Biology subjects

Rushmore, R. J.

Publications and source records attributed to Rushmore, R. J..

11 recordsLinked to original sources

bioRxiv2026

Multimodal characterization of putative pan-inhibitory viral constructs in macaque monkeys

Transgenic approaches and validated viral vector toolboxes have advanced our understanding of how inhibitory neurons shape cognition and motor control in mice and other rodents. However, such advances have been elusive in non-human primates (NHPs). While many studies demonstrate expression of reporter proteins, few studies have provided clear quantitative evidence of whether these viral constructs can be reliably used for assessment of in vivo and in vitro function in primates, which, in turn, has hindered widespread adoption by NHP researchers. Here, we characterize putative pan-inhibitory cell targeting vectors engineered with regions from the Dlx5-6 intergenic domain. Pan-inhibitory viral vectors are attractive because they enable ground-truth optotagging and modulation of multiple inhibitory subtypes in the same animal and, when combined with machine learning approaches, enable cell-type classifiers for NHPs. We combined in vivo anesthetized electrophysiological recordings, in vitro slice electrophysiology, and immunohistochemistry across seven rhesus macaque monkeys to assess the specificity, completeness and efficacy of three constructs in multiple sensory and higher-order association cortices. The vectors reliably restricted transgene expression to inhibitory neurons (81-97%). However, of the local GABAergic neurons only 32-64% expressed the transgene, depending on the construct. This incompleteness arose in part from uneven coverage across subtypes, with strong transgene expression in parvalbumin-positive interneurons (~60-90%), sparse expression in calbindin-positive interneurons (~1-7%), and near-complete avoidance of calretinin-positive interneurons. A construct pairing DLX2.0 with ChrimsonR was excellent for in vivo optotagging, while h56D paired with bReaChES most effectively suppressed neural activity in vivo. In the slice, activating terminals of transgene-expressing neurons optically evoked inhibitory currents in coupled pyramidal neurons confirming transsynaptic functionality of these constructs and their use for inhibitory circuit-specific synaptic assessments and manipulation. Collectively, the results provide rigorous functional characterization, and quantitative guidance for NHP researchers seeking to deploy GABAergic cell-type-specific tools in their experiments.

neuroscience↗

bioRxiv2026

Connectional neuroanatomy of U-fibers in the rhesus monkey brain

The superficial white matter (SWM), the region of white matter immediately beneath the gray matter-white matter (GM-WM) border, contains short cortico-cortical association fibers that interconnect neighboring cortical regions. The SWM is estimated to comprise the majority of axons in the cerebral white matter and is thus thought to play a major role in cortical information processing. Despite this prominence, and growing attention in the diffusion MRI (dMRI) field, the connectional organization of the SWM remains poorly defined. A major component of the SWM is U-shaped fiber bundles, classically depicted in brain dissections as bundles beneath sulci that interconnect adjacent gyri. The prevailing view, from both brain dissection and dMRI, considers U-fibers to be ubiquitous elements of the SWM that form symmetric connections between corresponding portions of adjacent gyri beneath all sulci, and they are routinely reconstructed in tractography as a layer of short association connections. However, their actual prevalence and organization in the primate brain have never been systematically evaluated with experimental tract tracing. To address this gap, we analyzed 28 archival macaque tract-tracing cases in which anterograde tracers were injected on gyri adjacent to major cortical sulci (intraparietal, central, principal, superior temporal), all of which have clear anatomical correspondences to sulci in the human cerebral cortex. Several organizational principles emerged. First, although short association fibers were present in every case, U-fibers - operationally defined as labeled fibers that left the injection site, passed beneath a sulcus, and terminated on the adjacent gyrus - were only observed in a minority of cases. Second, U-fiber incidence was sulcus-dependent: U-fibers were consistently present beneath the principal and central sulci, but uncommon beneath the intraparietal and superior temporal sulci. Third, when present, U-fibers did not follow a uniform trajectory - some took a course symmetric and orthogonal to the sulcus, whereas others followed oblique trajectories to more distant regions. In addition to U-fibers, we identified shorter association fiber bundles that terminated on the sulcal bank proximal to the injection, or on the opposing bank after they crossed the fundus of the sulcus, evidence that the SWM contains multiple classes of short association fiber bundles rather than a single canonical U-fiber system. We further identified a consistent 200-300 {micro}m band of white matter beneath cortical layer 6 that contained exclusively short association fibers on approach to their cortical terminations and was selectively avoided by deeper long cortico-cortical pathways. This band was present across all examined sulci, suggesting that it is a conserved feature of the cortical white matter. Notably, U-fibers were found both within this band and in the white matter below. We also identified deeper fiber bundles that adopted a U-shaped course beneath a sulcus but did not interconnect adjacent gyri. Thus, a U-shaped trajectory alone does not define a U-fiber. Together, these findings constitute the first systematic connectional study of cortical U-fibers in major sulci of the non-human primate brain and indicate that the white matter beneath the cortex is a highly complex system in which short association fiber bundle organization reflects the selective connectivity of the cortical areas separated by a sulcus, rather than a uniform U-fiber architecture imposed by the geometry of the overlying sulcus. These results have potential consequences for dMRI and anatomical studies of white matter and provide an anatomically grounded basis to better define SWM organization in anatomy and tractography.

