The Energy Landscape of Neurophysiological Activity Implicit in Brain Network Structure

Brain dynamics alterations induced by partial sleep deprivation: An energy landscape study

Partial sleep deprivation (PSD) alters neural activity of intrinsic brain networks involved in cognitive functions. However, the age-related time-varying properties of large-scale brain functional networks after PSD remain unknown. Our study applied energy landscape analysis to resting-state functional magnetic resonance imaging data to characterize the dominant brain activity patterns in 36 healthy young (19 females, 23.53 ± 2.36 years) and 33 healthy older (18 females, 68.81 ± 2.41 years) adults after full sleep (FS) and PSD. Dynamic properties of these patterns, including appearance probability, duration and transitions, were then calculated. Finally, a 105 steps numerical simulation was performed on each energy landscape. We found that the energy landscapes of the younger and older groups had similar hierarchical structures, including two major states and two minor states. The two major states showed complementary spontaneous activation patterns. But the PSD has altered the temporal evolution of these major brain states in younger participants, manifested by significantly higher appearance frequency of the major states and the direct transitions between major states than FS. These changes were not significant in older participants. Additionally, the weaker functional segregation between two modules assigned by two complementary major states was found during PSD than FS in young group. We further demonstrated that such abnormal brain network functional coordination was associated with the atypical brain dynamics and behaviors. These findings suggested a low-dimensional and restricted dynamic landscape of brain activity in young adults after PSD and provided new insight into understand the neural effects of PSD.

Entropy and Complexity Tools Across Scales in Neuroscience: A Review

Understanding the brain's intricate dynamics across multiple scales-from cellular interactions to large-scale brain behavior-remains one of the most significant challenges in modern neuroscience. Two key concepts, entropy and complexity, have been increasingly employed by neuroscientists as powerful tools for characterizing the interplay between structure and function in the brain across scales. The flexibility of these two concepts enables researchers to explore quantitatively how the brain processes information, adapts to changing environments, and maintains a delicate balance between order and disorder. This review illustrates the main tools and ideas to study neural phenomena using these concepts. This review does not delve into the specific methods or analyses of each study. Instead, it aims to offer a broad overview of how these tools are applied within the neuroscientific community and how they are transforming our understanding of the brain. We focus on their applications across scales, discuss the strengths and limitations of different metrics, and examine their practical applications and theoretical significance.

The brain selectively allocates energy to functional brain networks under cognitive control

Network energy has been conceptualized based on structural balance theory in the physics of complex networks. We utilized this framework to assess the energy of functional brain networks under cognitive control and to understand how energy is allocated across canonical functional networks during various cognitive control tasks. We extracted network energy from functional connectivity patterns of subjects who underwent fMRI scans during cognitive tasks involving working memory, inhibitory control, and cognitive flexibility, in addition to task-free scans. We found that the energy of the whole-brain network increases when exposed to cognitive control tasks compared to the task-free resting state, which serves as a reference point. The brain selectively allocates this elevated energy to canonical functional networks; sensory networks receive more energy to support flexibility for processing sensory stimuli, while cognitive networks relevant to the task, functioning efficiently, require less energy. Furthermore, employing network energy, as a global network measure, improves the performance of predictive modeling, particularly in classifying cognitive control tasks and predicting chronological age. Our results highlight the robustness of this framework and the utility of network energy in understanding brain and cognitive mechanisms, including its promising potential as a biomarker for mental conditions and neurological disorders.

Symmetry breaking organizes the brain's resting state manifold

Spontaneously fluctuating brain activity patterns that emerge at rest have been linked to the brain's health and cognition. Despite detailed descriptions of the spatio-temporal brain patterns, our understanding of their generative mechanism is still incomplete. Using a combination of computational modeling and dynamical systems analysis we provide a mechanistic description of the formation of a resting state manifold via the network connectivity. We demonstrate that the symmetry breaking by the connectivity creates a characteristic flow on the manifold, which produces the major data features across scales and imaging modalities. These include spontaneous high-amplitude co-activations, neuronal cascades, spectral cortical gradients, multistability, and characteristic functional connectivity dynamics. When aggregated across cortical hierarchies, these match the profiles from empirical data. The understanding of the brain's resting state manifold is fundamental for the construction of task-specific flows and manifolds used in theories of brain function. In addition, it shifts the focus from the single recordings towards the brain's capacity to generate certain dynamics characteristic of health and pathology.

The alterations of repetitive transcranial magnetic stimulation on the energy landscape of resting-state networks differ across the human cortex

Repetitive transcranial magnetic stimulation (rTMS) is a promising intervention tool for the noninvasive modulation of brain activity and behavior in neuroscience research and clinical settings. However, the resting-state dynamic evolution of large-scale functional brain networks following rTMS has rarely been investigated. Here, using resting-state fMRI images collected from 23 healthy individuals before (baseline) and after 1 Hz rTMS of the left frontal (FRO) and occipital (OCC) lobes, we examined the different effects of rTMS on brain dynamics across the human cortex. By fitting a pairwise maximum entropy model (pMEM), we constructed an energy landscape for the baseline and poststimulus conditions by fitting a pMEM. We defined dominant brain states (local minima) in the energy landscape with synergistic activation and deactivation patterns of large-scale functional networks. We calculated state dynamics including appearance probability, transitions and duration. The results showed that 1 Hz rTMS induced increased and decreased state probability, transitions and duration when delivered to the FRO and OCC targets, respectively. Most importantly, the shortest path and minimum cost between dominant brain states were altered after stimulation. The absolute sum of the costs from the source states to the destinations was lower after OCC stimulation than after FRO stimulation. In conclusion, our study characterized the dynamic trajectory of state transitions in the energy landscape and suggested that local rTMS can induce significant dynamic perturbation involving stimulated and distant functional networks, which aligns with the modern view of the dynamic and complex brain. Our results suggest low-dimensional mapping of rTMS-induced brain adaption, which will contribute to a broader and more effective application of rTMS in clinical settings.

