Biology subjects

Haber, S. N.

Publications and source records attributed to Haber, S. N..

11 recordsLinked to original sources

bioRxiv2026

A human subcortical connectome at 400 μm resolution

The fiber pathways of the human subcortex are of particular importance in clinical neuroscience, as they are targeted by neuromodulation therapies, such as deep brain stimulation (DBS) and lesion approaches, in various motor and psychiatric disorders. However, the complexity, size, and position of these pathways make them challenging to image non-invasively with diffusion MRI (dMRI). As a result, recent efforts in atlasing these pathways to guide neuromodulation have resorted to using synthetic data. Here we present the first extensive reconstruction of fiber pathways of the human subcortex with ultra-high-resolution dMRI. We leverage a unique, ex vivo dMRI dataset acquired by the BRAIN CONNECTS center for Large-scale Imaging of Neural Circuits (LINC) on the first-of-its-kind Connectome 2.0 scanner. Our contribution is two-fold. First, by showing the feasibility of reconstructing these pathways with non-invasive neuroimaging at the single subject level, we set the stage for future research into reconstructing them in vivo in individual patients. Second, we provide a high-definition atlas of basal-ganglia-thalamocortical circuits that is readily extensible via our publicly released data and annotations. As a first demonstration of its clinical validity, we align our atlas to "hotspots" from previous DBS studies and identify pathways associated with therapeutic or side effects.

neuroscience↗

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↗

bioRxiv2026

The modular nature of long-association pathways in the human brain

Human brain functions are organized within large-scale networks, yet the long-range structural pathways that support them remain only partly understood. Diffusion MRI tractography has enabled non-invasive mapping of these connections but its low resolution has also contributed to a view of white matter association bundles as monolithic entities linking distant cortical regions. This contrasts with anatomical studies in non-human primates and humans, which show these bundles act as conduits for complex systems of short- and long-range projections. Here we investigate the dorsal branch of the superior longitudinal fasciculus (SLF-I), the proposed structural backbone of the dorsal attention network, whose anatomy in humans is debated. Using anatomic tracing, polarization-sensitive optical coherence tomography, and in vivo and ex vivo diffusion MRI, we reconstruct the SLF-I across species, modalities, and scales. High resolution tractography (<750 m), consistent with tracer and PS-OCT data, reveals multiple fiber systems of varying lengths rather than uniform parieto-frontal connections observed at more conventional resolution (1.5 mm). Comparative analyses show a consistent organization: the SLF-I carries short-range cortico-cortical projections rostral to area 6 and longer, layered connections extending to parietal regions, while direct parieto-frontal connectivity is mostly supported by the adjacent cingulum bundle. These findings reconcile our understanding of the SLF-I across the scales of non-invasive neuroimaging and invasive anatomic studies and provide an updated framework for future investigations of large-scale networks in health and disease.

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bioRxiv2023

Self-supervised segmentation and characterization of fiber bundles in anatomic tracing data

Anatomic tracing is the gold standard tool for delineating brain connections and for validating more recently developed imaging approaches such as diffusion MRI tractography. A key step in the analysis of data from tracer experiments is the careful, manual charting of fiber trajectories on histological sections. This is a very time-consuming process, which limits the amount of annotated tracer data that are available for validation studies. Thus, there is a need to accelerate this process by developing a method for computer-assisted segmentation. Such a method must be robust to the common artifacts in tracer data, including variations in the intensity of stained axons and background, as well as spatial distortions introduced by sectioning and mounting the tissue. The method should also achieve satisfactory performance using limited manually charted data for training. Here we propose the first deep-learning method, with a self-supervised loss function, for segmentation of fiber bundles on histological sections from macaque brains that have received tracer injections. We address the limited availability of manual labels with a semi-supervised training technique that takes advantage of unlabeled data to improve performance. We also introduce anatomic and across-section continuity constraints to improve accuracy. We show that our method can be trained on manually charted sections from a single case and segment unseen sections from different cases, with a true positive rate of ~0.80. We further demonstrate the utility of our method by quantifying the density of fiber bundles as they travel through different white-matter pathways. We show that fiber bundles originating in the same injection site have different levels of density when they travel through different pathways, a finding that can have implications for microstructure-informed tractography methods. The code for our method is available at https://github.com/v-sundaresan/fiberbundle_seg_tracing.

