Subgraphs of functional brain networks identify dynamical constraints of cognitive control

MEA-NAP compares microscale functional connectivity, topology, and network dynamics in organoid or monolayer neuronal cultures

Microelectrode array (MEA) recordings are commonly used to compare firing and burst rates in neuronal cultures. MEA recordings can also reveal microscale functional connectivity, topology, and network dynamics-patterns seen in brain networks across spatial scales. Network topology is frequently characterized in neuroimaging with graph theoretical metrics. However, few computational tools exist for analyzing microscale functional brain networks from MEA recordings. Here, we present a MATLAB MEA network analysis pipeline (MEA-NAP) for raw voltage time-series acquired from single- or multi-well MEAs. Applications to 3D human cerebral organoids or 2D human-derived or murine cultures reveal differences in network development, including topology, node cartography, and dimensionality. MEA-NAP incorporates multi-unit template-based spike detection, probabilistic thresholding for determining significant functional connections, and normalization techniques for comparing networks. MEA-NAP can identify network-level effects of pharmacologic perturbation and/or disease-causing mutations and, thus, can provide a translational platform for revealing mechanistic insights and screening new therapeutic approaches.

Individual peak alpha frequency does not index individual differences in inhibitory cognitive control

Previous work has indicated that individual differences in cognitive performance can be predicted by characteristics of resting state oscillations, such as individual peak alpha frequency (IAF). Although IAF has previously been correlated with cognitive functions, such as memory, attention, or mental speed, its link to cognitive conflict processing remains unexplored. The current work investigated the relationship between IAF and incl-established conflict tasks, Stroop and Navon task, while also controlling for alpha power, theta power, and the 1/f offset of aperiodic broadband activity. In Bayesian analyses on a large sample of 127 healthy participants, we found substantial evidence against the assumption that IAF predicts individual abilities to spontaneously exert cognitive control. Similarly, our findings yielded substantial evidence against links between cognitive control and resting state power in the alpha and theta bands or between cognitive control and aperiodic 1/f offset. In sum, our results challenge frameworks suggesting that an individual's ability to spontaneously engage attentional control networks may be mirrored in resting state EEG characteristics.

Enhancing cognitive control with transcranial magnetic stimulation in subject-specific frontoparietal networks

BACKGROUND

Cognitive control processes, including those involving frontoparietal networks, are highly variable between individuals, posing challenges to basic and clinical sciences. While distinct frontoparietal networks have been associated with specific cognitive control functions such as switching, inhibition, and working memory updating functions, there have been few basic tests of the role of these networks at the individual level.

METHODS

To examine the role of cognitive control at the individual level, we conducted a within-subject excitatory transcranial magnetic stimulation (TMS) study in 19 healthy individuals that targeted intrinsic ("resting") frontoparietal networks. Person-specific intrinsic networks were identified with resting state functional magnetic resonance imaging scans to determine TMS targets. The participants performed three cognitive control tasks: an adapted Navon figure-ground task (requiring set switching), n-back (working memory), and Stroop color-word (inhibition).

OBJECTIVE

Hypothesis: We predicted that stimulating a network associated with externally oriented control [the "FPCN-B" (fronto-parietal control network)] would improve performance on the set switching and working memory task relative to a network associated with attention (the Dorsal Attention Network, DAN) and cranial vertex in a full within-subjects crossover design.

RESULTS

We found that set switching performance was enhanced by FPCN-B stimulation along with some evidence of enhancement in the higher-demand n-back conditions.

CONCLUSION

Higher task demands or proactive control might be a distinguishing role of the FPCN-B, and personalized intrinsic network targeting is feasible in TMS designs.