neuroscience↗

bioRxiv2026

Anatomically constrained and curated cerebellar tractography (ACCURAT): an open framework and a pathway-specific neuroanatomical reference

Cerebellar pathways form extensive structural circuits linking the cerebellum with the brainstem, thalamus, and cerebrum, underlying motor, cognitive, and affective functions. Diffusion MRI tractography provides the only non-invasive method for mapping these pathways in vivo, but reconstruction of cerebellar connectivity remains challenging due to crossing fibers, peduncular bottlenecks, decussations, multi-synaptic circuits, and numerous small nuclei that define pathway origins and terminations. Here we introduce Anatomically Constrained and CURAted Tractography (ACCURAT), an open framework for reconstructing cerebellar pathways from diffusion MRI using anatomical priors and rule-based streamline queries. ACCURAT combines anatomical segmentation, densely seeded tractography, and vertex-level evaluation of anatomical constraints along streamline trajectories, enabling the isolation of pathway segments within specific nuclei while preventing their propagation across synaptic boundaries. To define these constraints, we provide a concise, pathway-by-pathway synthesis of cerebellar connectional anatomy based on experimental tract-tracing literature and organized for tractography applications. We identify pathway-specific origins, trajectories, terminations, decussation patterns, and tractography challenges, and use this information to inform tractography-ready cerebellar pathway definitions. Using ultra-high-resolution submillimeter diffusion MRI (0.76 mm gSlider acquisition) from healthy participants, we reconstruct multiple extrinsic and intrinsic cerebellar pathways, including specific components of the inferior, middle, and superior cerebellar peduncles; challenging decussating pathways such as the olivocerebellar and dentato-olivary projections; and intrinsic cerebellar pathways, including Purkinje corticonuclear projections and intracortical parallel fibers. ACCURAT generalizes across tractography algorithms, producing comparable reconstructions with both probabilistic parallel transport tractography and deterministic unscented Kalman filter tractography. Together, the ACCURAT framework and accompanying neuroanatomical reference provide an anatomically grounded, tractography-oriented resource for reconstructing cerebellar pathways in vivo and for supporting future development and evaluation of cerebellar tractography methods.

neuroscience↗

bioRxiv2026

Neuroanatomy of substantia nigra and ventral tegmental area dopaminergic, and dorsal raphe serotonergic circuits in the human brain using T1-weighted and diffusion magnetic resonance imaging: A morphometric pilot study with estimate of reliability

