PUBLICATIONS
Zhou Z, Bai R*, Wang Z, Bryant H, Lang L, Merkle H, Munasinghe J, Tang L, Tang W, Tian R, Yu G, Ma Y, Niu G, Gao J, Chen X*
Williamson N, Ravin R, Benjamini D, Hellmut M, Falgairolle M, O’Donovan M, Blivis D. Bai R, Basser P* (2020)
Bai R1*, Wang B, Jia Y, Wang Z, Springer C, Li Z, Zhang Y, Liu Y* (2020)
Bai R1*, Li Z, Sun C, Hsu Y, Liang H, Basser P (2020) NeuroImage
Purpose: fMRI is widely used to study brain activity. Unfortunately, conventional fMRI methods assess neuronal activity only indirectly, through hemodynamic coupling. Here,we show that active, steady‐state transmembrane water cycling (AWC) could serve as a basis for a potential fMRI mechanism for direct neuronal activity detection.Methods: AWC and neuronal actitivity in rat organotypic cortical cultures were simultaneously measured with a hybrid MR‐fluorescence system. Perfusion with a paramagnetic MRI contrast agent, Gadoteridol, allows NMR determination of the kinetics of transcytolemmal water exchange. Changes in intracellular calcium concentration, [Cai2+] were used as a proxy of neuronal activity and were monitored by fluorescence imaging.Results: When we alter neuronal activity by titrating with extracellular [K+] near the normal value, we see an AWC response resembling Na+‐K+‐ATPase (NKA) Michaelis‐Menten behavior. When we treat with the voltage‐gated sodium channel inhibitor, or with an excitatory postsynaptic inhibitor cocktail, we see AWC decrease by up to 71%. AWC was found also to be positively correlated with the basal level of spontaneous activity, which varies in different cultures.
Ruiliang Bai1,4 | Charles S. Springer Jr.2 | Dietmar Plenz3 | Peter J. Basser4 Brain active transmembrane water cycling measured by MR is associated with neuronal activity.pdf
We present an algorithm to solve the two-dimensional Fredholm integral of the first kind with tensor product structure from a limited number of measurements, with the goal of using this method to speed up nuclear magnetic resonance spectroscopy. This is done by incorporating compressive sensing–type arguments to fill in missing measurements, using a priori knowledge of the structure of the data. In the first step we recover a compressed data matrix from measurements that form a tight frame, and establish that these measurements satisfy the restricted isometry property. Recovery can be done from as few as 10% of the total measurements. In the second and third steps, we solve the zeroth-order regularization minimization problem using the Venkataramanan–Song–H¨urlimann algorithm. We demonstrate the performance of this algorithm on simulated data and show that our approach is a realistic approach to speeding up the data acquisition.
A. Cloninger, W. Czaja, R. Bai, P.J. Basser, Solving 2D Fredholm integral from incomplete measurements using compressive sensing, SIAM J. Imaging Sci. 7 (2014) 1775–1798.
Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca2+ and Na+ Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na+ on the mobility of water molecules was practically undetectable. In contrast, addition of Ca2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced
R. Bai, P.J. Basser, R.M. Briber, F. Horkay, NMR water self-diffusion and relaxation studies on sodium polyacrylate solutions and gels in physiologic ionic solutions, J. Appl. Polym. Sci. 131 (2014) 1–7.
Measurement of the T2 distribution in tissues provides biologically relevant information about normal and abnormal microstructure and organization. Typically, the T2 distribution is obtained by fitting the magnitude MR images acquired by a multi-echo MRI pulse sequence using an inverse Laplace transform (ILT) algorithm. It is well known that the ideal magnitude MR signal follows a Rician distribution. Unfortunately, studies attempting to establish the validity and efficacy of the ILT algorithm assume that these input signals are Gaussian distributed. Violation of the normality (or Gaussian) assumption introduces unexpected artifacts, including spurious cerebrospinal fluid (CSF)-like long T2 components; bias of the true geometric mean T2 values and in the relative fractions of various components; and blurring of nearby T2 peaks in the T2 distribution. Here we apply and extend our previously proposed magnitude signal transformation framework to map noisy Rician-distributed magnitude multi-echo MRI signals into Gaussian-distributed signals with high accuracy and precision. We then perform an ILT on the transformed data to obtain an accurate T2 distribution. Additionally, we demonstrate, by simulations and experiments, that this approach corrects the aforementioned artifacts in magnitude multi-echo MR images over a large range of signal-to-noise ratios.
Bai R, Koay CG, Hutchinson E, and Basser PJ. (2014) A framework for accurate determination of the T2distribution from multiple echo magnitude MRI images. J Magn Reson. 244:53-63.
Recently, several new functional MRI contrast mechanisms including diffusion, phase imaging, proton density, etc.have been proposed to measure neuronal activity more directly and accurately than blood-oxygen-level dependent (BOLD) fMRI. However, these approaches have proved difficult to reproduce, mainly because of the dearth of reliable and robust test systems to vet and validate them. Here we describe the development and testing of such a test bed for non-BOLD fMRI. Organotypic cortical cultures were used as a stable and reproducible biological model of neuronal activity that shows spontaneous activity similar to that of in vivo brain cortex without any hemodynamic confounds. An open-access, single-sided magnetic resonance (MR) “profiler” consisting of four permanent magnets with magnetic field of 0.32 T was used in this study to perform MR acquisition. A fluorescence microscope with longworking distance objective was mounted on the top of a custom-designed chamber that keeps the organotypic culture vital, and the MR system was mounted on the bottom of the chamber to achieve real-time simultaneous calcium fluorescence optical imaging and MR acquisition on the same specimen. In this study, the reliability and performance of the proposed test bed were demonstrated by a conventional CPMG MR sequence acquired simultaneously with calcium imaging, which is a well-characterized measurement of neuronal activity. This experimental design will make it possible to correlate directly the other candidate functional MR signals to the optical indicia of neuronal activity in the future
Bai R, Klaus A, Bellay T, Stewart C, Pajevic S, Nevo U, Merkle H, Plenz D, and Basser PJ. 2015. Simultaneous calcium fluorescence imaging and MR of ex vivo organotypic cortical cultures: a new test bed for functional MRI. NMR Biomed 28(12):1726-38.
Potential applications of 2D relaxation spectrum NMR and MRI to characterize complex water dynamics (e.g., compartmental exchange) in biology and other disciplines have increased in recent years. However, the large amount of data and long MR acquisition times required for conventional 2D MR relaxometry limits its applicability for in vivo preclinical and clinical MRI. We present a new MR pipeline for 2D relaxometry that incorporates compressed sensing (CS) as a means to vastly reduce the amount of 2D relaxation data needed for material and tissue characterization without compromising data quality. Unlike the conventional CS reconstruction in the Fourier space (k-space), the proposed CS algorithm is directlyapplied onto the Laplace space (the joint 2D relaxation data) without compressing k-space to reduce the amount of data required for 2D relaxation spectra. This framework is validated using synthetic data, with NMR data acquired in a well-characterized urea/water phantom, and on fixed porcine spinal cord tissue. The quality of the CS-reconstructed spectra was comparable to that of the conventional 2D relaxation spectra, as assessed using global correlation, local contrast between peaks, peak amplitude and relaxation parameters, etc. This result brings this important type of contrast closer to being realized in preclinical, clinical, and other applications.
Bai R, Cloninger A, Czaja W, Basser PJ. 2015. Efficient 2D MRI relaxometry using compressed sensing. J Magn Reson. 255:88-99. PubMed