Executive function and underlying brain network distinctions for callous-unemotional traits and conduct problems in adolescents

The complexity of executive function (EF) impairments in youth antisocial phenotypes of callous-unemotional (CU) traits and conduct problems (CP) challenge identifying phenotypic specific EF deficits. We can redress these challenges by (1) accounting for EF measurement error and (2) testing distinct functional brain properties accounting for differences in EF. Thus, we employed a latent modeling approach for EFs (inhibition, shifting, fluency, common EF) and extracted connection density from matching contemporary EF brain models with a sample of 112 adolescents (ages 13-17, 42% female). Path analysis indicated CU traits associated with lower inhibition. Inhibition network density positively associated with inhibition, but this association was strengthened by CU and attenuated by CP. Common EF associated with three-way interactions between density*CP by CU for the inhibition and shifting networks. This suggests those higher in CU require their brain to work harder for lower inhibition, whereas those higher in CP have difficulty engaging inhibitory brain responses. Additionally, those with CP interacting with CU show distinct brain patterns for a more general EF capacity. Importantly, modeling cross-network connection density in contemporary EF models to test EF involvement in core impairments in CU and CP may accelerate our understanding of EF in these phenotypes.

Network targets for therapeutic brain stimulation: towards personalized therapy for pain

Precision neuromodulation of central brain circuits is a promising emerging therapeutic modality for a variety of neuropsychiatric disorders. Reliably identifying in whom, where, and in what context to provide brain stimulation for optimal pain relief are fundamental challenges limiting the widespread implementation of central neuromodulation treatments for chronic pain. Current approaches to brain stimulation target empirically derived regions of interest to the disorder or targets with strong connections to these regions. However, complex, multidimensional experiences like chronic pain are more closely linked to patterns of coordinated activity across distributed large-scale functional networks. Recent advances in precision network neuroscience indicate that these networks are highly variable in their neuroanatomical organization across individuals. Here we review accumulating evidence that variable central representations of pain will likely pose a major barrier to implementation of population-derived analgesic brain stimulation targets. We propose network-level estimates as a more valid, robust, and reliable way to stratify personalized candidate regions. Finally, we review key background, methods, and implications for developing network topology-informed brain stimulation targets for chronic pain.

Dynamic Functional Connectivity of Emotion Processing in Beta Band with Naturalistic Emotion Stimuli

While naturalistic stimuli, such as movies, better represent the complexity of the real world and are perhaps crucial to understanding the dynamics of emotion processing, there is limited research on emotions with naturalistic stimuli. There is a need to understand the temporal dynamics of emotion processing and their relationship to different dimensions of emotion experience. In addition, there is a need to understand the dynamics of functional connectivity underlying different emotional experiences that occur during or prior to such experiences. To address these questions, we recorded the EEG of participants and asked them to mark the temporal location of their emotional experience as they watched a video. We also obtained self-assessment ratings for emotional multimedia stimuli. We calculated dynamic functional the connectivity (DFC) patterns in all the frequency bands, including information about hubs in the network. The change in functional networks was quantified in terms of temporal variability, which was then used in regression analysis to evaluate whether temporal variability in DFC (tvDFC) could predict different dimensions of emotional experience. We observed that the connectivity patterns in the upper beta band could differentiate emotion categories better during or prior to the reported emotional experience. The temporal variability in functional connectivity dynamics is primarily related to emotional arousal followed by dominance. The hubs in the functional networks were found across the right frontal and bilateral parietal lobes, which have been reported to facilitate affect, interoception, action, and memory-related processing. Since our study was performed with naturalistic real-life resembling emotional videos, the study contributes significantly to understanding the dynamics of emotion processing. The results support constructivist theories of emotional experience and show that changes in dynamic functional connectivity can predict aspects of our emotional experience.

Detection of Brain Network Communities During Natural Speech Comprehension From Functionally Aligned EEG Sources

