The Japan Monkey Centre Primates Brain Imaging Repository for comparative neuroscience: an archive of digital records including records for endangered species

Advances in magnetic resonance imaging (MRI) and computational analysis technology have enabled comparisons among various primate brains in a three-dimensional electronic format. Results from comparative studies provide information about common features across primates and species-specific features of neuroanatomy. Investigation of various species of non-human primates is important for understanding such features, but the majority of comparative MRI studies have been based on experimental primates, such as common marmoset, macaques, and chimpanzee. A major obstacle has been the lack of a database that includes non-experimental primates’ brain MRIs. To facilitate scientific discoveries in the field of comparative neuroanatomy and brain evolution, we launched a collaborative project to develop an open-resource repository of non-human primate brain images obtained using ex vivo MRI. As an initial open resource, here we release a collection of structural MRI and diffusion tensor images obtained from 12 species: pygmy marmoset, owl monkey, white-fronted capuchin, crab-eating macaque, Japanese macaque, bonnet macaque, toque macaque, Sykes’ monkey, red-tailed monkey, Schmidt’s guenon, de Brazza’s guenon, and lar gibbon. Sixteen postmortem brain samples from the 12 species, stored in the Japan Monkey Centre (JMC), were scanned using a 9.4-T MRI scanner and made available through the JMC collaborative research program (http://www.j-monkey.jp/BIR/index_e.html). The expected significant contributions of the JMC Primates Brain Imaging Repository include (1) resources for comparative neuroscience research, (2) preservation of various primate brains, including those of endangered species, in a permanent digital form, (3) resources with higher resolution for identifying neuroanatomical features, compared to previous MRI atlases, (4) resources for optimizing methods of scanning large fixed brains, and (5) references for veterinary neuroradiology. User-initiated research projects beyond these contributions are also anticipated

Recommendations and guidelines from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 1 -- In vivo small-animal imaging

The value of in vivo preclinical diffusion MRI (dMRI) is substantial. Small-animal dMRI has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. Many of the influential works in this field were first performed in small animals or ex vivo samples. The steps from animal setup and monitoring, to acquisition, analysis, and interpretation are complex, with many decisions that may ultimately affect what questions can be answered using the data. This work aims to serve as a reference, presenting selected recommendations and guidelines from the diffusion community, on best practices for preclinical dMRI of in vivo animals. In each section, we also highlight areas for which no guidelines exist (and why), and where future work should focus. We first describe the value that small animal imaging adds to the field of dMRI, followed by general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in animal species and disease models and discuss how they are appropriate for different studies. We then give guidelines for in vivo acquisition protocols, including decisions on hardware, animal preparation, imaging sequences and data processing, including pre-processing, model-fitting, and tractography. Finally, we provide an online resource which lists publicly available preclinical dMRI datasets and software packages, to promote responsible and reproducible research. An overarching goal herein is to enhance the rigor and reproducibility of small animal dMRI acquisitions and analyses, and thereby advance biomedical knowledge.Comment: 69 pages, 6 figures, 1 tabl

Axonal T₂ estimation using the spherical variance of the strongly diffusion-weighted MRI signal.

In magnetic resonance imaging, the application of a strong diffusion weighting suppresses the signal contributions from the less diffusion-restricted constituents of the brain's white matter, thus enabling the estimation of the transverse relaxation time T <sub>2</sub> that arises from the more diffusion-restricted constituents such as the axons. However, the presence of cell nuclei and vacuoles can confound the estimation of the axonal T <sub>2</sub> , as diffusion within those structures is also restricted, causing the corresponding signal to survive the strong diffusion weighting. We devise an estimator of the axonal T <sub>2</sub> based on the directional spherical variance of the strongly diffusion-weighted signal. The spherical variance T <sub>2</sub> estimates are insensitive to the presence of isotropic contributions to the signal like those provided by cell nuclei and vacuoles. We show that with a strong diffusion weighting these estimates differ from those obtained using the directional spherical mean of the signal which contains both axonal and isotropically-restricted contributions. Our findings hint at the presence of an MRI-visible isotropically-restricted contribution to the signal in the white matter ex vivo fixed tissue (monkey) at 7T, and do not allow us to discard such a possibility also for in vivo human data collected with a clinical 3T system

