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Tangent functional connectomes uncover more unique phenotypic traits

Functional connectomes (FCs) containing pairwise estimations of functional couplings between pairs of brain regions are commonly represented by correlation matrices. As symmetric positive definite matrices, FCs can be transformed via tangent space projections, resulting into tangent-FCs. Tangent-FCs have led to more accurate models predicting brain conditions or aging. Motivated by the fact that tangent-FCs seem to be better biomarkers than FCs, we hypothesized that tangent-FCs have also a higher fingerprint. We explored the effects of six factors: fMRI condition, scan length, parcellation granularity, reference matrix, main-diagonal regularization, and distance metric. Our results showed that identification rates are systematically higher when using tangent-FCs across the “fingerprint gradient” (here including test-retest, monozygotic and dizygotic twins). Highest identification rates were achieved when minimally (0.01) regularizing FCs while performing tangent space projection using Riemann reference matrix and using correlation distance to compare the resulting tangent-FCs. Such configuration was validated in a second dataset (resting-state).

59 BASIC BIOLOGICAL SCIENCES↗

An open science resource for establishing reliability and reproducibility in functional connectomics

Efforts to identify meaningful functional imaging-based biomarkers are limited by the ability to reliably characterize inter-individual differences in human brain function. Although a growing number of connectomics-based measures are reported to have moderate to high test-retest reliability, the variability in data acquisition, experimental designs, and analytic methods precludes the ability to generalize results. The Consortium for Reliability and Reproducibility (CoRR) is working to address this challenge and establish test-retest reliability as a minimum standard for methods development in functional connectomics. Specifically, CoRR has aggregated 1,629 typical individuals’ resting state fMRI (rfMRI) data (5,093 rfMRI scans) from 18 international sites, and is openly sharing them via the International Data-sharing Neuroimaging Initiative (INDI). To allow researchers to generate various estimates of reliability and reproducibility, a variety of data acquisition procedures and experimental designs are included. Similarly, to enable users to assess the impact of commonly encountered artifacts (for example, motion) on characterizations of inter-individual variation, datasets of varying quality are included.

60 APPLIED LIFE SCIENCES↗

Brain Connectomics: Opportunities for High-Performance Computing (Final Report)

The human brain is estimated to contain approximately 100 trillion neural connections. This complex map of connectivity (human connectome) underlies cognitive processes and informs disease states, but until recently, studying the human connectome has been hampered by the difficulty of collecting and processing suitable data for analysis. In this context, an initiative denominated The Human Connectome Project (HCP) was created to acquire and collect the largest, most cohesive set of brain data to accelerate neuroscience research. Recently the HCP released a magnetic resonance (MR) dataset of brain imagery with unprecedented scale and organization, together with high quality spatial and temporal resolution; however, fully taking advantage of this high-resolution brain imagery to estimate neurological connectivity networks requires high-performance computing (HPC). In this project, we explored the feasibility of using HPC resources at Lawrence Livermore to effectively estimate brain connectivity networks from this large set of imagery. Specifically, we addressed one of the main current challenges in brain connectomics, which is to advance the computation of individual structural and functional connectomes.

42 ENGINEERING↗

Aging and functional brain networks

Aging is associated with changes in human brain anatomy and function and cognitive decline. Recent studies suggest the aging decline of major functional connectivity hubs in the 'default-mode' network (DMN). Aging effects on other networks, however, are largely unknown. We hypothesized that aging would be associated with a decline of short- and long-range functional connectivity density (FCD) hubs in the DMN. To test this hypothesis, we evaluated resting-state data sets corresponding to 913 healthy subjects from a public magnetic resonance imaging database using functional connectivity density mapping (FCDM), a voxelwise and data-driven approach, together with parallel computing. Aging was associated with pronounced long-range FCD decreases in DMN and dorsal attention network (DAN) and with increases in somatosensory and subcortical networks. Aging effects in these networks were stronger for long-range than for short-range FCD and were also detected at the level of the main functional hubs. Females had higher short- and long-range FCD in DMN and lower FCD in the somatosensory network than males, but the gender by age interaction effects were not significant for any of the networks or hubs. These findings suggest that long-range connections may be more vulnerable to aging effects than short-range connections and that, in addition to the DMN, the DAN is also sensitive to aging effects, which could underlie the deterioration of attention processes that occurs with aging.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Correspondence between structure and function in the human brain at rest

