Michal E. Komlosh

From single-pulsed field gradient to double-pulsed field gradient MR: gleaning new microstructural information and developing new forms of contrast in MRI.

One of the hallmarks of diffusion NMR and MRI is its ability to utilize restricted diffusion to probe compartments much smaller than the excited volume or the MRI voxel, respectively, and to extract microstructural information from them. Single‐pulsed field gradient (s‐PFG) MR methodologies have been employed with great success to probe microstructures in various disciplines, ranging from chemistry to neuroscience. However, s‐PFG MR also suffers from inherent shortcomings, especially when specimens are characterized by orientation or size distributions: in such cases, the microstructural information available from s‐PFG experiments is limited or lost. Double‐pulsed field gradient (d‐PFG) MR methodology, an extension of s‐PFG MR, has attracted attention owing to recent theoretical studies predicting that it can overcome certain inherent limitations of s‐PFG MR. In this review, we survey the microstructural features that can be obtained from conventional s‐PFG methods in the different q regimes, and highlight its limitations. The experimental aspects of d‐PFG methodology are then presented, together with an overview of its theoretical underpinnings and a general framework for relating the MR signal decay and material microstructure, affording new microstructural parameters. We then discuss recent studies that have validated the theory using phantoms in which the ground truth is well known a priori, a crucial step prior to the application of d‐PFG methodology in neuronal tissue. The experimental findings are in excellent agreement with the theoretical predictions and reveal, inter alia, zero‐crossings of the signal decay, robustness towards size distributions and angular dependences of the signal decay from which accurate microstructural parameters, such as compartment size and even shape, can be extracted. Finally, we show some initial findings in d‐PFG MR imaging. This review lays the foundation for future studies, in which accurate and novel microstructural information could be extracted from complex biological specimens, eventually leading to new forms of contrast in MRI. Copyright

Observation of microscopic diffusion anisotropy in the spinal cord using double-pulsed gradient spin echo MRI

A double‐pulsed gradient spin echo (d‐PGSE) filtered MRI sequence is proposed to detect microscopic diffusion anisotropy in heterogeneous specimen. The technique was developed, in particular, to characterize local microscopic anisotropy in specimens that are macroscopically isotropic, such as gray matter. In such samples, diffusion tensor MRI (DTI) produces an isotropic or nearly isotropic diffusion tensor despite the fact that the medium may be anisotropic at a microscopic length scale. Using d‐PGSE filtered MRI, microscopic anisotropy was observed in a “gray matter” phantom consisting of randomly oriented tubes filled with water, as well as in fixed pig spinal cord, within a range of b‐values that can be readily achieved on clinical and small animal MR scanners. These findings suggest a potential use for this new contrast mechanism in clinical studies and biological research applications. Magn Reson Med 59:803–809, 2008.

Pore diameter mapping using double pulsed-field gradient MRI and its validation using a novel glass capillary array phantom

Double pulsed-field gradient (d-PFG) MRI can provide quantitative maps of microstructural quantities and features within porous media and tissues. We propose and describe a novel MRI phantom, consisting of wafers of highly ordered glass capillary arrays (GCA), and its use to validate and calibrate a d-PFG MRI method to measure and map the local pore diameter. Specifically, we employ d-PFG Spin-Echo Filtered MRI in conjunction with a recently introduced theoretical framework, to estimate a mean pore diameter in each voxel within the imaging volume. This simulation scheme accounts for all diffusion and imaging gradients within the diffusion weighted MRI (DWI) sequence, and admits the violation of the short gradient pulse approximation. These diameter maps agree well with pore sizes measured using both optical microscopy and single PFG diffusion diffraction NMR spectroscopy using the same phantom. Pixel-by-pixel analysis shows that the local pore diameter can be mapped precisely and accurately within a specimen using d-PFG MRI.

Mapping average axon diameters in porcine spinal cord white matter and rat corpus callosum using d-PFG MRI.

Knowledge of microstructural features of nerve fascicles, such as their axon diameter, is crucial for understanding normal function in the central and peripheral nervous systems as well as assessing changes due to pathologies. In this study double-pulsed field gradient (d-PFG) filtered MRI was used to map the average axon diameter (AAD) in porcine spinal cord, which was then compared to AADs measured with optical microscopy of the same specimen, as a way to further validate this new MRI method. A novel 3D d-PFG acquisition scheme was used to obtain AADs in each voxel of a coronal slice of rat brain corpus callosum. AAD measurements were also acquired using optical microscopy performed on histological sections and validated using a glass capillary array phantom.