Power and reproducibility in the external validation of brain-phenotype predictions

Brain-phenotype predictive models seek to identify reproducible and generalizable brain-phenotype associations. External validation, or the evaluation of a model in external datasets, is the gold standard in evaluating the generalizability of models in neuroimaging. Unlike typical studies, external validation involves two sample sizes: the training and the external sample sizes. Thus, traditional power calculations may not be appropriate. Here we ran over 900 million resampling-based simulations in functional and structural connectivity data to investigate the relationship between training sample size, external sample size, phenotype effect size, theoretical power and simulated power. Our analysis included a wide range of datasets: the Healthy Brain Network, the Adolescent Brain Cognitive Development Study, the Human Connectome Project (Development and Young Adult), the Philadelphia Neurodevelopmental Cohort, the Queensland Twin Adolescent Brain Project, and the Chinese Human Connectome Project; and phenotypes: age, body mass index, matrix reasoning, working memory, attention problems, anxiety/depression symptoms and relational processing. High effect size predictions achieved adequate power with training and external sample sizes of a few hundred individuals, whereas low and medium effect size predictions required hundreds to thousands of training and external samples. In addition, most previous external validation studies used sample sizes prone to low power, and theoretical power curves should be adjusted for the training sample size. Furthermore, model performance in internal validation often informed subsequent external validation performance (Pearson's r difference <0.2), particularly for well-harmonized datasets. These results could help decide how to power future external validation studies.

A Dynamic Entropy Approach Reveals Reduced Functional Network Connectivity Trajectory Complexity in Schizophrenia

Over the past decade and a half, dynamic functional imaging has revealed low-dimensional brain connectivity measures, identified potential common human spatial connectivity states, tracked the transition patterns of these states, and demonstrated meaningful transition alterations in disorders and over the course of development. Recently, researchers have begun to analyze these data from the perspective of dynamic systems and information theory in the hopes of understanding how these dynamics support less easily quantified processes, such as information processing, cortical hierarchy, and consciousness. Little attention has been paid to the effects of psychiatric disease on these measures, however. We begin to rectify this by examining the complexity of subject trajectories in state space through the lens of information theory. Specifically, we identify a basis for the dynamic functional connectivity state space and track subject trajectories through this space over the course of the scan. The dynamic complexity of these trajectories is assessed along each dimension of the proposed basis space. Using these estimates, we demonstrate that schizophrenia patients display substantially simpler trajectories than demographically matched healthy controls and that this drop in complexity concentrates along specific dimensions. We also demonstrate that entropy generation in at least one of these dimensions is linked to cognitive performance. Overall, the results suggest great value in applying dynamic systems theory to problems of neuroimaging and reveal a substantial drop in the complexity of schizophrenia patients' brain function.

Enhancing neural encoding models for naturalistic perception with a multi-level integration of deep neural networks and cortical networks

Cognitive neuroscience aims to develop computational models that can accurately predict and explain neural responses to sensory inputs in the cortex. Recent studies attempt to leverage the representation power of deep neural networks (DNNs) to predict the brain response and suggest a correspondence between artificial and biological neural networks in their feature representations. However, typical voxel-wise encoding models tend to rely on specific networks designed for computer vision tasks, leading to suboptimal brain-wide correspondence during cognitive tasks. To address this challenge, this work proposes a novel approach that upgrades voxel-wise encoding models through multi-level integration of features from DNNs and information from brain networks. Our approach combines DNN feature-level ensemble learning and brain atlas-level model integration, resulting in significant improvements in predicting whole-brain neural activity during naturalistic video perception. Furthermore, this multi-level integration framework enables a deeper understanding of the brain's neural representation mechanism, accurately predicting the neural response to complex visual concepts. We demonstrate that neural encoding models can be optimized by leveraging a framework that integrates both data-driven approaches and theoretical insights into the functional structure of the cortical networks.

Diagnostically distinct resting state fMRI energy distributions: A subject-specific maximum entropy modeling study

Objective

Existing neuroimaging studies of psychotic and mood disorders have reported brain activation differences (first-order properties) and altered pairwise correlation-based functional connectivity (second-order properties). However, both approaches have certain limitations that can be overcome by integrating them in a pairwise maximum entropy model (MEM) that better represents a comprehensive picture of fMRI signal patterns and provides a system-wide summary measure called energy. This study examines the applicability of individual-level MEM for psychiatry and identifies image-derived model coefficients related to model parameters.

Method

MEMs are fit to resting state fMRI data from each individual with schizophrenia/schizoaffective disorder, bipolar disorder, and major depression (n=132) and demographically matched healthy controls (n=132) from the UK Biobank to different subsets of the default mode network (DMN) regions.

Results

The model satisfactorily explained observed brain energy state occurrence probabilities across all participants, and model parameters were significantly correlated with image-derived coefficients for all groups. Within clinical groups, averaged energy level distributions were higher in schizophrenia/schizoaffective disorder but lower in bipolar disorder compared to controls for both bilateral and unilateral DMN. Major depression energy distributions were higher compared to controls only in the right hemisphere DMN.