In recent years, electroencephalograph (EEG) studies on speech comprehension have been extended from a controlled paradigm to a natural paradigm. Under the hypothesis that the brain can be approximated as a linear time-invariant system, the neural response to natural speech has been investigated extensively using temporal response functions (TRFs). However, most studies have modeled TRFs in the electrode space, which is a mixture of brain sources and thus cannot fully reveal the functional mechanism underlying speech comprehension. In this paper, we propose methods for investigating the brain networks of natural speech comprehension using TRFs on the basis of EEG source reconstruction. We first propose a functional hyper-alignment method with an additive average method to reduce EEG noise. Then, we reconstruct neural sources within the brain based on the EEG signals to estimate TRFs from speech stimuli to source areas, and then investigate the brain networks in the neural source space on the basis of the community detection method. To evaluate TRF-based brain networks, EEG data were recorded in story listening tasks with normal speech and time-reversed speech. To obtain reliable structures of brain networks, we detected TRF-based communities from multiple scales. As a result, the proposed functional hyper-alignment method could effectively reduce the noise caused by individual settings in an EEG experiment and thus improve the accuracy of source reconstruction. The detected brain networks for normal speech comprehension were clearly distinctive from those for non-semantically driven (time-reversed speech) audio processing. Our result indicates that the proposed source TRFs can reflect the cognitive processing of spoken language and that the multi-scale community detection method is powerful for investigating brain networks.

Investigation of functional brain network reconfiguration during exposure to naturalistic stimuli using graph-theoretical analysis

Objective.One of the most significant features of the human brain is that it can dynamically reconfigure itself to adapt to a changing environment. However, dynamic interaction characteristics of the brain networks in naturalistic scenes remain unclear.Approach.We used open-source functional magnetic resonance imaging (fMRI) data from 15 participants who underwent fMRI scans while watching an audio-visual movie 'Forrest Gump'. The community detection algorithm based on inter-subject functional correlation was used to study the time-varying functional networks only induced by the movie stimuli. The whole brain reconfiguration patterns were quantified by the temporal co-occurrence matrix that describes the probability of two brain regions engage in the same community (or putative functional module) across time and the time-varying brain modularity. Four graph metrics of integration, recruitment, spatio-temporal diversity and within-community normalised centrality were further calculated to summarise the brain network dynamic roles and hub features in their spatio-temporal topology.Main results.Our results suggest that the networks that were involved in attention and audio-visual information processing, such as the visual network, auditory network, and dorsal attention network, were considered to play a role of 'stable loners'. By contrast, 'unstable loner' networks such as the default mode network (DMN) and fronto-parietal network tended to interact more flexibly with the other networks. In addition, global brain network showed significant fluctuations in modularity. The 'stable loner' networks always maintained high functional connectivity (FC) strength while 'unstable loner' networks, especially the DMN, exhibited high intra- and inter-network FC only during a low modularity period. Finally, changes in brain modularity were significantly associated with variations in emotions induced by the movie.Significance.Our findings provide new insight for understanding the dynamic interaction characteristics of functional brain networks during naturalistic stimuli.

Long-term brain network reorganization predicts responsive neurostimulation outcomes for focal epilepsy

Responsive neurostimulation (RNS) devices, able to detect imminent seizures and to rapidly deliver electrical stimulation to the brain, are effective in reducing seizures in some patients with focal epilepsy. However, therapeutic response to RNS is often slow, is highly variable, and defies prognostication based on clinical factors. A prevailing view holds that RNS efficacy is primarily mediated by acute seizure termination; yet, stimulations greatly outnumber seizures and occur mostly in the interictal state, suggesting chronic modulation of brain networks that generate seizures. Here, using years-long intracranial neural recordings collected during RNS therapy, we found that patients with the greatest therapeutic benefit undergo progressive, frequency-dependent reorganization of interictal functional connectivity. The extent of this reorganization scales directly with seizure reduction and emerges within the first year of RNS treatment, enabling potential early prediction of therapeutic response. Our findings reveal a mechanism for RNS that involves network plasticity and may inform development of next-generation devices for epilepsy.

