Biology subjects

Keil, B.

Publications and source records attributed to Keil, B..

14 recordsLinked to original sources

bioRxiv2026

Multi-dimensional diffusion MRI at ultra-high gradient strength for mapping axonal architecture and microstructure in the primate brain

We present the most comprehensive sampling of the macaque and human brain with diffusion MRI to date. As part of the BRAIN CONNECTS center for Large-scale Imaging of Neural Circuits, we leverage ultra-high-gradient MRI systems, including the first-of-its-kind Connectome 2.0, for post-mortem acquisitions. Each sample is imaged for [~]250 hours at multiple spatial resolutions down to 0.25 mm isotropic for whole macaque brains and 0.4 mm isotropic for human hemispheres. Our optimized protocols allow us to sample both species across [~]50 diffusion shells varying in b-value, diffusion time, and echo time, reaching ultra-high b-values up to 64000 s/mm2 with high signal-to-noise ratio. We demonstrate that these multi-dimensional data resolve not only white matter connectional architecture but also cortical and subcortical cytoarchitectonic boundaries, at a level of detail previously inaccessible in whole-brain noninvasive imaging. As such, these data are an important resource for both technical development and basic and clinical neuroscience.

neuroscience↗

bioRxiv2025

How infant brains fold: Sulcal deepening is linked to development of sulcal span, thickness, curvature, and microstructure

Cortical folding begins in utero as sulci emerge and continues postnatally as sulci deepen. However, the timeline and mechanisms underlying postnatal sulcal development remain unknown. Using structural and quantitative magnetic resonance imaging in infants from birth to one year of age, we longitudinally measured macroanatomical and microstructural development in major sulci that emerge in utero between the 16th and 31st gestational weeks. We find that sulci that emerge earlier in utero are deeper at birth and deepen at a slower rate postnatally than later emerging sulci. Sulci also become wider, thicker, and microstructurally denser, while their curvature decreases. Notably, mean sulcal depth is predicted by a weighted sum of sulcal span, thickness, curvature, and tissue microstructure, with differential weights across sulci. Analysis of local depth along the sulcus also reveals that deeper portions of sulci (fundi) have higher curvature and higher microstructural density than the surrounding sulcal walls. These data reveal that postnatal sulcal deepening is nonuniform and depends on the time of emergence in utero, tissue microstructure, and multiple macroanatomical factors. Together, these findings have important ramifications for theories of cortical folding and elucidating neurodevelopmental disorders and delays.

neuroscience↗

bioRxiv2024

White matter connections of human ventral temporal cortex are organized by cytoarchitecture, eccentricity, and category-selectivity from birth

Category-selective regions in ventral temporal cortex (VTC) have a consistent anatomical organization, which is hypothesized to be scaffolded by white matter connections. However, it is unknown how white matter connections are organized from birth. Here, we scanned newborn to 6-month-old infants and adults to determine the organization of the white matter connections of VTC. We find that white matter connections are organized by cytoarchitecture, eccentricity, and category from birth. Connectivity profiles of functional regions in the same cytoarchitectonic area are similar from birth and develop in parallel, with decreases in endpoint connectivity to lateral occipital, and parietal, and somatosensory cortex, and increases to lateral prefrontal cortex. Additionally, connections between VTC and early visual cortex are organized topographically by eccentricity bands and predict eccentricity biases in VTC. These data show that there are both innate organizing principles of white matter connections of VTC, and the capacity for white matter connections to change over development.

neuroscience↗

bioRxiv2024

DEAD-box ATPase Dbp2 mediates mRNA release after 3'-end formation

mRNA biogenesis in the eukaryotic nucleus is a highly complex process. The numerous RNA processing steps are tightly coordinated to ensure that only fully processed transcripts are released from chromatin for export from the nucleus. Here, we present the hypothesis that fission yeast Dbp2, a ribonucleoprotein complex (RNP) remodelling ATPase of the DEAD-box family, is the key enzyme in an RNP assembly checkpoint at the 3-end of genes. We show that Dbp2 interacts with the cleavage and polyadenylation complex (CPAC) and localizes to cleavage bodies, which are enriched for 3-end processing factors and proteins involved in nuclear RNA surveillance. Upon loss of Dbp2, 3-processed, polyadenylated RNAs accumulate on chromatin and in cleavage bodies, and CPAC components are depleted from the soluble pool. Under these conditions, cells display an increased likelihood to skip polyadenylation sites and a delayed transcription termination, suggesting that levels of free CPAC components are insufficient to maintain normal levels of 3-end processing. Our data support a model in which Dbp2 is the active component of an mRNP remodelling checkpoint that licenses RNA export and is coupled to CPAC release.