To further understanding of basic and complex cognitive functions, previous connectome research has identified functional and structural connections of the human brain. Functional connectivity is often measured by using resting-state functional magnetic resonance imaging (rs-fMRI) and is generally interpreted as an indirect measure of neuronal activity. Gray matter (GM) primarily consists of neuronal and glia cell bodies; therefore, it is surprising that the majority of connectome research has excluded GM measures. Therefore, we propose that by exploring where GM corresponds to function would aid in the understanding of both structural and functional connectivity and in turn the human connectome. A cohort of 603 healthy participants underwent structural and functional scanning on the same 3 T scanner at the Mind Research Network. To investigate the spatial correspondence between structure and function, spatial independent component analysis (ICA) was applied separately to both GM density (GMD) maps and to rs-fMRI data. ICA of GM delineates structural components based on the covariation of GMD regions among subjects. For the rs-fMRI data, ICA identified spatial patterns with common temporal features. These decomposed structural and functional components were then compared by spatial correlation. Basal ganglia components exhibited the highest structural to resting-state functional spatial correlation (r = 0.59). Cortical components generally show correspondence between a single structural component and several resting-state functional components. We also studied relationships between the weights of different structural components and identified the precuneus as a hub in GMD structural network correlations. In addition, we analyzed relationships between component weights, age, and gender; concluding that age has a significant effect on structural components.

59 BASIC BIOLOGICAL SCIENCES↗

A Principled Framework to Assess the Information-Theoretic Fitness of Brain Functional Sub-Circuits

In systems and network neuroscience, many common practices in brain connectomic analysis are often not properly scrutinized. One such practice is mapping a predetermined set of sub-circuits, like functional networks (FNs), onto subjects’ functional connectomes (FCs) without adequately assessing the information-theoretic appropriateness of the partition. Another practice that goes unchallenged is thresholding weighted FCs to remove spurious connections without justifying the chosen threshold. This paper leverages recent theoretical advances in Stochastic Block Models (SBMs) to formally define and quantify the information-theoretic fitness (e.g., prominence) of a predetermined set of FNs when mapped to individual FCs under different fMRI task conditions. Our framework allows for evaluating any combination of FC granularity, FN partition, and thresholding strategy, thereby optimizing these choices to preserve the important topological features of the human brain connectomes. By applying to the Human Connectome Project with Schaefer parcellations at multiple levels of granularity, the framework showed that the common thresholding value of 0.25 was indeed information-theoretically valid for group-average FCs, despite its previous lack of justification. Our results pave the way for the proper use of FNs and thresholding methods, and provide insights for future research in individualized parcellations.

Duong-Tran, Duy (ORCID:0009000944967575)↗

The connectome of the adult Drosophila mushroom body provides insights into function

Making inferences about the computations performed by neuronal circuits from synapse-level connectivity maps is an emerging opportunity in neuroscience. The mushroom body (MB) is well positioned for developing and testing such an approach due to its conserved neuronal architecture, recently completed dense connectome, and extensive prior experimental studies of its roles in learning, memory, and activity regulation. Here, we identify new components of the MB circuit in Drosophila , including extensive visual input and MB output neurons (MBONs) with direct connections to descending neurons. We find unexpected structure in sensory inputs, in the transfer of information about different sensory modalities to MBONs, and in the modulation of that transfer by dopaminergic neurons (DANs). We provide insights into the circuitry used to integrate MB outputs, connectivity between the MB and the central complex and inputs to DANs, including feedback from MBONs. Our results provide a foundation for further theoretical and experimental work.

Li, Feng↗

Discriminative analysis of schizophrenia patients using graph convolutional networks: A combined multimodal MRI and connectomics analysis