Conclusions

Diagnostically distinct energy states suggest that probability distributions of temporal changes in synchronously active nodes may underlie each diagnostic entity. Subject-specific MEMs allow for factoring in the individual variations compared to traditional group-level inferences, offering an improved measure of biologically meaningful correlates of brain activity that may have potential clinical utility.

Re-awakening the brain: Forcing transitions in disorders of consciousness by external in silico perturbation

A fundamental challenge in neuroscience is accurately defining brain states and predicting how and where to perturb the brain to force a transition. Here, we investigated resting-state fMRI data of patients suffering from disorders of consciousness (DoC) after coma (minimally conscious and unresponsive wakefulness states) and healthy controls. We applied model-free and model-based approaches to help elucidate the underlying brain mechanisms of patients with DoC. The model-free approach allowed us to characterize brain states in DoC and healthy controls as a probabilistic metastable substate (PMS) space. The PMS of each group was defined by a repertoire of unique patterns (i.e., metastable substates) with different probabilities of occurrence. In the model-based approach, we adjusted the PMS of each DoC group to a causal whole-brain model. This allowed us to explore optimal strategies for promoting transitions by applying off-line in silico probing. Furthermore, this approach enabled us to evaluate the impact of local perturbations in terms of their global effects and sensitivity to stimulation, which is a model-based biomarker providing a deeper understanding of the mechanisms underlying DoC. Our results show that transitions were obtained in a synchronous protocol, in which the somatomotor network, thalamus, precuneus and insula were the most sensitive areas to perturbation. This motivates further work to continue understanding brain function and treatments of disorders of consciousness.

Cocaine diminishes functional network robustness and destabilizes the energy landscape of neuronal activity in the medial prefrontal cortex

We present analysis of neuronal activity recordings from a subset of neurons in the medial prefrontal cortex of rats before and after the administration of cocaine. Using an underlying modern Hopfield model as a description for the neuronal network, combined with a machine learning approach, we compute the underlying functional connectivity of the neuronal network. We find that the functional connectivity changes after the administration of cocaine with both functional-excitatory and functional-inhibitory neurons being affected. Using conventional network analysis, we find that the diameter of the graph, or the shortest length between the two most distant nodes, increases with cocaine, suggesting that the neuronal network is less robust. We also find that the betweenness centrality scores for several of the functional-excitatory and functional-inhibitory neurons decrease significantly, while other scores remain essentially unchanged, to also suggest that the neuronal network is less robust. Finally, we study the distribution of neuronal activity and relate it to energy to find that cocaine drives the neuronal network towards destabilization in the energy landscape of neuronal activation. While this destabilization is presumably temporary given one administration of cocaine, perhaps this initial destabilization indicates a transition towards a new stable state with repeated cocaine administration. However, such analyses are useful more generally to understand how neuronal networks respond to perturbations.

Brain dynamics predictive of response to psilocybin for treatment-resistant depression

Psilocybin therapy for depression has started to show promise, yet the underlying causal mechanisms are not currently known. Here, we leveraged the differential outcome in responders and non-responders to psilocybin (10 and 25 mg, 7 days apart) therapy for depression-to gain new insights into regions and networks implicated in the restoration of healthy brain dynamics. We used large-scale brain modelling to fit the spatiotemporal brain dynamics at rest in both responders and non-responders before treatment. Dynamic sensitivity analysis of systematic perturbation of these models enabled us to identify specific brain regions implicated in a transition from a depressive brain state to a healthy one. Binarizing the sample into treatment responders (>50% reduction in depressive symptoms) versus non-responders enabled us to identify a subset of regions implicated in this change. Interestingly, these regions correlate with in vivo density maps of serotonin receptors 5-hydroxytryptamine 2a and 5-hydroxytryptamine 1a, which psilocin, the active metabolite of psilocybin, has an appreciable affinity for, and where it acts as a full-to-partial agonist. Serotonergic transmission has long been associated with depression, and our findings provide causal mechanistic evidence for the role of brain regions in the recovery from depression via psilocybin.

Neural Network Connectivity Following Opioid Dependence is Altered by a Common Genetic Variant in the µ-Opioid Receptor, OPRM1 A118G

Opioid use disorder is a chronic, relapsing disease associated with persistent changes in brain plasticity. A common single nucleotide polymorphism (SNP) in the µ-opioid receptor gene, OPRM1 A118G, is associated with altered vulnerability to opioid addiction. Reconfiguration of neuronal connectivity may explain dependence risk in individuals with this SNP. Mice with the equivalent Oprm1 variant, A112G, demonstrate sex-specific alterations in the rewarding properties of morphine and heroin. To determine whether this SNP influences network-level changes in neuronal activity, we compared FOS expression in male and female mice that were opioid-naive or opioid-dependent. Network analyses identified significant differences between the AA and GG Oprm1 genotypes. Based on several graph theory metrics, including small-world analysis and degree centrality, we show that GG females in the opioid-dependent state exhibit distinct patterns of connectivity compared to other groups of the same genotype. Using a network control theory approach, we identified key cortical brain regions that drive the transition between opioid-naive and opioid-dependent brain states; however, these regions are less influential in GG females leading to sixfold higher average minimum energy needed to transition from the acute to the dependent state. In addition, we found that the opioid-dependent brain state is significantly less stable in GG females compared to other groups. Collectively, our findings demonstrate sex- and genotype-specific modifications in local, mesoscale, and global properties of functional brain networks following opioid exposure and provide a framework for identifying genotype differences in specific brain regions that play a role in opioid dependence.