IntroductionWe present here a methodology for morphometric analysis of the substantia nigra (SN), the ventral tegmental area (VTA), the dorsal raphe nucleus (DRN) and their respective structural brain circuits. MethodsOur analyses were based on multimodal T1-weighted MRI and diffusion MRI (dMRI) segmentation and tractography in 12 human subjects drawn from the Human Connectome Project (HCP) repository. ResultsWe were able to demonstrate strong connections of the SN, VTA and DRN with several brain regions, in particular the dorsolateral prefrontal cortex (DLPFC) and the cerebellum. More specifically, we created comprehensive visualizations of the SN and VTA dopaminergic as well as the DRN serotonergic structural circuits in the human brain, which, although preliminary, demonstrate the potential of multimodal neuroimaging to investigate these circuits quantitatively in clinical conditions. Finally, we created a pilot dataset for the most frequently observed structural connections, specifically those that were present more than 92% of the time among all subjects. Discussion This pilot morphometric report examines the structural circuits of the SN, VTA and DRN, which are critically involved in several biobehaviors and clinical conditions such as addiction, stress, Parkinsons disease (PD), schizophrenia, obsessive-compulsive disorder, post-traumatic stress disorder, attention deficit hyperactivity disorder, mood disorders, COVID-19 and long COVID. Importantly, the strong structural connectivity of the DLPFC and cerebellum with the SN, VTA and DRN is expected to be a potential target of noninvasive neuromodulation treatments in neuropsychiatry. Our findings demonstrate the potential of current clinical multimodal neuroimaging to delineate the dopaminergic (DA) and serotonergic (5-HT) circuits in the human brain in clinical conditions.

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bioRxiv2025

Study of Sex Differences in the Whole Brain White Matter Using Diffusion MRI Tractography and Suprathreshold Fiber Cluster Statistics

Sex-specific characteristics demonstrate a substantial influence on the brain white matter (WM), suggesting distinct structural connectivity patterns between females and males. Diffusion MRI (dMRI) tractography is an important tool in assessing WM connectivity and brain tissue microstructure across different populations. Whole brain tractography analysis for group statistical comparison is a challenging task due to the large number of WM connections. This work studies whole-brain WM connectivity differences between females and males using dMRI tractography. We study a large cohort of 707 subjects from the Human Connectome Project Young Adult dataset. By applying a well-established fiber clustering pipeline and a suprathreshold fiber cluster statistical method, we analyze tracts in the cerebral cortex and understudied pathways like those connecting to the cerebellum. We identify several tracts with significant sex differences in terms of their fractional anisotropy and/or mean diffusivity. These include deep tracts like the arcuate fasciculus, corticospinal tract, and corpus callosum, superficial tracts in the frontal lobe, and cerebellar tracts. Finally, correlation analysis reveals that these WM differences are linked to a range of neurobehavioral measures, with the strongest and most consistent associations observed for motor function, suggesting motor circuits as a potential key focus for future research.

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bioRxiv2025

The superficial white matter in language processing: Broca's area connections are bilaterally associated with individual performance in children and adults

While deeper white matter connections, such as the arcuate fasciculus and frontal aslant tract, are well known for their role in language and show leftward asymmetries in adults, the contribution of the short-range cortico-cortical superficial white matter (SWM) connections remains less understood. In this preregistered study, we examined white matter connections of Brocas area and its right hemisphere homolog in early adolescents and young adults using two large, publicly available datasets: the Adolescent Brain Cognitive Development Study and the Human Connectome Project Young Adult Study, totaling over 10,000 participants. We anatomically curated the ODonnell Research Group (ORG) tractography atlas to identify SWM fiber clusters intersecting Brocas area (pars opercularis and pars triangularis), confirmed through expert visual inspection. We investigated the microstructure, structural connectivity, and lateralization of Brocas area SWM and its relationship with language performance (Picture Vocabulary and Oral Reading Recognition assessments), in comparison to the deeper white matter connections of the frontal aslant tract and arcuate fasciculus. The arcuate fasciculus demonstrated the strongest and most consistent leftward lateralization of both microstructure (fractional anisotropy, FA) and structural connectivity (number of streamlines, NoS), with structure-function associations that were bilateral in adolescents and left-dominant in adults. Interestingly, despite weaker lateralization than the arcuate fasciculus, both the SWM and the frontal aslant tract demonstrated comparable associations with language performance. The frontal aslant tract showed greater leftward lateralization (FA and NoS) with age and was bilaterally associated with language performance, particularly in adolescents. Compared to these deeper tracts, Brocas area SWM demonstrated left-lateralized FA and right-lateralized NoS in both adolescents and adults, with stronger FA lateralization in adults. Bilateral SWM FA and NoS were significantly associated with language performance in both hemispheres and age groups. Overall, these results suggest that Brocas area SWM may support language in a more bilaterally distributed manner and highlight the importance of considering SWM connections in studies of language development and neurosurgical planning.