Introduction Recent studies in human brain connectomics with multimodal magnetic resonance imaging (MRI) data have widely reported abnormalities in brain structure, function and connectivity associated with schizophrenia (SZ). However, most previous discriminative studies of SZ patients were based on MRI features of brain regions, ignoring the complex relationships within brain networks. Methods We applied a graph convolutional network (GCN) to discriminating SZ patients using the features of brain region and connectivity derived from a combined multimodal MRI and connectomics analysis. Structural magnetic resonance imaging (sMRI) and resting-state functional magnetic resonance imaging (rs-fMRI) data were acquired from 140 SZ patients and 205 normal controls. Eighteen types of brain graphs were constructed for each subject using 3 types of node features, 3 types of edge features, and 2 brain atlases. We investigated the performance of 18 brain graphs and used the TopK pooling layers to highlight salient brain regions (nodes in the graph). Results The GCN model, which used functional connectivity as edge features and multimodal features (sMRI + fMRI) of brain regions as node features, obtained the highest average accuracy of 95.8%, and outperformed other existing classification studies in SZ patients. In the explainability analysis, we reported that the top 10 salient brain regions, predominantly distributed in the prefrontal and occipital cortices, were mainly involved in the systems of emotion and visual processing. Discussion Our findings demonstrated that GCN with a combined multimodal MRI and connectomics analysis can effectively improve the classification of SZ at an individual level, indicating a promising direction for the diagnosis of SZ patients. The code is available at https://github.com/CXY-scut/GCN-SZ.git .

Chen, Xiaoyi↗

Editorial: Functional microcircuits in the brain and in artificial intelligent systems

Fundamental principles underlying higher-order cognitive functions remain elusive, but recent breakthroughs in neurophysiology and deep learning offer new perspectives. First, experimental studies have uncovered neural circuit motifs consisting of various neuron types; see Brain Initiative Cell Census Network (https://www.nature.com/collections/cicghheddj). For example, inhibitory neuron types expressing exclusive genes have specific targets and distinct functions (Pfeffer et al., 2013). Furthermore, diverse neuron types in cortex and their connectomes were identified in cortical columns (Jiang et al., 2015); see also Barth et al. (2016) for a debate on neuron types. Second, artificial neural networks were originally inspired by structures of the brain (McCulloch and Pitts, 1943) and could be trained to perform complex functions similar to human perception/cognition by deep learning (DL) (Lecun et al., 2015).

59 BASIC BIOLOGICAL SCIENCES↗

Mean Field Theory of Self‐Organizing Memristive Connectomes

Abstract Biological neuronal networks are characterized by nonlinear interactions and complex connectivity. Given the growing impetus to build neuromorphic computers, understanding physical devices that exhibit structures and functionalities similar to biological neural networks is an important step toward this goal. Self‐organizing circuits of nanodevices are at the forefront of the research in neuromorphic computing, as their behavior mimics synaptic plasticity features of biological neuronal circuits. However, an effective theory to describe their behavior is lacking. This study provides for the first time an effective mean field theory for the emergent voltage‐induced polymorphism of circuits of a nanowire connectome, showing that the behavior of these circuits can be explained by a low‐dimensional dynamical equation. The equation can be derived from the microscopic dynamics of a single memristive junction in analytical form. The effective model is tested on experiments of nanowire networks and show that it fits both the potentiation and depression of these synapse‐mimicking circuits. It is shown that this theory applies beyond the case of nanowire networks by formulating a general mean‐field theory of conductance transitions in self‐organizing memristive connectomes.

Caravelli, Francesco↗

Diversity of visual inputs to Kenyon cells of the Drosophila mushroom body

The arthropod mushroom body is well-studied as an expansion layer representing olfactory stimuli and linking them to contingent events. However, 8% of mushroom body Kenyon cells in Drosophila melanogaster receive predominantly visual input, and their function remains unclear. Here, we identify inputs to visual Kenyon cells using the FlyWire adult whole-brain connectome. Input repertoires are similar across hemispheres and connectomes with certain inputs highly overrepresented. Many visual neurons presynaptic to Kenyon cells have large receptive fields, while interneuron inputs receive spatially restricted signals that may be tuned to specific visual features. Individual visual Kenyon cells randomly sample sparse inputs from combinations of visual channels, including multiple optic lobe neuropils. These connectivity patterns suggest that visual coding in the mushroom body, like olfactory coding, is sparse, distributed, and combinatorial. However, the specific input repertoire to the smaller population of visual Kenyon cells suggests a constrained encoding of visual stimuli.