Impact of Network Topology on Neural Synchrony in a Model of the Subthalamic Nucleus-Globus Pallidus Circuit

Synchronous neural oscillations within the beta frequency range are observed across the parkinsonian basal ganglia network, including within the subthalamic nucleus (STN) - globus pallidus (GPe) subcircuit. The emergence of pathological synchrony in Parkinson's disease is often attributed to changes in neural properties or connection strength, and less often to the network topology, i.e. the structural arrangement of connections between neurons. This study investigates the relationship between network structure and neural synchrony in a model of the STN-GPe circuit comprised of conductance-based spiking neurons. Changes in net synaptic input were controlled for through a synaptic scaling rule, which facilitated separation of the effects of network structure from net synaptic input. Five topologies were examined as structures for the STN-GPe circuit: Watts-Strogatz, preferential attachment, spatial, stochastic block, k-regular random. Beta band synchrony generally increased as the number of connections increased, however the exact relationship was topology specific. Varying the wiring pattern while maintaining a constant number of connections caused network synchrony to be enhanced or suppressed, demonstrating the ability of purely structural changes to alter synchrony. This relationship was well-captured by the algebraic connectivity of the network, the second smallest eigenvalue of the network's Laplacian matrix. The structure-synchrony relationship was further investigated in a network model designed to emulate the action selection role of the STN-GPe circuit. It was found that increasing the number of connections and/or the overlap of action selection channels could lead to a rapid transition to synchrony, which was also predicted by the algebraic connectivity.

Altered dynamical integration/segregation balance during anesthesia-induced loss of consciousness

In recent years, brain imaging studies have begun to shed light on the neural correlates of physiologically-reversible altered states of consciousness such as deep sleep, anesthesia, and psychedelic experiences. The emerging consensus is that normal waking consciousness requires the exploration of a dynamical repertoire enabling both global integration i.e., long-distance interactions between brain regions, and segregation, i.e., local processing in functionally specialized clusters. Altered states of consciousness have notably been characterized by a tipping of the integration/segregation balance away from this equilibrium. Historically, functional MRI (fMRI) has been the modality of choice for such investigations. However, fMRI does not enable characterization of the integration/segregation balance at sub-second temporal resolution. Here, we investigated global brain spatiotemporal patterns in electrocorticography (ECoG) data of a monkey (Macaca fuscata) under either ketamine or propofol general anesthesia. We first studied the effects of these anesthetics from the perspective of band-specific synchronization across the entire ECoG array, treating individual channels as oscillators. We further aimed to determine whether synchrony within spatially localized clusters of oscillators was differently affected by the drugs in comparison to synchronization over spatially distributed subsets of ECoG channels, thereby quantifying changes in integration/segregation balance on physiologically-relevant time scales. The findings reflect global brain dynamics characterized by a loss of long-range integration in multiple frequency bands under both ketamine and propofol anesthesia, most pronounced in the beta (13-30 Hz) and low-gamma bands (30-80 Hz), and with strongly preserved local synchrony in all bands.

A pattern of cognitive resource disruptions in childhood psychopathology

The Hurst exponent (H) isolated in fractal analyses of neuroimaging time series is implicated broadly in cognition. Within this literature, H is associated with multiple mental disorders, suggesting that H is transdimensionally associated with psychopathology. Here, we unify these results and demonstrate a pattern of decreased H with increased general psychopathology and attention-deficit/hyperactivity factor scores during a working memory task in 1,839 children. This pattern predicts current and future cognitive performance in children and some psychopathology in 703 adults. This pattern also defines psychological and functional axes associating psychopathology with an imbalance in resource allocation between fronto-parietal and sensorimotor regions, driven by reduced resource allocation to fronto-parietal regions. This suggests the hypothesis that impaired working memory function in psychopathology follows from a reduced cognitive resource pool and a reduction in resources allocated to the task at hand.

Event-related variability is modulated by task and development

In carefully designed experimental paradigms, cognitive scientists interpret the mean event-related potentials (ERP) in terms of cognitive operations. However, the huge signal variability from one trial to the next, questions the representability of such mean events. We explored here whether this variability is an unwanted noise, or an informative part of the neural response. We took advantage of the rapid changes in the visual system during human infancy and analyzed the variability of visual responses to central and lateralized faces in 2-to 6-month-old infants compared to adults using high-density electroencephalography (EEG). We observed that neural trajectories of individual trials always remain very far from ERP components, only moderately bending their direction with a substantial temporal jitter across trials. However, single trial trajectories displayed characteristic patterns of acceleration and deceleration when approaching ERP components, as if they were under the active influence of steering forces causing transient attraction and stabilization. These dynamic events could only partly be accounted for by induced microstate transitions or phase reset phenomena. Importantly, these structured modulations of response variability, both between and within trials, had a rich sequential organization, which in infants, was modulated by the task difficulty and age. Our approaches to characterize Event Related Variability (ERV) expand on classic ERP analyses and provide the first evidence for the functional role of ongoing neural variability in human infants.

Triple-network analysis of Alzheimer's disease based on the energy landscape

Introduction

Research on the brain activity during resting state has found that brain activation is centered around three networks, including the default mode network (DMN), the salient network (SN), and the central executive network (CEN), and switches between multiple modes. As a common disease in the elderly, Alzheimer's disease (AD) affects the state transitions of functional networks in the resting state.