A Primate View on Multiple Sclerosis

MS is a chronic disease affecting the CNS with an average disease onset in the third or fourth decade of life. Clinical symptoms are caused by changes in the motor, sensory, visual, and autonomic systems. Most common symptoms include visual and balance disturbances, spasticity, bladder dysfunction, pain, and fatigue. At a later disease stage, paralysis may occur. Other symptoms are Lhermitte’s symptom, an electrical sensation running down the spine or limbs when the neck bends, and Uhthoff phenomenon, worsening of symptoms when the core body temperature increases

In-vivo-Magnetresonanzmikroskopie des humanen Auges [In vivo MR microscopy of the human eye]

MR microscopy using an ultra high-field MR system is a novel non-invasive imaging technique to explore the human eye without optical distortions. This review aims to provide an insight into the technique. Normal MR microscopic anatomy of the human eye in vivo is demonstrated and clinical applications of MR microscopy are discussed

Development of Diffusion MRI Methodology to Quantify White Matter Integrity Underlying Post-Stroke Anomia

In 1909 German neurologist Korbinian Brodmann wrote “functional localization of the cerebral cortex without the lead of anatomy is impossible... In all domains, physiology has its firmest foundations in anatomy [1”. While histology is the current gold standard for studying brain microstructure, it is primarily a post-mortem technique that has an average resolution of one micrometer making it impractical for studying the entire brain. Diffusion Magnetic Resonance Imaging (dMRI) is ideally suited to study whole-brain tissue microstructure by sensitizing the MRI contrast to water diffusion, which has a length scale on the order of micrometers. Even though dMRI is applied clinically for the detection of acute ischemia, the relation between tissue microstructure and the dMRI signal is complex and not fully understood. The focus of this dissertation was the validation and development of a new biophysical model of the dMRI signal. Notwithstanding, it is important to keep in mind the potential clinical applications of these models, so in parallel we studied the relationship between white matter integrity and language impairments in post-stroke anomia. This application is of interest since response to language treatment is variable and it is currently difficult to predict which patients will benefit. A better understanding of the underlying brain damage could help inform on functionality and recovery potential. Our work resulted in 9 peer-reviewed papers in international journals and 13 abstracts in proceedings at national and international conferences. Using data collected from 32 chronic stroke patients with language impairments, we studied the relation between baseline naming impairments and microstructural integrity of the residual white matter. An existing dMRI technique, Diffusional Kurtosis Imaging (DKI), was used to assess the tissue microstructure along the length of two major white matter bundles: the Inferior Longitudinal Fasciculus (ILF) and the Superior Longitudinal Fasciculus (SLF). The frequency of semantic paraphasias was strongly associated with ILF axonal loss, whereas phonemic paraphasias were strongly associated with SLF axonal loss. This double dissociation between semantic and phonological processing is in agreement with the dual stream model of language processing and corroborates the concept that, during speech production, knowledge association (semantics) depends on the integrity of ventral pathways (ILF), whereas form encoding (phonological encoding) is more localized to dorsal pathways (SLF). Using a smaller dataset of 8 chronic stroke subjects whom underwent speech entrainment therapy, we assessed if naming improvements were supported by underlying changes in microstructure. Remarkably, we saw that a decrease in semantic errors during confrontational naming was related to a renormalization of the microstructure of the ILF. Together, these two studies support the idea that white matter integrity (in addition to regional gray matter damage) impacts baseline stroke impairments and disease progression. Acquiring accurate information about a patient’s linguistic disorder and the underlying neuropathology is often an integral part to developing an appropriate intervention strategy. However, DKI metrics describe the general physical process of diffusion, which can be difficult to interpret biologically. Different pathological processes could lead to similar DKI changes further complicating interpretation and possibly decreasing its specificity to disease. A multitude of biophysical models have been developed to improve the specificity of dMRI. Due to the complexity of biological tissue, assumptions are necessary, which can differ in stringency depending on the dMRI data at hand. One such assumption is that axons can be approximated by water confined to impermeable thin cylinders. In this dissertation, we provide evidence for this “stick model”. Using data from 2 healthy controls we show that the dMRI signal decay behaves as predicted from theory, particularly at strong diffusion weightings. This work validated the foundation of a biophysical model known as Fiber Ball Imaging (FBI), which allows for the calculation of the angular dependence of fiber bundles. Here, we extend FBI by introducing the technique Fiber Ball White Matter (FBWM) modeling that in addition provides estimations for the Axonal Water Fraction (AWF) and compartmental diffusivities. The ability to accurately estimate compartment specific diffusion dynamics could provide the opportunity to distinguish between different disease processes that affect axons differently than the extra-axonal environment (e.g. gliosis). Lastly, we were able to show that FBI data can also be used to calculate compartmental transverse relaxation times (T2). These metrics can be used as biomarkers, aid in the calculation of the myelin content, or be used to reduce bias in diffusion modeling metrics. Future work should focus on the application of FBI and FBWM to the study of white matter in post-stroke anomia. Since FBWM offers the advantage of isolating the diffusion dynamics of the intra- and extra- axonal environments, it could be used to distinguish between pathological processes such as glial cell infiltration and axonal degeneration. A more specific assessment of the structural integrity underlying anomia could provide information on an individual’s recovery potential and could pave the way for more targeted treatment strategies. The isolation of intra-axonal water is also beneficial for a technique known as dMRI tractography, which delineates the pathway of fiber bundles in the brain. dMRI tractography is a popular research tool for studying brain networks but it is notoriously challenging to do in post-stroke brains. In damaged brain tissue, the high extra-cellular water content masks the directionality of fibers; however, since FBI provides the orientational dependence of solely intra-axonal water, it is not affected by this phenomenon. It is important to understand that caution should be taken when applying biophysical models (FBWM/FBI vs. DKI) to the diseased brain as the validation we provided in this work was only for healthy white matter and these experiments should be repeated in pathological white matter