Atypical core-periphery brain dynamics in autism

The intrinsic function of the human brain is dynamic, giving rise to numerous behavioral subtypes that fluctuate distinctively at multiple timescales. One of the key dynamical processes that takes place in the brain is the interaction between core-periphery brain regions, which undergoes constant fluctuations associated with developmental time frames. Core-periphery dynamical changes associated with macroscale brain network dynamics span multiple timescales and may lead to atypical behavior and clinical symptoms. For example, recent evidence suggests that brain regions with shorter intrinsic timescales are located at the periphery of brain networks (e.g., sensorimotor hand, face areas) and are implicated in perception and movement. On the contrary, brain regions with longer timescales are core hub regions. These hubs are important for regulating interactions between the brain and the body during self-related cognition and emotion. In this review, we summarize a large body of converging evidence derived from time-resolved fMRI studies in autism to characterize atypical core-periphery brain dynamics and how they relate to core and contextual sensory and cognitive profiles.

Multimodal in vivo recording using transparent graphene microelectrodes illuminates spatiotemporal seizure dynamics at the microscale

Neurological disorders such as epilepsy arise from disrupted brain networks. Our capacity to treat these disorders is limited by our inability to map these networks at sufficient temporal and spatial scales to target interventions. Current best techniques either sample broad areas at low temporal resolution (e.g. calcium imaging) or record from discrete regions at high temporal resolution (e.g. electrophysiology). This limitation hampers our ability to understand and intervene in aberrations of network dynamics. Here we present a technique to map the onset and spatiotemporal spread of acute epileptic seizures in vivo by simultaneously recording high bandwidth microelectrocorticography and calcium fluorescence using transparent graphene microelectrode arrays. We integrate dynamic data features from both modalities using non-negative matrix factorization to identify sequential spatiotemporal patterns of seizure onset and evolution, revealing how the temporal progression of ictal electrophysiology is linked to the spatial evolution of the recruited seizure core. This integrated analysis of multimodal data reveals otherwise hidden state transitions in the spatial and temporal progression of acute seizures. The techniques demonstrated here may enable future targeted therapeutic interventions and novel spatially embedded models of local circuit dynamics during seizure onset and evolution.

Learning Clique Subgraphs in Structural Brain Network Classification with Application to Crystallized Cognition

Structural brain networks constructed from diffusion MRI are important biomarkers for understanding human brain structure and its relation to cognitive functioning. There is increasing interest in learning differences in structural brain networks between groups of subjects in neuroimaging studies, leading to a variable selection problem in network classification. Traditional methods often use independent edgewise tests or unstructured generalized linear model (GLM) with regularization on vectorized networks to select edges distinguishing the groups, which ignore the network structure and make the results hard to interpret. In this paper, we develop a symmetric bilinear logistic regression (SBLR) with elastic-net penalty to identify a set of small clique subgraphs in network classification. Clique subgraphs, consisting of all the interconnections among a subset of brain regions, have appealing neurological interpretations as they may correspond to some anatomical circuits in the brain related to the outcome. We apply this method to study differences in the structural connectome between adolescents with high and low crystallized cognitive ability, using the crystallized cognition composite score, picture vocabulary and oral reading recognition tests from NIH Toolbox. A few clique subgraphs containing several small sets of brain regions are identified between different levels of functioning, indicating their importance in crystallized cognition.

Transcranial direct current stimulation modulates brain functional connectivity in autism

Autism spectrum disorder (ASD) is characterized by deficits in social interactions, impairments in language and communication, and highly restricted behavioral interests. Transcranial direct current stimulation (tDCS) is a widely used form of noninvasive stimulation and may have therapeutic potential for ASD. So far, despite the widespread use of this technique in the neuroscience field, its effects on network-level neural activity and the underlying mechanisms of any effects are still unclear. In the present study, we used electroencephalography (EEG) to investigate tDCS induced brain network changes in children with ASD before and after active and sham stimulation. We recorded 5 min of resting state EEG before and after a single session of tDCS (of approximately 20 min) over dorsolateral prefrontal cortex (DLPFC). Two network-based methods were applied to investigate tDCS modulation on brain networks: 1) temporal network dynamics were analyzed by comparing "flexibility" changes before vs after stimulation, and 2) frequency specific network changes were identified using non-negative matrix factorization (NMF). We found 1) an increase in network flexibility following tDCS (rapid network configuration of dynamic network communities), 2) specific increase in interhemispheric connectivity within the alpha frequency band following tDCS. Together, these results demonstrate that tDCS could help modify both local and global brain network dynamics, and highlight stimulation-induced differences in the manifestation of network reconfiguration. Meanwhile, frequency-specific subnetworks, as a way to index local and global information processing, highlight the core modulatory effects of tDCS on the modular architecture of the functional connectivity patterns within higher frequency bands.