neuroscience↗

bioRxiv2025

Neuroanatomy of catecholaminergic circuits in the brainstem and hypothalamus using T1-weighted and diffusion magnetic resonance imaging in humans: implications for brain-immune interactions, cardiovascular disease, neuropsychiatric disorders, stress response, and COVID-19

Neuroimaging allows the study of brain structures that previously were undetectable due to their small size and location. Herein we focused on the core catecholaminergic circuitries in the human brain, involving the coerulean noradrenergic (or norepi-nephrine, NE) and dopaminergic (DA) systems. Using T1-weighted MRI morphometry and dMRI tractography, this study was carried out in one post-mortem human ultra-high-resolution dataset of the brainstem and diencephalon and in healthy human datasets from the Human Connectome Project repository. We investigated 26 connections of brainstem origin (13 in the left side and 13 in the right side) associated with the NE and DA circuitries. We delineated the coerulean NE and DA core central catechol-aminergic circuitries of the brainstem and hypothalamus in the post-mortem dataset, including all targeted fiber connections. Importantly, this was also achieved in the HCP datasets. These results emphasize the importance of multispectral neuroimaging in the study of chemical neuroanatomical circuitries and its application in clinical conditions such as cardiovascular disease, major depression, schizophrenia, and other disorders associated with chronic stress and brain-immune interactions such as COVID-19.

neuroscience↗

bioRxiv2025

Towards an informed choice of diffusion MRI image contrasts for cerebellar segmentation

The fine-grained segmentation of cerebellar structures is an essential step towards supplying increasingly accurate anatomically informed analyses, including, for example, white matter diffusion magnetic resonance imaging (MRI) tractography. Cerebellar tissue segmentation is typically performed on structural magnetic resonance imaging data, such as T1-weighted data, while connectivity between segmented regions is mapped using diffusion MRI tractography data. Small deviations in structural to diffusion MRI data co-registration may negatively impact connectivity analyses. Reliable segmentation of brain tissue performed directly on diffusion MRI data helps to circumvent such inaccuracies. Diffusion MRI enables the computation of many image contrasts, including a variety of tissue microstructure maps. While multiple methods have been proposed for the segmentation of cerebellar structures using diffusion MRI, little attention has been paid to the systematic evaluation of the performance of different available input image contrasts for the segmentation task. In this work, we evaluate and compare the segmentation performance of diffusion MRI-derived contrasts on the cerebellar segmentation task. Specifically, we include spherical mean (diffusion-weighted image average) and b0 (non-diffusion-weighted image average) contrasts, local signal parameterization contrasts (diffusion tensor and kurtosis fit maps), and the structural T1-weighted MRI contrast that is most commonly employed for the task. We train a popular deep-learning architecture using a publicly available dataset (HCP-YA), leveraging cerebellar region labels from the atlas-based SUIT cerebellar segmentation pipeline. By training and testing using many diffusion-MRI-derived image inputs, we find that the spherical mean image computed from b=1000 s/mm2 shell data provides stable performance across different metrics and significantly outperforms the tissue microstructure contrasts that are traditionally used in machine learning segmentation methods for diffusion MRI. Key pointsO_LIWe provide evidence about the performance of different dMRI contrasts for cerebellar structure segmentation using a deep learning neural network. C_LIO_LIThe diffusion MRI spherical mean provides improved and stable cerebellar structure segmentation performance. C_LIO_LIThe spherical mean is easy to compute and can be used for cerebellar structure segmentation on retrospective clinical diffusion MRI data. C_LI

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bioRxiv2025

Consistent cerebellar pathway-cognition associations across pre-adolescents & young adults: a diffusion MRI study of 9000+ participants