Methods

Energy landscape, as a new method, can intuitively and quickly grasp the statistical distribution of system states and information related to state transition mechanisms. Therefore, this study mainly uses the energy landscape method to study the changes of the triple-network brain dynamics in AD patients in the resting state.

Results

AD brain activity patterns are in an abnormal state, and the dynamics of patients with AD tend to be unstable, with an unusually high flexibility in switching between states. Also , the subjects' dynamic features are correlated with clinical index.

Discussion

The atypical balance of large-scale brain systems in patients with AD is associated with abnormally active brain dynamics. Our study are helpful for further understanding the intrinsic dynamic characteristics and pathological mechanism of the resting-state brain in AD patients.

Is the tendency to maximise energy distribution an optimal collective activity for biological purposes? A proposal for a global principle of biological organization

Our purpose is to address the biological problem of finding foundations of the organization in the collective activity among cell networks in the nervous system, at the meso/macroscale, giving rise to cognition and consciousness. But in doing so, we encounter another problem related to the interpretation of methods to assess the neural interactions and organization of the neurodynamics, because thermodynamic notions, which have precise meaning only under specific conditions, have been widely employed in these studies. The consequence is that apparently contradictory results appear in the literature, but these contradictions diminish upon the considerations of the specific circumstances of each experiment. After clarifying some of these controversial points and surveying some experimental results, we propose that a necessary condition for cognition/consciousness to emerge is to have available enough energy, or cellular activity; and a sufficient condition is the multiplicity of configurations in which cell networks can communicate, resulting in non-uniform energy distribution, the generation and dissipation of energy gradients due to the constant activity. The diversity of sensorimotor processing of higher animals needs a flexible, fluctuating web on neuronal connections, and we review results supporting such multiplicity of configurations among brain regions associated with conscious awareness and healthy brain states. These ideas may reveal possible fundamental principles of brain organization that could be extended to other natural phenomena and how healthy activity may derive to pathological states.

Gender effects on the controllability of hemispheric white matter networks

Male and female adults exhibited significant group differences in brain white matter (WM) asymmetry and WM network controllability. However, gender differences in controllability of hemispheric WM networks between males and females remain to be determined. Based on 1 principal atlas and 1 replication atlas, this work characterized the average controllability (AC) and modal controllability (MC) of hemispheric WM network based on 1 principal dataset and 2 replication datasets. All results showed that males had higher AC of left hemispheric networks than females. And significant hemispheric asymmetry was revealed in regional AC and MC. Furthermore, significant gender differences in the AC asymmetry were mainly found in regions lie in the frontoparietal network, and the MC asymmetry was found in regions involving auditory and emotion process. Finally, we found significant associations between regional controllability and cognitive features. Taken together, this work could provide a novel perspective for understanding gender differences in hemispheric WM asymmetry and cognitive function between males and females.

Driving brain state transitions in major depressive disorder through external stimulation

Major depressive disorder (MDD) as a dysfunction of neural circuits and brain networks has been established in modern neuroimaging sciences. However, the brain state transitions between MDD and health through external stimulation remain unclear, which limits translation to clinical contexts and demonstrable clinical utility. We propose a framework of the large-scale whole-brain network model for MDD linking the underlying anatomical connectivity with functional dynamics obtained from diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI). Then, we further explored the optimal brain regions to promote the transition of brain states between MDD and health through external stimulation of the model. Based on the whole-brain model successfully fitting the brain state space in MDD and the health, we demonstrated that the transition from MDD to health is achieved by the excitatory activation of the limbic system and from health to MDD by the inhibitory stimulation of the reward circuit. Our finding provides novel biophysical evidence for the neural mechanism of MDD and its recovery and allows the discovery of new stimulation targets for MDD recovery.

Controllability of Structural Brain Networks and the Waxing and Waning of Negative Affect in Daily Life

Background

The waxing and waning of negative affect in daily life is normative, reflecting an adaptive capacity to respond flexibly to changing circumstances. However, understanding of the brain structure correlates of affective variability in naturalistic settings has been limited. Using network control theory, we examine facets of brain structure that may enable negative affect variability in daily life.

Methods

We used diffusion-weighted imaging data from 95 young adults (age [in years]: mean = 20.19, SD = 1.80; 56 women) to construct structural connectivity networks that map white matter fiber connections between 200 cortical and 14 subcortical regions. We applied network control theory to these structural networks to estimate the degree to which each brain region's pattern of structural connectivity facilitates the spread of activity to other brain systems. We examined how the average controllability of functional brain systems relates to negative affect variability, computed by taking the standard deviation of negative affect self-reports collected via smartphone-based experience sampling twice per day over 28 days as participants went about their daily lives.

Results

We found that high average controllability of the cingulo-insular system is associated with increased negative affect variability. We also found that greater negative affect variability is related to the presence of more depressive symptoms, yet average controllability of the cingulo-insular system was not associated with depressive symptoms.

Conclusions

Our results highlight the role that brain structure plays in affective dynamics as observed in the context of daily life, suggesting that average controllability of the cingulo-insular system promotes normative negative affect variability.