59 BASIC BIOLOGICAL SCIENCES↗

Whole nervous system expression of glutamate receptors reveals distinct receptor roles in sensorimotor circuits

A goal of connectomics is to reveal the links between neural circuits and behavior. Larvae of the primitive chordateCionaare well-suited to make contributions in this area. In addition to having a described connectome,Cionalarvae have a range of readily-quantified behaviors. Moreover, the small number of neurons in the larval CNS (∼180) holds the promise of a comprehensive characterization of individual neurons. We present single-neuron predictions for glutamate receptor (GlutR) expression based onin situhybridization. Included are both ionotropic receptors (AMPA, NMDA, and Kainate), and metabotropic receptors. The predicted glutamate receptor expression dataset is discussed in the context of known circuits driving behaviors such as phototaxis, mechanosensation, and looming shadow response. The predicted expression of AMPA and NMDA receptors may help to resolve issues regarding the co-production of GABA and glutamate by a subset of photoreceptors. The targets of these photoreceptors in the midbrain appear to express NMDA receptors, but not AMPA receptors. This is in agreement with previous results indicating that GABA is the primary neurotransmitter from the photoreceptors evoking a swimming response through a disinhibition mechanism, and that glutamate may, therefore, have only a modulatory action in this circuit. Other findings reported here are more unexpected. For example, many of the targets of glutamatergic epidermal sensory neurons (ESNs) do not express any of the ionotropic receptors, yet the ESNs themselves express metabotropic receptors. Thus, we speculate that their production of glutamate may be for communication with neighboring ESNs, rather than to their interneuron targets. Significance StatementSimple invertebrates offer a tractable alternative to complex vertebrate brains, facilitating holistic understanding of brain function. One such invertebrate is the marine chordateCiona, which has the benefit of a complete synaptic wiring diagram for its swimming larva. This “connectome” allowed identification of putative neural circuits driving defined behaviors. Fuller understanding of neural circuits, however, requires a description of the attributes of individual neurons. This study focuses on the excitatory neurotransmitter glutamate, which signals via a complex set of both ionotropic and metabotropic receptors. Here, we present a nervous system-wide prediction of GlutR expression inCionaat the individual neuron level, considered in the context of neural circuits, with emphasis on how GlutR expression accounts for function of neural circuits.

Neurosciences & Neurology↗

CRCNS US-France Research Proposal: Collaborative Research: Encoding reward expectation in Drosophilia

The fruit fly Drosophila melanogaster has been a valuable model for investigating the genetic and neural bases that underlie learning and memory. Early and most current studies use basic behavior conditioning protocols to study learning in controlled laboratory settings. More recently, the ability to transgenically manipulate many of the brain neurons in the fruit fly with exquisite specificity, and the recent knowledge of the synaptic ‘connectome’ of the fruit fly brain, makes these animals almost unique as a comprehensive model for studies of learning, memory and motivated behavior. In fact, the connectome has revealed many types of new connections that had until now been overlooked. Within this context, the thesis of this proposal is that studies of learning and memory will be greatly enhanced by using more sophisticated means for evaluating memory representations, such as have been developed in vertebrates, and combining those studies with information from the connectome guided by computational modelling. We propose to push beyond the boundaries of existing conditioning protocols for fruit flies to investigate more complex memory representations. In particular, we will investigate the function of reinforcement pathways in relation to the absence of expected reinforcement. More specifically, we propose a series of experiments designed to investigate the memory representations in fruit flies when an expected consequence of a Conditioned Stimulus (CS) fails to occur. Although studies have evaluated how this failure can establish extinction memory for the CS, our studies will go beyond studying extinction. Specifically, we predict that in Drosophila when a CS is associated with a failed expectation of an appetitive food reinforcement it will acquire aversive value, and vice versa for a failed expectation of an aversive reinforcer. We combine these studies with manipulations of reinforcement pathways in the CNS inspired from the connectome, iteratively knitted in with established computational models. Intellectual Merit: The concept of reinforcement expectation and incentive contrast have been influential in the development of studies of associative learning in mammals. These questions are particularly challenging to answer in vertebrates because they require exquisite cellular, temporal, and genetic specificity of experimental manipulations. The recent development of work with identified neurons and their connectomes makes the larval and adult fly brains ripe as models for pushing our understanding of neural bases for these higher- order conditioning phenomena. Broader Impacts: Public health: These analyses and the conceptual framework of prediction error processing underlying them have a profound impact on our understanding of reinforcement-related behavior in humans, including monetary rewards and the mnemonic consequences of traumatic experiences, and for pathologies of the dopamine reinforcement system. Educational: This project will provide interdisciplinary training for postdoctoral researchers, Ph.D. and undergraduate students. The PIs will act as co-supervisors or mentors of students working in the different labs via face-to-face and internet-based technologies. We will also work with ASU’s award-winning Ask- A-Biologist program. This is an online science program designed to enrich the learning experiences of students of all ages and to provide classroom material for use by K-12 teachers. We will develop an extension of a game developed under a prior NSF award, and the new game will include modules to teach K-12 students about how insects learn. We will also integrate into the AAB site a program developed by a collaborator (B Gerber) at the Leibniz Institut für Neurobiologie, Magdeburg, and now in use in schools in Germany, to teach K-12 students how to train animals using the fruit fly larval learning paradigm. Underrepresented groups: All PIs will work with their university offices of Academic Diversity and Equal Opportunity for reaching underrepresented students.