Structural Controllability Predicts Functional Patterns and Brain Stimulation Benefits Associated with Working Memory

The brain is an inherently dynamic system, and much work has focused on the ability to modify neural activity through both local perturbations and changes in the function of global network ensembles. Network controllability is a recent concept in network neuroscience that purports to predict the influence of individual cortical sites on global network states and state changes, thereby creating a unifying account of local influences on global brain dynamics. While this notion is accepted in engineering science, it is subject to ongoing debates in neuroscience as empirical evidence linking network controllability to brain activity and human behavior remains scarce. Here, we present an integrated set of multimodal brain-behavior relationships derived from fMRI, diffusion tensor imaging, and online repetitive transcranial magnetic stimulation (rTMS) applied during an individually calibrated working memory task performed by individuals of both sexes. The modes describing the structural network system dynamics showed direct relationships to brain activity associated with task difficulty, with difficult-to-reach modes contributing to functional brain states in the hard task condition. Modal controllability (a measure quantifying the contribution of difficult-to-reach modes) at the stimulated site predicted both fMRI activations associated with increasing task difficulty and rTMS benefits on task performance. Furthermore, fMRI explained 64% of the variance between modal controllability and the working memory benefit associated with 5 Hz online rTMS. These results therefore provide evidence toward the functional validity of network control theory, and outline a clear technique for integrating structural network topology and functional activity to predict the influence of stimulation on subsequent behavior.SIGNIFICANCE STATEMENT The network controllability concept proposes that specific cortical nodes are able to steer the brain into certain physiological states. By applying external perturbation to these control nodes, it is theorized that brain stimulation is able to selectively target difficult-to-reach states, potentially aiding processing and improving performance on cognitive tasks. The current study used rTMS and fMRI during a working memory task to test this hypothesis. We demonstrate that network controllability correlates with fMRI modulation because of working memory load and with the behavioral improvements that result from a multivisit intervention using 5 Hz rTMS. This study demonstrates the validity of network controllability and offers a new targeting approach to improve efficacy.

Functional brain network reconfiguration during learning in a dynamic environment

When learning about dynamic and uncertain environments, people should update their beliefs most strongly when new evidence is most informative, such as when the environment undergoes a surprising change or existing beliefs are highly uncertain. Here we show that modulations of surprise and uncertainty are encoded in a particular, temporally dynamic pattern of whole-brain functional connectivity, and this encoding is enhanced in individuals that adapt their learning dynamics more appropriately in response to these factors. The key feature of this whole-brain pattern of functional connectivity is stronger connectivity, or functional integration, between the fronto-parietal and other functional systems. Our results provide new insights regarding the association between dynamic adjustments in learning and dynamic, large-scale changes in functional connectivity across the brain.

Identifying brain network topology changes in task processes and psychiatric disorders

A central goal in neuroscience is to understand how dynamic networks of neural activity produce effective representations of the world. Advances in the theory of graph measures raise the possibility of elucidating network topologies central to the construction of these representations. We leverage a result from the description of lollipop graphs to identify an iconic network topology in functional magnetic resonance imaging data and characterize changes to those networks during task performance and in populations diagnosed with psychiatric disorders. During task performance, we find that task-relevant subnetworks change topology, becoming more integrated by increasing connectivity throughout cortex. Analysis of resting state connectivity in clinical populations shows a similar pattern of subnetwork topology changes; resting scans becoming less default-like with more integrated sensory paths. The study of brain network topologies and their relationship to cognitive models of information processing raises new opportunities for understanding brain function and its disorders.