Complexity changes in functional state dynamics suggest focal connectivity reductions

The past two decades have seen an explosion in the methods and directions of neuroscience research. Along with many others, complexity research has rapidly gained traction as both an independent research field and a valuable subdiscipline in computational neuroscience. In the past decade alone, several studies have suggested that psychiatric disorders affect the spatiotemporal complexity of both global and region-specific brain activity (Liu et al., 2013; Adhikari et al., 2017; Li et al., 2018). However, many of these studies have not accounted for the distributed nature of cognition in either the global or regional complexity estimates, which may lead to erroneous interpretations of both global and region-specific entropy estimates. To alleviate this concern, we propose a novel method for estimating complexity. This method relies upon projecting dynamic functional connectivity into a low-dimensional space which captures the distributed nature of brain activity. Dimension-specific entropy may be estimated within this space, which in turn allows for a rapid estimate of global signal complexity. Testing this method on a recently acquired obsessive-compulsive disorder dataset reveals substantial increases in the complexity of both global and dimension-specific activity versus healthy controls, suggesting that obsessive-compulsive patients may experience increased disorder in cognition. To probe the potential causes of this alteration, we estimate subject-level effective connectivity via a Hopf oscillator-based model dynamic model, the results of which suggest that obsessive-compulsive patients may experience abnormally high connectivity across a broad network in the cortex. These findings are broadly in line with results from previous studies, suggesting that this method is both robust and sensitive to group-level complexity alterations.

The longitudinal neural dynamics changes of whole brain connectome during natural recovery from poststroke aphasia

Poststroke aphasia is one of the most dramatic functional deficits that results from direct damage of focal brain regions and dysfunction of large-scale brain networks. The reconstruction of language function depends on the hierarchical whole-brain dynamic reorganization. However, investigations into the longitudinal neural changes of large-scale brain networks for poststroke aphasia remain scarce. Here we characterize large-scale brain dynamics in left-frontal-stroke aphasia through energy landscape analysis. Using fMRI during an auditory comprehension task, we find that aphasia patients suffer serious whole-brain dynamics perturbation in the acute and subacute stages after stroke, in which the brains were restricted into two major activity patterns. Following spontaneous recovery process, the brain flexibility improved in the chronic stage. Critically, we demonstrated that the abnormal neural dynamics are correlated with the aberrant brain network coordination. Taken together, the energy landscape analysis exhibited that the acute poststroke aphasia has a constrained, low dimensional brain dynamics, which were replaced by less constrained and high dimensional dynamics at chronic aphasia. Our study provides a new perspective to profoundly understand the pathological mechanisms of poststroke aphasia.

Understanding brain states across spacetime informed by whole-brain modelling

In order to survive in a complex environment, the human brain relies on the ability to flexibly adapt ongoing behaviour according to intrinsic and extrinsic signals. This capability has been linked to specific whole-brain activity patterns whose relative stability (order) allows for consistent functioning, supported by sufficient intrinsic instability needed for optimal adaptability. The emergent, spontaneous balance between order and disorder in brain activity over spacetime underpins distinct brain states. For example, depression is characterized by excessively rigid, highly ordered states, while psychedelics can bring about more disordered, sometimes overly flexible states. Recent developments in systems, computational and theoretical neuroscience have started to make inroads into the characterization of such complex dynamics over space and time. Here, we review recent insights drawn from neuroimaging and whole-brain modelling motivating using mechanistic principles from dynamical system theory to study and characterize brain states. We show how different healthy and altered brain states are associated to characteristic spacetime dynamics which in turn may offer insights that in time can inspire new treatments for rebalancing brain states in disease. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Inferring excitation-inhibition dynamics using a maximum entropy model unifying brain structure and function

Neural activity coordinated across different scales from neuronal circuits to large-scale brain networks gives rise to complex cognitive functions. Bridging the gap between micro- and macroscale processes, we present a novel framework based on the maximum entropy model to infer a hybrid resting-state structural connectome, representing functional interactions constrained by structural connectivity. We demonstrate that the structurally informed network outperforms the unconstrained model in simulating brain dynamics, wherein by constraining the inference model with the network structure we may improve the estimation of pairwise BOLD signal interactions. Further, we simulate brain network dynamics using Monte Carlo simulations with the new hybrid connectome to probe connectome-level differences in excitation-inhibition balance between apolipoprotein E (APOE)-ε4 carriers and noncarriers. Our results reveal sex differences among APOE-ε4 carriers in functional dynamics at criticality; specifically, female carriers appear to exhibit a lower tolerance to network disruptions resulting from increased excitatory interactions. In sum, the new multimodal network explored here enables analysis of brain dynamics through the integration of structure and function, providing insight into the complex interactions underlying neural activity such as the balance of excitation and inhibition.

Control energy assessment of spatial interactions among macro‐scale brain networks

Many recent studies have revealed that spatial interactions of functional brain networks derived from fMRI data can well model functional connectomes of the human brain. However, it has been rarely explored what the energy consumption characteristics are for such spatial interactions of macro‐scale functional networks, which remains crucial for the understanding of brain organization, behavior, and dynamics. To explore this unanswered question, this article presents a novel framework for quantitative assessment of energy consumptions of macro‐scale functional brain network's spatial interactions via two main effective computational methodologies. First, we designed a novel scheme combining dictionary learning and hierarchical clustering to derive macro‐scale consistent brain network templates that can be used to define a common reference space for brain network interactions and energy assessments. Second, the control energy consumption for driving the brain networks during their spatial interactions is computed from the viewpoint of the linear network control theory. Especially, the energetically favorable brain networks were identified and their energy characteristics were comprehensively analyzed. Experimental results on the Human Connectome Project (HCP) task‐based fMRI (tfMRI) data showed that the proposed methods can reveal meaningful, diverse energy consumption patterns of macro‐scale network interactions. In particular, those networks present remarkable differences in energy consumption. The energetically least favorable brain networks are stable and consistent across HCP tasks such as motor, language, social, and working memory tasks. In general, our framework provides a new perspective to characterize human brain functional connectomes by quantitative assessment for the energy consumption of spatial interactions of macro‐scale brain networks.