molecular biology↗

bioRxiv2023

Eddy current-induced artifacts correction in high gradient strength diffusion MRI with dynamic field monitoring: demonstration in ex vivo human brain imaging

PurposeTo demonstrate the advantages of spatiotemporal magnetic field monitoring to correct eddy current-induced artifacts (ghosting and geometric distortions) in high gradient strength diffusion MRI (dMRI). MethodsA dynamic field camera with 16 NMR field probes was used to characterize eddy current fields induced from diffusion gradients for different gradients strengths (up to 300 mT/m), diffusion directions, and shots in a 3D multi-shot EPI sequence on a 3T Connectom scanner. The efficacy of dynamic field monitoring-based image reconstruction was demonstrated on high-resolution whole brain ex vivo dMRI. A 3D multi-shot image reconstruction framework was informed with the actual nonlinear phase evolution measured with the dynamic field camera, thereby accounting for high-order eddy currents fields on top of the image encoding gradients in the image formation model. ResultsEddy current fields from diffusion gradients at high gradient strength in a 3T Connectom scanner are highly nonlinear in space and time, inducing high-order spatial phase modulations between odd/even echoes and shots that are not static during the readout. Superior reduction of ghosting and geometric distortion was achieved with dynamic field monitoring compared to ghosting approaches such as navigator- and structured low-rank-based methods or MUSE, followed by image-based distortion correction with eddy. Improved dMRI analysis is demonstrated with diffusion tensor imaging and high-angular resolution diffusion imaging. ConclusionStrong eddy current artifacts characteristic of high gradient strength dMRI can be well corrected with dynamic field monitoring-based image reconstruction, unlike the two-step approach consisting of ghosting correction followed by geometric distortion reduction with eddy.

bioengineering↗

bioRxiv2023

8-channel Tx dipole and 20-channel Rx loop coil array for MRI of the cervical spinal cord at 7 Tesla

The quality of cervical spinal cord images can be improved by the use of tailored radiofrequency coil solutions for ultra-high field imaging; however, very few commercial and research 7 Tesla radiofrequency coils currently exist for the spinal cord, and in particular those with parallel transmit capabilities. This work presents the design, testing and validation of a pTx/Rx coil for the human neck and cervical/upper-thoracic spinal cord. The pTx portion is composed of 8 dipoles to ensure high homogeneity over this large region of the spinal cord. The Rx portion is made of 20 semi-adaptable overlapping loops to produce high Signal-to-noise ratio (SNR) across the patient population. The coil housing is designed to facilitate patient positioning and comfort, while being tight fitting to ensure high sensitivity. We demonstrate RF shimming capabilities to optimize B1+ uniformity, power efficiency and/or specific absorption rate (SAR) efficiency. B1+ homogeneity, SNR and g-factor was evaluated in adult volunteers and demonstrated excellent performance from the occipital lobe down to the T4-T5 level. We compared the proposed coil with two state-of-the-art head and head/neck coils, confirming its superiority in the cervical and upper-thoracic regions of the spinal cord. This coil solution therefore provides a convincing platform for producing the high image quality necessary for clinical and research scanning of the upper spinal cord.

bioengineering↗

bioRxiv2022

Effect of field strength on RF power deposition near conductive leads: A simulation study of SAR in DBS lead models during MRI at 1.5 T - 10.5 T

