identify the overlaps to be eliminated and the gaps and mismatches to be resolved with unused contigs. The process was repeated until a sequence with full coverage and alignment with the whole genome map was achieved. Using this method we were able to achieved 100% WGRM coverage without a paired-end library. We assembled complete sequences for three distinct genetic components of a clinical isolate of Providencia stuartii: a bacterial chromosome, a novel bla NDM-1 plasmid, and a novel bacteriophage, without separately purifying them to homogeneity.
| S-EPMC3629165 | biostudies-literature
Project description:PurposeTo explore the impact of temporal motion-induced coil sensitivity changes on CEST-MRI at 7T and its correction using interleaved volumetric EPI navigators, which are applied for real-time motion correction.MethodsFive healthy volunteers were scanned via CEST. A 4-fold correction pipeline allowed the mitigation of (1) motion, (2) motion-induced coil sensitivity variations, ΔB1- , (3) motion-induced static magnetic field inhomogeneities, ΔB0 , and (4) spatially varying transmit RF field fluctuations, ΔB1+ . Four CEST measurements were performed per session. For the first 2, motion correction was turned OFF and then ON in absence of voluntary motion, whereas in the other 2 controlled head rotations were performed. During post-processing ΔB1- was removed additionally for the motion-corrected cases, resulting in a total of 6 scenarios to be compared. In all cases, retrospective ∆B0 and - ΔB1+ corrections were performed to compute artifact-free magnetization transfer ratio maps with asymmetric analysis (MTRasym ).ResultsDynamic ΔB1- correction successfully mitigated signal deviations caused by head motion. In 2 frontal lobe regions of volunteer 4, induced relative signal errors of 10.9% and 3.9% were reduced to 1.1% and 1.0% after correction. In the right frontal lobe, the motion-corrected MTRasym contrast deviated 0.92%, 1.21%, and 2.97% relative to the static case for Δω = 1, 2, 3 ± 0.25 ppm. The additional application of ΔB1- correction reduced these deviations to 0.10%, 0.14%, and 0.42%. The fully corrected MTRasym values were highly consistent between measurements with and without intended head rotations.ConclusionTemporal ΔB1- cause significant CEST quantification bias. The presented correction pipeline including the proposed retrospective ΔB1- correction significantly reduced motion-related artifacts on CEST-MRI.
| S-EPMC7839562 | biostudies-literature
Project description:The aim of this work is to develop a data-driven quantitative dynamic contrast-enhanced (DCE) MRI technique using Golden-angle RAdial Sparse Parallel (GRASP) MRI with high spatial resolution and high flexible temporal resolution and pharmacokinetic (PK) analysis with an arterial input function (AIF) estimated directly from the data obtained from each patient. DCE-MRI was performed on 13 patients with gynecological malignancy using a 3-T MRI scanner with a single continuous golden-angle stack-of-stars acquisition and image reconstruction with two temporal resolutions, by exploiting a unique feature in GRASP that reconstructs acquired data with user-defined temporal resolution. Joint estimation of the AIF (both AIF shape and delay) and PK parameters was performed with an iterative algorithm that alternates between AIF and PK estimation. Computer simulations were performed to determine the accuracy (expressed as percentage error [PE]) and precision of the estimated parameters. PK parameters (volume transfer constant [Ktrans ], fractional volume of the extravascular extracellular space [ve ], and blood plasma volume fraction [vp ]) and normalized root-mean-square error [nRMSE] (%) of the fitting errors for the tumor contrast kinetic data were measured both with population-averaged and data-driven AIFs. On patient data, the Wilcoxon signed-rank test was performed to compare nRMSE. Simulations demonstrated that GRASP image reconstruction with a temporal resolution of 1 s/frame for AIF estimation and 5 s/frame for PK analysis resulted in an absolute PE of less than 5% in the estimation of Ktrans and ve , and less than 11% in the estimation of vp . The nRMSE (mean ± SD) for the dual temporal resolution image reconstruction and data-driven AIF was 0.16 ± 0.04 compared with 0.27 ± 0.10 (p < 0.001) with 1 s/frame using population-averaged AIF, and 0.23 ± 0.07 with 5 s/frame using population-averaged AIF (p < 0.001). We conclude that DCE-MRI data acquired and reconstructed with the GRASP technique at dual temporal resolution can successfully be applied to jointly estimate the AIF and PK parameters from a single acquisition resulting in data-driven AIFs and voxelwise PK parametric maps.