Prefrontal contributions to the stability and variability of thought and conscious experience

The human prefrontal cortex is a structurally and functionally heterogenous brain region, including multiple subregions that have been linked to different large-scale brain networks. It contributes to a broad range of mental phenomena, from goal-directed thought and executive functions to mind-wandering and psychedelic experience. Here we review what is known about the functions of different prefrontal subregions and their affiliations with large-scale brain networks to examine how they may differentially contribute to the diversity of mental phenomena associated with prefrontal function. An important dimension that distinguishes across different kinds of conscious experience is the stability or variability of mental states across time. This dimension is a central feature of two recently introduced theoretical frameworks-the dynamic framework of thought (DFT) and the relaxed beliefs under psychedelics (REBUS) model-that treat neurocognitive dynamics as central to understanding and distinguishing between different mental phenomena. Here, we bring these two frameworks together to provide a synthesis of how prefrontal subregions may differentially contribute to the stability and variability of thought and conscious experience. We close by considering future directions for this work.

Situational Understanding in the Human and the Machine

The Air Force research programs envision developing AI technologies that will ensure battlespace dominance, by radical increases in the speed of battlespace understanding and decision-making. In the last half century, advances in AI have been concentrated in the area of machine learning. Recent experimental findings and insights in systems neuroscience, the biophysics of cognition, and other disciplines provide converging results that set the stage for technologies of machine understanding and machine-augmented Situational Understanding. This paper will review some of the key ideas and results in the literature, and outline new suggestions. We define situational understanding and the distinctions between understanding and awareness, consider examples of how understanding-or lack of it-manifest in performance, and review hypotheses concerning the underlying neuronal mechanisms. Suggestions for further R&D are motivated by these hypotheses and are centered on the notions of Active Inference and Virtual Associative Networks.

Empirical Bayes estimation of pairwise maximum entropy model for nonlinear brain state dynamics

The pairwise maximum entropy model (pMEM) has recently gained widespread attention to exploring the nonlinear characteristics of brain state dynamics observed in resting-state functional magnetic resonance imaging (rsfMRI). Despite its unique advantageous features, the practical application of pMEM for individuals is limited as it requires a much larger sample than conventional rsfMRI scans. Thus, this study proposes an empirical Bayes estimation of individual pMEM using the variational expectation-maximization algorithm (VEM-MEM). The performance of the VEM-MEM is evaluated for several simulation setups with various sample sizes and network sizes. Unlike conventional maximum likelihood estimation procedures, the VEM-MEM can reliably estimate the individual model parameters, even with small samples, by effectively incorporating the group information as the prior. As a test case, the individual rsfMRI of children with attention deficit hyperactivity disorder (ADHD) is analyzed compared to that of typically developed children using the default mode network, executive control network, and salient network, obtained from the Healthy Brain Network database. We found that the nonlinear dynamic properties uniquely established on the pMEM differ for each group. Furthermore, pMEM parameters are more sensitive to group differences and are better associated with the behavior scores of ADHD compared to the Pearson correlation-based functional connectivity. The simulation and experimental results suggest that the proposed method can reliably estimate the individual pMEM and characterize the dynamic properties of individuals by utilizing empirical information of the group brain state dynamics.

Causal roles of prefrontal cortex during spontaneous perceptual switching are determined by brain state dynamics

The prefrontal cortex (PFC) is thought to orchestrate cognitive dynamics. However, in tests of bistable visual perception, no direct evidence supporting such presumable causal roles of the PFC has been reported except for a recent work. Here, using a novel brain-state-dependent neural stimulation system, we identified causal effects on percept dynamics in three PFC activities—right frontal eye fields, dorsolateral PFC (DLPFC), and inferior frontal cortex (IFC). The causality is behaviourally detectable only when we track brain state dynamics and modulate the PFC activity in brain-state-/state-history-dependent manners. The behavioural effects are underpinned by transient neural changes in the brain state dynamics, and such neural effects are quantitatively explainable by structural transformations of the hypothetical energy landscapes. Moreover, these findings indicate distinct functions of the three PFC areas: in particular, the DLPFC enhances the integration of two PFC-active brain states, whereas IFC promotes the functional segregation between them. This work resolves the controversy over the PFC roles in spontaneous perceptual switching and underlines brain state dynamics in fine investigations of brain-behaviour causality.

A cube that seems to shift its spatial arrangement as you keep looking; the elegant silhouette of a pirouetting dancer, which starts to spin in the opposite direction the more you stare at it; an illustration that shows two profiles – or is it a vase? These optical illusions are examples of bistable visual perception. Beyond their entertaining aspect, they provide a way for scientists to explore the dynamics of human consciousness, and the neural regions involved in this process.

Some studies show that bistable visual perception is associated with the activation of the prefrontal cortex, a brain area involved in complex cognitive processes. However, it is unclear whether this region is required for the illusions to emerge. Some research has showed that even if sections of the prefrontal cortex are temporally deactivated, participants can still experience the illusions.