Parsimonious Model Selection for Tissue Segmentation and Classification Applications: A Study Using Simulated and Experimental DTI Data

One aim of this work is to investigate the feasibility of using a hierarchy of models to describe diffusion tensor magnetic resonance (MR) data in fixed tissue. Parsimonious model selection criteria are used to choose among different models of diffusion within tissue. Using this information, we assess whether we can perform simultaneous tissue segmentation and classification. Both numerical phantoms and diffusion weighted imaging (DWI) data obtained from excised pig spinal cord are used to test and validate this model selection framework. Three hierarchical approaches are used for parsimonious model selection: the Schwarz criterion (SC), the F-test t-test (F-t), proposed by Hext, and the F-test F-test (F-F), adapted from Snedecor. The F-t approach is more robust than the others for selecting between isotropic and general anisotropic (full tensor) models. However, due to its high sensitivity to the variance estimate and bias in sorting eigenvalues, the F-F and SC are preferred for segmenting models with transverse isotropy (cylindrical symmetry). Additionally, the SC method is easier to implement than the F-t and F-F methods and has better performance. As such, this approach can be efficiently used for evaluating large MRI data sets. In addition, the proposed voxel-by-voxel segmentation framework is not susceptible to artifacts caused by the inhomogeneity of the variance in neighboring voxels with different degrees of anisotropy, which might contaminate segmentation results obtained with the techniques based on voxel averaging.

Solution NMR Structures of Productive and Non-productive Complexes between the A and B Domains of the Cytoplasmic Subunit of the Mannose Transporter of the Escherichia coli Phosphotransferase System.

Solution structures of complexes between the isolated A (IIAMan) and B (IIBMan) domains of the cytoplasmic component of the mannose transporter of Escherichia coli have been solved by NMR. The complex of wild-type IIAMan and IIBMan is a mixture of two species comprising a productive, phosphoryl transfer competent complex and a non-productive complex with the two active site histidines, His-10 of IIAMan and His-175 of IIBMan, separated by ∼25Å. Mutation of the active site histidine, His-10, of IIAMan to a glutamate, to mimic phosphorylation, results in the formation of a single productive complex. The apparent equilibrium dissociation constants for the binding of both wild-type and H10E IIAMan to IIBMan are approximately the same (KD ∼ 0.5 mm). The productive complex can readily accommodate a transition state involving a pentacoordinate phosphoryl group with trigonal bipyramidal geometry bonded to the Nϵ2 atom of His-10 of IIAMan and the Nδ1 atom of His-175 of IIBMan with negligible (<0.2Å) local backbone conformational changes in the immediate vicinity of the active site. The non-productive complex is related to the productive one by a ∼90° rotation and ∼37Å translation of IIBMan relative to IIAMan, leaving the active site His-175 of IIBMan fully exposed to solvent in the non-productive complex. The interaction surface on IIAMan for the non-productive complex comprises a subset of residues used in the productive complex and in both cases involves both subunits of IIAMan. The selection of the productive complex by IIAMan(H10E) can be attributed to neutralization of the positively charged Arg-172 of IIBMan at the center of the interface. The non-productive IIAMan-IIBMan complex may possibly be relevant to subsequent phosphoryl transfer from His-175 of IIBMan to the incoming sugar located on the transmembrane IICMan-IIDMan complex.

A system and mathematical framework to model shear flow effects in biomedical DW‐imaging and spectroscopy