More Flexible Integration of Functional Systems After Musical Training in Young Adults

Musical training, because it involves the interaction and integration of diverse functional systems, is an excellent model to investigate training-induced brain plasticity. The human brain functions in a network architecture in which dynamic modules and subgraphs are considered to enable efficient information communication. However, it remains largely unknown how the dynamic integration of functional systems changes with musical training, which may provide new insight into musical training-induced brain plasticity and further the use of music therapy for neuropsychiatric disease and brain injury. Here, 29 healthy young adult novices who received 24 weeks of piano training, and another 27 novices without any intervention were scanned at three time points-before and after musical training and 12 weeks after training. We used nonnegative matrix factorization to identify a set of subgraphs and their corresponding time-dependent coefficients from a concatenated functional network of all the subjects in sliding time windows. The energy and entropy of the time-dependent coefficients were computed to quantify the subgraph's dynamic changes in expression. The training group showed a significantly increased energy of the time-dependent coefficients of 3 subgraphs after training. Furthermore, one of the subgraphs, comprised of primary functional systems and cingulo-opercular task control and salience systems, showed significantly changed entropy in the training group after training. Our results suggest that the integration of functional systems undergoes increased flexibility in fine-scale dynamics after musical training, which reveals how brain functional systems engage in musical performance. The efficacy of musical training induced brain plasticity may provide new therapeutic strategies for brain injury and neuropsychiatric disorders.

Developmental Maturation of the Precuneus as a Functional Core of the Default Mode Network

Efforts to map the functional architecture of the developing human brain have shown that connectivity between and within functional neural networks changes from childhood to adulthood. Although prior work has established that the adult precuneus distinctively modifies its connectivity during task versus rest states [Utevsky, A. V., Smith, D. V., & Huettel, S. A. Precuneus is a functional core of the default-mode network. Journal of Neuroscience, 34, 932-940, 2014], it remains unknown how these connectivity patterns emerge over development. Here, we use fMRI data collected at two longitudinal time points from over 250 participants between the ages of 8 and 26 years engaging in two cognitive tasks and a resting-state scan. By applying independent component analysis to both task and rest data, we identified three canonical networks of interest-the rest-based default mode network and the task-based left and right frontoparietal networks (LFPN and RFPN, respectively)-which we explored for developmental changes using dual regression analyses. We found systematic state-dependent functional connectivity in the precuneus, such that engaging in a task (compared with rest) resulted in greater precuneus-LFPN and precuneus-RFPN connectivity, whereas being at rest (compared with task) resulted in greater precuneus-default mode network connectivity. These cross-sectional results replicated across both tasks and at both developmental time points. Finally, we used longitudinal mixed models to show that the degree to which precuneus distinguishes between task and rest states increases with age, due to age-related increasing segregation between precuneus and LFPN at rest. Our results highlight the distinct role of the precuneus in tracking processing state, in a manner that is both present throughout and strengthened across development.

Centralized and distributed cognitive task processing in the human connectome

A key question in modern neuroscience is how cognitive changes in a human brain can be quantified and captured by functional connectivity (FC). A systematic approach to measure pairwise functional distance at different brain states is lacking. This would provide a straightforward way to quantify differences in cognitive processing across tasks; also, it would help in relating these differences in task-based FCs to the underlying structural network. Here we propose a framework, based on the concept of Jensen-Shannon divergence, to map the task-rest connectivity distance between tasks and resting-state FC. We show how this information theoretical measure allows for quantifying connectivity changes in distributed and centralized processing in functional networks. We study resting state and seven tasks from the Human Connectome Project dataset to obtain the most distant links across tasks. We investigate how these changes are associated with different functional brain networks, and use the proposed measure to infer changes in the information-processing regimes. Furthermore, we show how the FC distance from resting state is shaped by structural connectivity, and to what extent this relationship depends on the task. This framework provides a well-grounded mathematical quantification of connectivity changes associated with cognitive processing in large-scale brain networks.

Correction: Subgraphs of functional brain networks identify dynamical constraints of cognitive control

[This corrects the article DOI: 10.1371/journal.pcbi.1006234.].