Quantitative analysis of the focused ultrasound-induced blood-brain barrier opening with applications in neurodegenerative disorders

The blood-brain barrier poses a formidable impediment to the treatment of adult-onset neurodegenerative disorders, by prevention of most drugs from gaining access to the brain parenchyma. Focused ultrasound (FUS), in conjunction with systemically administered microbubbles, has been shown to open the blood-brain barrier (BBB) locally, reversibly and non invasively both in rodents and in non-human-primates. Initially, we demonstrate a monotonic increase of the BBB opening volume with close to normal incidence angle, detectable by diffusion tensor imaging; the employed contrast-free magnetic resonance protocol that revealed the anisotropic nature of the diffusion gradient. Implementation of this optimized BBB opening technique in Parkinsonian mice, coupled with the administration of trophic growth factors, induced restorative effects in the dopaminergic neurons, the main cellular target of the pathological process in Parkinson’s disease. The immune response initiated by the FUS-induced BBB disruption has been proven pivotal in reducing proteinaceous aggregates from the brain through the activation of a gliosis cascade. Therefore, we investigated this immunomodulatory effect in Alzheimer’s disease. The neuropathological hallmarks of Alzheimer’s disease include aggregation of amyloid beta into plaques and accumulation of tau protein into neurofibrillary tangles. Tau pathology correlates well with impaired neuronal activity and dementia and was found to be attenuated after the application of ultrasound that correlated with increased microglia activity. Given the beneficial effect of this methodology on the Alzheimer’s pathologies when studied separately, we explored the application of FUS in brains subjected concurrently to amyloidosis and tau phosphorylation. Our findings indicate the reduction of tau protein and decrease in the amyloid load from brains treated with ultrasound, accompanied by spatial memory improvement. Overall, in this dissertation, we established an optimized targeting and detection protocol, pre-clinical implementation of which confirmed its ameliorative effects as a drug-delivery adjuvant or an immune response stimulant. These preclinical findings support the immense potential of such a methodology that significantly contributes to the treatment of different neurodegenerative disorders curbing their progression