neuroscience↗

bioRxiv2023

Single nucleus transcriptomics of human and monkey striatum implicates DNA damage, neuroinflammation, and neurodegeneration signaling in opioid use disorder

The striatum in the brain is involved in various behavioral functions, including reward, and disease processes, such as opioid use disorder (OUD). Further understanding of the role of striatal subregions in reward behaviors and their potential associations with OUD requires molecular identification of specific striatal cell types in human brain. The human striatum contains subregions based on different anatomical, functional, and physiological properties, with the dorsal striatum further divided into caudate and putamen. Both caudate and putamen are involved in altered reward processing, formation of habits, and development of negative affect states associated with OUD. Using single nuclei RNA-sequencing of human postmortem caudate and putamen, we identified canonical neuronal cell types in striatum (e.g., dopamine receptor 1 or 2 expressing neurons, D1 or D2) and less abundant subpopulations, including D1/D2-hybrid neurons and multiple classes of interneurons. By comparing unaffected subjects to subjects with OUD, we found neuronal-specific differences in pathways related to neurodegeneration, interferon response, and DNA damage. DNA damage markers were also elevated in striatal neurons of rhesus macaques following chronic opioid administration. We also identified sex-dependent differences in the expression of stress-induced transcripts among astrocytes and oligodendrocytes from female subjects with OUD. Thus, we describe striatal cell types and leverage these data to gain insights into molecular alterations in human striatum associated with opioid addiction.

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bioRxiv2022

The rostral zona incerta: a subcortical integrative hub and potential DBS target for OCD

BackgroundThe zona incerta (ZI) is involved in mediating survival behaviors and is connected to a wide range of cortical and subcortical structures, including key basal ganglia nuclei. Based on these connections and their links to behavioral modulation, we propose the ZI is a connectional hub for in mediating between top-down and bottom-up control and a possible target for deep brain stimulation for obsessive compulsive disorder. MethodsWe analyzed the trajectory of cortical fibers to the ZI in nonhuman and human primates, based on tracer injections in monkeys and high-resolution diffusion MRI in humans. The organization of cortical and subcortical connections with the ZI were identified in the nonhuman primate studies. ResultsMonkey anatomic data and human dMRI data showed a similar trajectory of fibers/streamlines to the ZI. PFC/ACC terminals all converge within the rostral ZI (ZIr), with dorsal and lateral areas most prominent. Motor areas terminate caudally. Dense subcortical reciprocal connections included the thalamus, medial hypothalamus, substantia nigra/ventral tegmental area, reticular formation, and pedunculopontine nucleus and a dense nonreciprocal projection to the lateral habenula (LHb). Additional connections included amygdala, dorsal raphe nucleus, and periaqueductal grey. ConclusionsDense connections with dorsal and lateral PFC/ACC cognitive control areas and LHb and SN/VTA coupled with inputs from the amygdala, hypothalamus, and brainstem, suggests that the ZIr is a subcortical hub positioned to modulate between top-down and bottom-up control. A DBS electrode placed in the ZIr would involve both connections common to other DBS sites, but also would capture several critically distinctive connections.

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bioRxiv2021

Anatomical and functional connectivity support the existence of a salience network node within the caudal ventrolateral prefrontal cortex

Three large-scale brain networks are considered essential to cognitive flexibility: the ventral and dorsal attention (VAN and DAN) and salience (SN) networks. The ventrolateral prefrontal cortex (vlPFC) is a known component of the VAN and DAN, but there is an important gap in the current knowledge regarding its involvement in the SN. In this study, we used a translational and multimodal approach to fulfill this gap and demonstrate the existence of a SN node within the vlPFC. First, we used tract-tracing methods in non-human primates (NHP) to quantify the anatomic connectivity strength between the different vlPFC areas and the frontal and insular cortices. The strongest connections with the dorsal anterior cingulate cortex (dACC) and anterior insula (AI) locations comprising the two main cortical SN nodes were derived from the caudal area 47/12. This location also has strong axonal projections to subcortical structures of the salience network, including the dorsomedial thalamus, hypothalamus, sublenticular extended amygdala, and periaqueductal gray. Second, we used a seed-based functional connectivity analysis in NHP resting-state functional MRI (rsfMRI) data to validate the caudal area 47/12 as an SN node. Third, we used the same approach in human rsfMRI data to identify a homologous structure in caudal area 47/12, also showing strong connections with the SN cortical nodes, thus confirming the caudal area 47/12 as the SN node in the vlPFC. Taken together, the vlPFC contains nodes for all three cognitive networks, the VAN, DAN, and SN. Thus, the vlPFC is in a position to switch between these three cognitive networks, pointing to a key role as an attentional hub. Its tight additional connections to the orbitofrontal, dorsolateral, and ventral premotor cortices, places the vlPFC at the center for switching behaviors based on environmental stimuli, computing value and cognitive control.