The cerebellum, long implicated in movement, is now recognized as a contributor to higher-order cognition. The cerebellar pathways provide key structural links between the cerebellum and cerebral regions integral to language, memory, and executive function. Here, we present a large-scale, cross-sectional diffusion MRI (dMRI) analysis investigating the relationships between cerebellar pathway microstructure and cognitive performance in over 9,000 participants spanning pre-adolescence (n>8,000 from the ABCD dataset) and young adulthood (n>900 from the HCP-YA dataset). We assessed the microstructure of five cerebellar pathways--the inferior, middle, and superior cerebellar peduncles; the parallel fibers; and input/Purkinje fibers--using three dMRI measures of fractional anisotropy, mean diffusivity, and number of streamlines. Cognitive performance was evaluated using seven NIH Toolbox assessments of language, executive function, and memory. In both datasets, we found numerous significant associations between cerebellar pathway microstructure and cognitive performance. These associations showed a strong correlation across the two datasets (r = 0.47, p < 0.0001), underscoring the reliability of cerebellar dMRI-cognition relationships in pre-adolescents and young adults. In both datasets, the strongest associations were found between the superior cerebellar peduncle and performance on language assessments, suggesting this pathway plays an important role in language function across age groups. In young adults, but not pre-adolescents, parallel fiber microstructure was linked to inhibitory control, suggesting that contributions to attentional processes may emerge or strengthen with maturation. Overall, our findings highlight the important role of cerebellar pathways in cognition and the utility of large-scale datasets for advancing our understanding of brain-cognition relationships. SignificanceThis study provides strong evidence linking cerebellar pathway tissue microstructure to cognition across large populations of preadolescent children and young adults. By leveraging diffusion MRI tractography and cognitive performance data from two major datasets, we identify significant relationships between cerebellar pathway microstructure and cognitive performance. Importantly, findings are significantly correlated across datasets, pointing to the consistency of these relationships, bridging age groups and acquisitions. These results highlight the cerebellar pathways integral role in cognitive functioning and underscore the value of large-scale, population-based studies in advancing our understanding of brain-cognition relationships. Classification 1) Biological Sciences, Neuroscience; 2) Social Sciences, Psychological and Cognitive Sciences

neuroscience↗

bioRxiv2019

3D Exploration of the Brainstem in 50-micron Resolution MRI

The brainstem, a structure of vital importance in the mammals, is currently becoming a principal focus in cognitive, affective and clinical neuroscience. Midbrain, pontine and medullar structures are the epicenter of conduit, cranial nerve and such integrative functions as consciousness, emotional processing, pain and motivation. In this study, we parcellated the nuclear masses and the principal fiber pathways that were visible in a high resolution T2-weighted MRI dataset of 50-micron isotropic voxels of a postmortem human brainstem. Based on this analysis, we generated a detailed map of the human brainstem. To assess the validity of our maps, we compared our observations with histological maps of traditional human brainstem atlases. Moreover, we reconstructed the motor, sensory and integrative neural systems of the brainstem and rendered them in 3D representations. We anticipate the utilization of these maps by the neuroimaging community at large for applications in basic neuroscience as well as in neurology, psychiatry and neurosurgery, due to their versatile computational nature in 2D and 3D representations in a publicly available capacity.

neuroscience↗

bioRxiv2019

MRI-based Parcellation and Morphometry of the Individual Rhesus Monkey Brain: a translational system referencing a standardized ontology

The rhesus macaque is the closest animal model to the human, and investigations into the brain of the rhesus monkey has shed light on the function and organization of the primate brain at a scale and resolution not yet possible in studies of the human brain A cornerstone of the linkage between non-human primate and human studies of the brain is magnetic resonance imaging, which allows for an association to be made between the detailed structural and physiological analysis of the non-human primate and that of the human brain. To further this end, we present a novel parcellation system for the rhesus monkey brain, referred to as the monkey Harvard Oxford Atlas (mHOA) which is based on the human Harvard-Oxford Atlas (HOA) and grounded in an ontological and taxonomic framework. Consistent anatomical features were used to delimit and parcellate brain regions in the macaque, which were then categorized according to functional systems. This system of parcellation will be expanded with advances in technology and like the HOA, will provide a framework upon which the results from other experimental studies (e.g., functional magnetic resonance imaging (fMRI), physiology, connection, graph theory) can be interpreted.

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