A novel mechanism of contrast in MRI: pseudo super-diffusion of water molecules unveils microstructural details in biological tissues

The goal of this work is to investigate the properties of the contrast provided by Anomalous Diffusion (AD) γ-imaging technique and to test its potential in detecting tissue microstructure. The collateral purpose is to implement this technique by optimizing data acquisition and data processing, with the long term perspective of adoption in massive in vitro, in vivo and clinical studies. The AD γ-imaging technique is a particular kind of Diffusion Weighted- Magnetic Resonance Imaging (DW-MRI). It represents a refinement of conventionally used DW-MRI methods, sharing with them the advantage of being non invasive, since it uses water as an endogenous contrast agent. Besides, it is more suitable to the study of complex tissues, because it is based on a theoretical model that overcomes the simplistic Gaussian assumption. While the Gaussian assumption predicates the linearity between the average molecular displacement of water and the diffusing time, as in case of diffusion in isotropic, homogeneous and infinite environments, a number of experiments performed in vitro and in vivo on both animals and humans showed an anomalous behavior of water molecules, with a non linear relation between the distance travelled and the elapsed time. In particular, the γ-parameter quantifies water pseudo super-diffusion, a peculiarity due to the fact that water diffusion occurs in multi-compartments and it is probed by means of MRI. In fact, a restricted diffusion is rather predicted for water diffusing in biological tissues. Recently, the trick that allows to make the traditional DW-MRI acquisition sequence suitable for pseudo super-diffusion quantification has been unveiled, and in short it consists in performing DW experiments varying the diffusion gradient strengths, at a constant diffusive time. The γ-parameter is extracted by fitting DW-data to a stretched-exponential function. Finally, probing water diffusion in different directions allows to reconstruct a γ-tensor, with scalar invariants that quantify the entity of AD and its anisotropy in a given volume element. In vitro results on inert materials revealed that γ correlates with internal gradients arising from magnetic susceptibility differences (Δ) between neighboring compartments, and that it reflects the multi-compartmentalization of the space explored by diffusing molecules. Furthermore, values of γ compatible with a description of super-diffusive motion were found. This anomaly can be explained considering that the presence of Δ induce an additional attenuation to the signal, simulating a pseudo super-diffusion. Finally, In vivo results on human brain showed that γ is more effective in discriminating among different brain regions compared to conventional DWMRI parameters. These studies suggest that the contrast provided by AD γ-imaging is influenced by an interplay of two factors, Δ -effects on one hand, multicompartmentalization on the other hand, through which γ could reflect tissue microstructure. With the aim to shed some light on this issue I performed AD γ-imaging in excised mouse spinal cord (MSC) at 9.4 T and healthy human brain at 3.0 T. The adoption of MSC was motivated by its current use in studies of demyelination due to an induced pathology that mimics Multiple Sclerosis alterations, and by its simplified geometry. I acquired DW-data with parameters optimized for the particular system chosen: the MSC was scanned along 3 orthogonal directions, thus an apparent γ was derived; for the in vivo studies I used more directions and I extracted a γ-tensor. I found that γ and its anisotropy reflected the microstructure of spinal cord tracts (such as the axon diameters and the axonal density). I investigated both in MSC and human brain the relation between γ and the rate of relaxation (R2*), a parameter well-known to reflect Δ, and found significant linear correlations. Because of this γ was able to differentiate white matter regions on the basis of their spatial orientation, and gray matter regions on the basis of their intrinsic iron content in human brain imaged at 3.0 T. These results suggest that AD γ-imaging could be an alternative or complementary technique to DW-MRI in the field of neuroscience. Indeed it could be useful for the assessment of the bulk susceptibility inhomogeneity, which reflects iron deposition, the hallmark of several neurodegenerative diseases. The part of this thesis work concerning the in vivo experiment in human brain gave rise to a paper published on NeuroImage, a relevant scientific journal in the field of MRI applied to brain investigation