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bioRxiv2021

Post mortem mapping of connectional anatomy for the validation of diffusion MRI

Despite the impressive advances in diffusion MRI (dMRI) acquisition and analysis that have taken place during the Human Connectome era, dMRI tractography is still an imperfect source of information on the circuitry of the brain. In this review, we discuss methods for post mortem validation of dMRI tractography, fiber orientations, and other microstructural properties of axon bundles that are typically extracted from dMRI data. These methods include anatomic tracer studies, Klinglers dissection, myelin stains, label-free optical imaging techniques, and others. We provide an overview of the basic principles of each technique, its limitations, and what it has taught us so far about the accuracy of different dMRI acquisition and analysis approaches.

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bioRxiv2020

Corticostriatal Projections of Macaque Area 44

Ventrolateral frontal area 44 is implicated in inhibitory motor functions and facilitating prefrontal control over vocalization. Yet, the corticostriatal circuitry that may contribute to area 44 functions is not clear, as prior investigation of area 44 corticostriatal projections is limited. Here, we used anterograde and retrograde tracing in macaques to map the innervation zone of area 44 corticostriatal projections, quantify their strengths, and evaluate their convergence with corticostriatal projections from non-motor and motor-related frontal regions. First, terminal fields from a rostral area 44 injection site were found primarily in the central caudate nucleus, whereas those from a caudal area 44 injection site were found primarily in the ventrolateral putamen. Second, amongst sampled striatal retrograde injection sites, area 44 input as a percentage of total frontal cortical input was highest in the ventral putamen at the level of the anterior commissure. Third, area 44 projections converged with both orofacial premotor area 6VR and other motor related projections (in the putamen), and with non-motor prefrontal projections (in the caudate nucleus). These findings support the role of area 44 as an interface between motor and non-motor functional domains, possibly facilitated by rostral and caudal area 44 subregions with distinct corticostriatal connectivity profiles.

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bioRxiv2019

A neural network for information seeking

Humans and other animals often show a strong desire to know the uncertain rewards their future has in store, even when they cannot use this information to influence the outcome. However, it is unknown how the brain predicts opportunities to gain information and motivates this information seeking behavior. Here we show that neurons in a network of interconnected subregions of primate anterior cingulate cortex and basal ganglia predict the moment of gaining information about uncertain rewards. Spontaneous increases in their information prediction signals are followed by gaze shifts toward objects associated with resolving uncertainty, and pharmacologically disrupting this network reduces the motivation to seek information. These findings demonstrate a cortico-basal ganglia mechanism responsible for motivating actions to resolve uncertainty by seeking knowledge about the future.

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bioRxiv2018

A connectional hub in the rostral anterior cingulate cortex links areas of emotion and cognitive control

We investigated afferent inputs from all areas in the frontal cortex (FC) to different subregions in the rostral anterior cingulate cortex (rACC). Using retrograde tracing in macaque monkeys, we quantified projection strength by counting retrogradely labeled cells in each FC area. The projection from different FC regions varied across injection sites in strength, following different spatial patterns. Importantly, a site at the rostral end of the cingulate sulcus stood out as having strong inputs from many areas in diverse FC regions. Moreover, it was at the integrative conjunction of three projection trends across sites. This site marks a connectional hub inside the rACC that integrates FC inputs across functional modalities. Tractography with monkey diffusion magnetic resonance imaging (dMRI) located a similar hub region comparable to the tracing result. Applying the same tractography method to human dMRI data, we demonstrated that a similar hub can be located in the human rACC.

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