BackgroundSince the advent of magnetic resonance imaging (MRI) nearly four decades ago, there has been a quest for ever-higher magnetic field strengths. Strong incentives exist to do so, as increasing the magnetic field strength increases the signal-to-noise ratio of images. However, ensuring patient safety becomes more challenging at high and ultrahigh field MRI (i.e., [≥]3 T) compared to lower fields. The problem is exacerbated for patients with conductive implants, such as those with deep brain stimulation (DBS) devices, as excessive local heating can occur around implanted lead tips. Despite extensive effort to assess radio frequency (RF) heating of implants during MRI at 1.5 T, a comparative study that systematically examines the effects of field strength and various exposure limits on RF heating is missing. PurposeThis study aims to perform numerical simulations that systematically compare RF power deposition near DBS lead models during MRI at common clinical and ultra-high field strengths, namely 1.5, 3, 7, and 10.5 T. Furthermore, we assess the effects of different exposure constraints on RF power deposition by imposing limits on either the B1+ or global head specific absorption rate (SAR) as these two exposure limits commonly appear in MRI guidelines. MethodsWe created 33 unique DBS lead models based on postoperative computed tomography (CT) images of patients with implanted DBS devices and performed electromagnetic simulations to evaluate the SAR of RF energy in the tissue surrounding lead tips during RF exposure at frequencies ranging from 64 MHz (1.5 T) to 447 MHz (10.5 T). The RF exposure was implemented via realistic MRI RF coil models created based on physical prototypes built in our institutions. We systematically examined the distribution of local SAR at different frequencies with the input coil power adjusted to either limit the B1+ or the global head SAR. ResultsThe MRI RF coils at higher resonant frequencies generated lower SARs around the lead tips when the global head SAR was constrained. The trend was reversed when the constraint was imposed on B1+. ConclusionAt higher static fields, MRI is not necessarily more dangerous than at lower fields for patients with conductive leads. Specifically, when a conservative safety criterion, such as constraints on the global SAR, is imposed, coils at a higher resonant frequency tend to generate a lower local SAR around implanted leads due to the decreased B1+ and, by proxy, E field levels.

biophysics↗

bioRxiv2021

High-fidelity, high-spatial-resolution diffusion MRI of the ex-vivo whole human brain on the 3T Connectom scanner using structured low-rank EPI ghost correction

Diffusion MRI (dMRI) of whole, intact, fixed postmortem human brain at high spatial resolution serves as key bridging technology for 3D mapping of structural connectivity and tissue microstructure at the mesoscopic scale. Ex vivo dMRI offers superior spatial resolution compared to in vivo dMRI but comes with its own technical challenges due to the significantly reduced T2 relaxation times and decreased diffusivity incurred by tissue fixation. The altered physical properties of fixed tissue necessitate the use of alternative acquisition strategies to preserve SNR and achieve sufficient diffusion weighting. Multi-shot or segmented 3D echo planar imaging (EPI) sequences have been used to shorten echo times (TEs) with reduced distortions from field inhomogeneity and eddy currents on small-bore MR scanners and have been adopted for high b-value dMRI of ex vivo whole human brain specimens. The advent of stronger gradients on human MRI scanners has led to improved image quality and a wider range of diffusion-encoding parameters for dMRI but at the cost of more severe eddy currents that result in spatial and temporal variations in the background magnetic field, which cannot be corrected for using standard vendor-provided ghost correction solutions. In this work, we show that conventional ghost correction techniques based on navigators and linear phase correction may be insufficient for EPI sequences using strong diffusion-sensitizing gradients in ex vivo dMRI experiments, resulting in orientationally biased dMRI estimates. This previously unreported problem is a critical roadblock in any effort to leverage scanners with ultra-high gradients for high-precision mapping of human neuroanatomy at the mesoscopic scale. We propose an advanced reconstruction method based on structured low-rank matrix modeling that reduces the ghosting substantially. We show that this method leads to more accurate and reliable dMRI metrics, as exemplified by diffusion tensor imaging and high angular diffusion imaging analyses in distributed neuroanatomical areas of fixed whole human brain specimens. Our findings advocate for the use of advanced reconstruction techniques for recovering unbiased metrics from ex vivo dMRI acquisitions and represent a crucial step toward making full use of strong diffusion-encoding gradients for neuroscientific studies seeking to study brain structure at multiple spatial scales.