The pulsed‐field gradient (PFG) MR experiment enables one to measure particle displacements, velocities, and even higher moments of complex fluid motions. In diffusion‐weighted MRI (DWI) in living tissue, where the PFG MRI experiment is used to measure diffusion, Brownian motion is assumed to dominate the displacements causing the observed signal loss. However, motions of water molecules caused by various active biological processes occurring at different length and time scales may also cause additional dephasing of magnetization and signal loss. To help understand their relative effects on the DWI signal attenuation, we used an integrated experimental and theoretical framework: a Rheo‐NMR, which served as an experimental model system to precisely prescribe a microscopic velocity distribution; and a mathematical model that relates the DW signal intensity in the Rheo‐NMR to experimental parameters that characterize the impressed velocity field. A technical innovation reported here is our use of ‘natural’ (in this case, polar) coordinates both to simplify the description the fluid motion within the Couette cell of the Rheo‐NMR, as well as to acquire and reconstruct magnitude and phase MR images obtained within it. We use this integrated model system to demonstrate how shear flows appears as pseudo‐diffusion in magnitude DW MR signals obtained using PFG spin‐echo (PGSE) NMR and MRI sequences. Our results lead us to reinterpret the possible causes of signal loss in DWI in vivo, in particular to revise and generalize the previous notion of intra‐voxel incoherent motion (IVIM) in order to describe activity driven flows that appear as pseudo‐diffusion over multiple length and time scales in living tissues. Copyright

White matter microstructure from nonparametric axon diameter distribution mapping

We report the development of a double diffusion encoding (DDE) MRI method to estimate and map the axon diameter distribution (ADD) within an imaging volume. A variety of biological processes, ranging from development to disease and trauma, may lead to changes in the ADD in the central and peripheral nervous systems. Unlike previously proposed methods, this ADD experimental design and estimation framework employs a more general, nonparametric approach, without a priori assumptions about the underlying form of the ADD, making it suitable to analyze abnormal tissue. In the current study, this framework was used on an ex vivo ferret spinal cord, while emphasizing the way in which the ADD can be weighted by either the number or the volume of the axons. The different weightings, which result in different spatial contrasts, were considered throughout this work. DDE data were analyzed to derive spatially resolved maps of average axon diameter, ADD variance, and extra-axonal volume fraction, along with a novel sub-micron restricted structures map. The morphological information contained in these maps was then used to segment white matter into distinct domains by using a proposed k-means clustering algorithm with spatial contiguity and left-right symmetry constraints, resulting in identifiable white matter tracks. The method was validated by comparing histological measures to the estimated ADDs using a quantitative similarity metric, resulting in good agreement. With further acquisition acceleration and experimental parameters adjustments, this ADD estimation framework could be first used preclinically, and eventually clinically, enabling a wide range of neuroimaging applications for improved understanding of neurodegenerative pathologies and assessing microstructural changes resulting from trauma.

Double pulsed field gradient (double-PFG) MR imaging (MRI) as a means to measure the size of plant cells†

Measurement of diffusion in porous materials and biological tissues with the pulsed field gradient (PFG) MR techniques has proven useful in characterizing the microstructure of such specimens noninvasively. A natural extension of the traditional PFG technique comprises multiple pairs of diffusion gradients. This approach has been shown to provide the ability to characterize anisotropy at different length scales without the need to employ very strong gradients. In this work, the double‐PFG imaging technique was used on a specimen involving a series of glass capillary arrays with different diameters. The experiments on the phantom demonstrated the ability to create a quantitative and accurate map of pore sizes. The same technique was subsequently employed to image a celery stalk. A diffusion tensor image (DTI) of the same specimen was instrumental in accurately delineating the regions of vascular tissue and determining the local orientation of cells. This orientation information was incorporated into a theoretical double‐PFG framework and the technique was employed to estimate the cell size in the vascular bundles of the celery stalk. The findings suggest that the double‐PFG MRI framework could provide important new information regarding the microstructure of many plants and other food products. Copyright

Characterization and mapping of dipolar interactions within macromolecules in tissues using a combination of DQF, MT and UTE MRI

This study shows that by combining a double‐quantum filtered magnetization transfer (DQF‐MT) with an ultra‐short TE (UTE) MRI that it is possible to obtain contrast between tissue compartments based on the following characteristics: (a) the residual dipolar coupling interaction within the biomacromolecules, which depends on their structure, (b) residual dipolar interactions within water molecules, and (c) the magnetization exchange rate between biomacromolecules and water. The technique is demonstrated in rat‐tail specimens, where the collagenous tissue such as tendons and the annulus pulposus of the disc are highlighted in these images, and their macromolecular properties along with those of bones and muscles can be characterized. DQF‐MT UTE MRI also holds promise because collagenous tissues that are typically invisible in conventional MRI experiments produce significant signal intensities using this approach. Copyright