59 BASIC BIOLOGICAL SCIENCES↗

Structural connectivity in schizophrenia and its impact on the dynamics of spontaneous functional networks

The neuropathology of schizophrenia remains unclear. Some insight has come from modern neuroimaging techniques, which offer an unparalleled opportunity to explore in vivo the structure and function of the brain. Using functional magnetic resonance imaging, it has been found that the large-scale resting-state functional connectivity (rsFC) in schizophrenia — measured as the temporal correlations of the blood-oxygen-level-dependent (BOLD) signal — exhibit altered network topology, with lower small-world index. The origin of these rsFC alterations and link with the underlying structural connectivity remain unclear. In this work, we used a computational model of spontaneous large-scale brain activity to explore the role of the structural connectivity in the large-scale dynamics of the brain in health and schizophrenia. The structural connectomes from 15 adolescent patients with early-onset schizophrenia and 15 age- and gender-matched controls were built from diffusion tensor imaging data to detect the white matter tracts between 90 brain areas. Brain areas, simulated using a reduced dynamic mean-field model, receive excitatory input from other areas in proportion to the number of fibre tracts between them. The simulated mean field activity was transformed into BOLD signal, and the properties of the simulated functional networks were analyzed. Our results suggest that the functional alterations observed in schizophrenia are not directly linked to alterations in the structural topology. Instead, subtly randomized and less small-world functional networks appear when the brain operates with lower global coupling, which shifts the dynamics from the optimal healthy regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Brain Connectivity Workshop Series Report

The National Institutes of Health (NIH) BRAIN Initiative aims to accelerate development and application of technologies that show how individual brain cells in complex neural circuits interact at the speed of thought and action. Complete wiring diagrams of the mammalian brain will revolutionize the capabilities of researchers to formulate and test models of how activity within brain circuits drives coordinated function and behavior. A top priority for the BRAIN Initiative, motivated by the strategic guidance of the BRAIN 2.0 Working Group report, is to muster the resources and foster the collaborations needed to generate these wiring diagrams at the level of long-range projections (“projectomes”) and synapses (“connectomes”) in whole mammalian brains, including those from rodents, humans, and other large-brained mammals. Achieving the scale and resolution necessary to characterize and use these projectomes and connectomes will not only push the boundaries of current imaging and computational capabilities to generate faster, cheaper, and more scalable technologies, but also drive broad innovation in data science, artificial intelligence, and machine learning.

42 ENGINEERING↗

Attend and Decode: 4D fMRI Task State Decoding Using Attention Models

Source code for Brain Attend and Decode paper. Functional magnetic resonance imaging (fMRI) is a neuroimaging modality that captures the blood oxygen level in a subject's brain while the subject either rests or performs a variety of functional tasks under different conditions. Given fMRI data, the problem of inferring the task, known as task state decoding, is challenging due to the high dimensionality (hundreds of million sampling points per datum) and complex spatio-temporal blood flow patterns inherent in the data. In this work, we propose to tackle the fMRI task state decoding problem by casting it as a 4D spatiotemporal classification problem. We present a novel architecture called Brain Attend and Decode (BAnD), that uses residual convolutional neural networks for spatial feature extraction and self-attention mechanisms for temporal modeling. We achieve significant performance gain compared to previous works on a 7-task benchmark from the large-scale Human Connectome Project-Young Adult (HCP-YA) dataset. We also investigate the transferability of BAnD's extracted features on unseen HCP tasks, either by freezing the spatial feature extraction layers and retraining the temporal model, or finetuning the entire model. The pre-trained features from BAnD are useful on similar tasks while finetuning them yields competitive results on unseen tasks/conditions.

Ng, BrendaM.↗