neuroscience↗

bioRxiv2021

A 48-Channel Receive Array Coil for Mesoscopic Diffusion-Weighted MRI of Human ex vivo Brain Imaging on the 3T Connectome Scanner

In vivo diffusion-weighted magnetic resonance imaging is limited in signal-to-noise-ratio (SNR) and acquisition time, which constrains spatial resolution to the macroscale regime. Ex vivo imaging, which allows for arbitrarily long scan times, is critical for exploring human brain structure in the mesoscale regime without loss of SNR. Standard head array coils designed for patients are sub-optimal for imaging ex vivo whole brain specimens. The goal of this work was to design and construct a 48-channel ex vivo whole brain array coil for high-resolution and high b-value diffusion-weighted imaging on a 3T Connectome scanner. The coil was validated with bench measurements and characterized by imaging metrics on an agar brain phantom and an ex vivo human brain sample. The two-segment coil former was constructed for a close fit to a whole human brain, with small receive elements distributed over the entire brain. Imaging tests including SNR and G-factor maps were compared to a 64-channel head coil designed for in vivo use. There was a 2.9-fold increase in SNR in the peripheral cortex and a 1.3-fold gain in the center when compared to the 64-ch head coil. The 48-channel ex vivo whole brain coil also decreases noise amplification in highly parallel imaging, allowing acceleration factors of approximately one unit higher for a given noise amplification level. The acquired diffusion-weighted images in a whole ex vivo brain specimen demonstrate the applicability of the developed coil for high-resolution and high b-value diffusion-weighted ex vivo brain MRI studies.

bioengineering↗

bioRxiv2020

Ultra-high field (7T) functional magnetic resonance imaging in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of the central nervous system that results in a progressive loss of motor function and ultimately death. It is critical, yet also challenging, to develop non-invasive biomarkers to identify, localize, measure and/or track biological mechanisms implicated in ALS. Such biomarkers may also provide clues to identify potential molecular targets for future therapeutic trials. Herein we report on a pilot study involving twelve participants with ALS and nine age-matched healthy controls who underwent high-resolution resting state functional magnetic resonance imaging at an ultra-high field of 7 Tesla. A group-level whole-brain analysis revealed a disruption in long-range functional connectivity between the superior sensorimotor cortex (in the precentral gyrus) and bilateral cerebellar lobule VI. Post hoc analyses using atlas-derived left and right cerebellar lobule VI revealed decreased functional connectivity in ALS participants that predominantly mapped to bilateral postcentral and precentral gyri. Cerebellar lobule VI is a transition zone between anterior motor networks and posterior non-motor networks in the cerebellum, and is associated with a wide range of key functions including complex motor and cognitive processing tasks. Our observation of the involvement of cerebellar lobule VI adds to the growing number of studies implicating the cerebellum in ALS. Future avenues of scientific investigation should consider how high-resolution imaging at 7T may be leveraged to visualize differences in functional connectivity disturbances in various genotypes and phenotypes of ALS along the ALS-frontotemporal dementia spectrum.

neuroscience↗

bioRxiv2020

In vivo human whole-brain Connectom diffusion MRI dataset at 760 μm isotropic resolution

We present a whole-brain in vivo diffusion MRI (dMRI) dataset acquired at 760 m isotropic resolution and sampled at 1260 q-space points across 9 two-hour sessions on a single healthy subject. The creation of this benchmark dataset is possible through the synergistic use of advanced acquisition hardware and software including the high-gradient-strength Connectom scanner, a custom-built 64-channel phased-array coil, a personalized motion-robust head stabilizer, a recently developed SNR-efficient dMRI acquisition method, and parallel imaging reconstruction with advanced ghost reduction algorithm. With its unprecedented resolution, SNR and image quality, we envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance the understanding of human brain structures and connectivity. This comprehensive dataset can also be used as a test bed for new modeling, sub-sampling strategies, denoising and processing algorithms, potentially providing a common testing platform for further development of in vivo high resolution dMRI techniques. Whole brain anatomical T1-weighted and T2-weighted images at submillimeter scale along with field maps are also made available.