| S-EPMC9203940 | biostudies-literature
Project description:PurposeTo extend the pH detection range of iopamidol-based ratiometric chemical exchange saturation transfer (CEST) MRI at sub-high magnetic field and establish quantitative renal pH MRI.MethodsChemical exchange saturation transfer imaging was performed on iopamidol phantoms with pH of 5.5 to 8.0 and in vivo on rat kidneys (n = 5) during iopamidol administration at a 4.7 T. Iopamidol CEST effects were described using a multipool Lorentzian model. A generalized ratiometric analysis was conducted by ratioing resolved iopamidol CEST effects at 4.3 and 5.5 ppm obtained under 1.0 and 2.0 µT, respectively. The pH detection range was established for both the standard ratiometric analysis and the proposed resolved approach. Renal pH was mapped in vivo with regional pH assessed by one-way analysis of variance.ResultsGood-fitting performance was observed in multipool Lorentzian resolving of CEST effects (R2 s > 0.99). The proposed approach extends the in vitro pH detection range to 5.5 to 7.5 at 4.7 T. In vivo renal pH was measured to be 7.0 ± 0.1, 6.8 ± 0.1, and 6.5 ± 0.2 for cortex, medulla and calyx, respectively (P < 0.05).ConclusionsThe proposed ratiometric approach extended the iopamidol pH detection range, enabling the renal pH mapping in vivo, which is promising for pH imaging studies at sub-high or low fields with potential clinical applicability. Magn Reson Med 79:1553-1558, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
| S-EPMC5756701 | biostudies-literature
Project description:Tomato (Solanum lycopersicum) is an established model for studying fruit biology; however, most studies of tomato fruit growth and ripening are based on homogenized pericarp, and do not consider the internal tissues, or the expression signatures of individual cell and tissue types. We present a spatiotemporally resolved transcriptome analysis of tomato fruit ontogeny, using laser microdissection (LM) or hand dissection coupled with RNA-Seq analysis. Regulatory and structural gene networks, including families of transcription factors and hormone synthesis and signaling pathways, are defined across tissue and developmental spectra. The ripening program is revealed as comprising gradients of gene expression, initiating in internal tissues then radiating outward, and basipetally along a latitudinal axis. We also identify spatial variations in the patterns of epigenetic control superimposed on ripening gradients. Functional studies elucidate previously masked regulatory phenomena and relationships, including those associated with fruit quality traits, such as texture, color, aroma, and metabolite profiles.
| S-EPMC5785480 | biostudies-literature
Project description:Malaria is a serious threat to global health, with over [Formula: see text] of the cases reported in 2020 by the World Health Organization in African countries, including Sudan. Sudan is a low-income country with a limited healthcare system and a substantial burden of malaria. The epidemiology of malaria in Sudan is rapidly changing due to factors including the rapidly developing resistance to drugs and insecticides among the parasites and vectors, respectively; the growing population living in humanitarian settings due to political instability; and the recent emergence of Anopheles stephensi in the country. These factors contribute to changes in the distribution of the parasites species as well as malaria vectors in Sudan, and the shifting patterns of malaria epidemiology underscore the need for investment in improved situational awareness, early preparedness, and a national prevention and control strategy that is updated, evidence based, and proactive. A key component of this strategy is accurate, high-resolution endemicity maps of species-specific malaria. Here, we present a spatiotemporal Bayesian model, developed in collaboration with the Sudanese Ministry of Health, that predicts a fine-scale (1 km [Formula: see text] 1 km) clinical incidence and seasonality profiles for Plasmodium falciparum and Plasmodium vivax across the country. We use monthly malaria case counts for both species collected via routine surveillance between January 2017 and December 2019, as well as a suite of high-resolution environmental covariates to inform our predictions. These epidemiological maps provide a useful resource for strategic planning and cost-effective implementation of malaria interventions, thus informing policymakers in Sudan to achieve success in malaria control and elimination.
| S-EPMC9387890 | biostudies-literature