neuroscience↗

bioRxiv2020

Application of Surgical Lead Management and Reconfigurable Coil Technology to Reduce RF Heating of DBS Implants during MRI at 3T Under Variant Body Compositions

Patients with active implants such as deep brain stimulation (DBS) devices, have limited access to magnetic resonance imaging (MRI) due to risks of RF heating. With an aging population, the prevalence of neurodegenerative and vascular disease increases; and so does the indication for MRI exams in patients with such implants. In response to this growing need for MRI, many groups have investigated strategies to mitigate the RF heating of the implants. These efforts, however, have relied either on simulations with homogenous body models or simplified phantom experiments (box shaped phantom with single tissue). It is well established, however, that the shape and heterogeneity of human body affects the distribution of MRI electric fields, which by proxy, alters the RF heating of an implant inside the body. In this contribution, we applied numerical simulations and phantom experiments to examine the effectiveness of RF heating mitigation strategies under variant patient body compositions, focusing on two recently proposed techniques: (a) surgical modification of DBS lead trajectories inside the body, and (b) use of a patient-adjustable reconfigurable MRI coil, both aiming to reduce the coupling of implanted leads and MRI electric fields. Our results demonstrated that both techniques perform well under variant body compositions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioengineering↗

bioRxiv2018

Reconfigurable MRI coil technology can substantially reduce RF heating at the tips of bilateral deep brain stimulation implants

Patients with deep brain stimulation (DBS) implants can significantly benefit from magnetic resonance imaging (MRI) examination, however, access to MRI is restricted in this patients because of safety concerns due to RF heating of the leads. Recently we introduced a patient-adjustable reconfigurable MRI coil system to reduce the SAR at the tip of deep brain stimulation implants during MRI at 1.5T. A simulation study with realistic models of single (unilateral) DBS leads demonstrated a substantial reduction in the local SAR up to 500-fold could be achieved using the coil system compared to quadrature birdcage coils. Many patients however, have bilateral DBS implants and the question arises whether the rotating coil system can be used in for them. This work reports the results of phantom experiments measuring the temperature rise at the tips of bilateral DBS implants with realistic trajectories extracted from postoperative CT images of 10 patients (20 leads in total). A total of 200 measurements were performed to record temperature rise at the tips of the leads during 2 minutes of scanning with the coil rotated to cover all accessible rotation angles. In all patients, we were able to find an optimum coil rotation angle and reduced the heating of both left and right leads to a level below the heating produced by the body coil. An average heat reduction of 65% was achieved for bilateral leads. Reconfigurable coil technology introduces a promising approach for imaging of patients with DBS implants.

biophysics↗

bioRxiv2018

Reducing RF-Induced Heating Near Implanted Leads Through High-Dielectric Capacitive Bleeding of Current (CBLOC)

Patients with implanted medical devices such as deep brain stimulation or spinal cord stimulation are often unable to receive magnetic resonance imaging (MRI). This is because once the device is within the radiofrequency (RF) field of the MRI scanner, electrically conductive leads act as antenna, amplifying the RF energy deposition in the tissue and causing possible excessive tissue heating. Here we propose a novel concept in lead design in which 40cm lead wires are coated with a ~1.2mm layer of high dielectric constant material (155 <{varepsilon} r < 250) embedded in a weakly conductive insulation ({sigma} = 20 S/m). The technique called High-Dielectric Capacitive Bleeding of Current, or CBLOC, works by forming a distributed capacitance along the lengths of the lead, efficiently dissipating RF energy before it reaches the exposed tip. Measurements during RF exposure at 64 MHz and 123 MHz demonstrated that CBLOC leads generated 20-fold less heating at 1.5 T, and 40-fold less heating at 3 T compared to control leads. Numerical simulations of RF exposure at 297 MHz (7T) predicted a 15-fold reduction in specific absorption rate (SAR) of RF energy around the tip of CBLOC leads compared to control leads.

biophysics↗