Instead, Takamitsu Watanabe proposes that bistable visual perception is a process tied to dynamic brain states – that is, that distinct regions of the prefontal cortex are required for this fluctuating visual awareness, depending on the state of the whole brain. Such causal link cannot be observed if brain activity is not tracked closely.

To investigate this, the brain states of 65 participants were recorded as individuals were experiencing the optical illusions; the activity of their various brain regions could therefore be mapped, and then areas of the prefrontal cortex could precisely be inhibited at the right time using transcranial magnetic stimulation. This revealed that, indeed, prefrontal cortex regions were necessary for bistable visual perception, but not in a simple way. Instead, which ones were required and when depended on activity dynamics taking place in the whole brain. Overall, these results indicate that monitoring brain states is necessary to better understand – and ultimately, control – the neural pathways underlying perception and behaviour.

Distributed Subnetworks of Depression Defined by Direct Intracranial Neurophysiology

Major depressive disorder is a common and disabling disorder with high rates of treatment resistance. Evidence suggests it is characterized by distributed network dysfunction that may be variable across patients, challenging the identification of quantitative biological substrates. We carried out this study to determine whether application of a novel computational approach to a large sample of high spatiotemporal resolution direct neural recordings in humans could unlock the functional organization and coordinated activity patterns of depression networks. This group level analysis of depression networks from heterogenous intracranial recordings was possible due to application of a correlational model-based method for inferring whole-brain neural activity. We then applied a network framework to discover brain dynamics across this model that could classify depression. We found a highly distributed pattern of neural activity and connectivity across cortical and subcortical structures that was present in the majority of depressed subjects. Furthermore, we found that this depression signature consisted of two subnetworks across individuals. The first was characterized by left temporal lobe hypoconnectivity and pathological beta activity. The second was characterized by a hypoactive, but hyperconnected left frontal cortex. These findings have applications toward personalization of therapy.

Functional harmonics reveal multi-dimensional basis functions underlying cortical organization

The human brain consists of specialized areas that flexibly interact to form a multitude of functional networks. Complementary to this notion of modular organization, brain function has been shown to vary along a smooth continuum across the whole cortex. We demonstrate a mathematical framework that accounts for both of these perspectives: harmonic modes. We calculate the harmonic modes of the brain's functional connectivity graph, called "functional harmonics," revealing a multi-dimensional, frequency-ordered set of basis functions. Functional harmonics link characteristics of cortical organization across several spatial scales, capturing aspects of intra-areal organizational features (retinotopy, somatotopy), delineating brain areas, and explaining macroscopic functional networks as well as global cortical gradients. Furthermore, we show how the activity patterns elicited by seven different tasks are reconstructed from a very small subset of functional harmonics. Our results suggest that the principle of harmonicity, ubiquitous in nature, also underlies functional cortical organization in the human brain.

A Multivariate Randomized Controlled Experiment about the Effects of Mindfulness Priming on EEG Neurofeedback Self-Regulation Serious Games

Neurofeedback training (NFT) is a technique often proposed to train brain activity SR with promising results. However, some criticism has been raised due to the lack of evaluation, reliability, and validation of its learning effects. The current work evaluates the hypothesis that SR learning may be improved by priming the subject before NFT with guided mindfulness meditation (MM). The proposed framework was tested in a two-way parallel-group randomized controlled intervention with a single session alpha NFT, in a simplistic serious game design. Sixty-two healthy naïve subjects, aged between 18 and 43 years, were divided into MM priming and no-priming groups. Although both the EG and CG successfully attained the up-regulation of alpha rhythms (F(1,59) = 20.67, p < 0.001, ηp2 = 0.26), the EG showed a significantly enhanced ability (t(29) = 4.38, p < 0.001) to control brain activity, compared to the CG (t(29) = 1.18, p > 0.1). Furthermore, EG superior performance on NFT seems to be explained by the subject’s lack of awareness at pre-intervention, less vigour at post-intervention, increased task engagement, and a relaxed non-judgemental attitude towards the NFT tasks. This study is a preliminary validation of the proposed assisted priming framework, advancing some implicit and explicit metrics about its efficacy on NFT performance, and a promising tool for improving naïve “users” self-regulation ability.

Characterising Alzheimer's Disease with EEG-based Energy Landscape Analysis

Alzheimer's disease (AD) is one of the most common neurodegenerative diseases, with around 50 million patients worldwide. Accessible and non-invasive methods of diagnosing and characterising AD are therefore urgently required. Electroencephalography (EEG) fulfils these criteria and is often used when studying AD. Several features derived from EEG were shown to predict AD with high accuracy, e.g. signal complexity and synchronisation. However, the dynamics of how the brain transitions between stable states have not been properly studied in the case of AD and EEG. Energy landscape analysis is a method that can be used to quantify these dynamics. This work presents the first application of this method to both AD and EEG. Energy landscape assigns energy value to each possible state, i.e. pattern of activations across brain regions. The energy is inversely proportional to the probability of occurrence. By studying the features of energy landscapes of 20 AD patients and 20 age-matched healthy counterparts (HC), significant differences are found. The dynamics of AD patients' EEG are shown to be more constrained - with more local minima, less variation in basin size, and smaller basins. We show that energy landscapes can predict AD with high accuracy, performing significantly better than baseline models. Moreover, these findings are replicated in a separate dataset including 9 AD and 10 HC above 70 years old.

Brain States and Transitions: Insights from Computational Neuroscience

Within the field of computational neuroscience there are great expectations of finding new ways to rebalance the complex dynamic system of the human brain through controlled pharmacological or electromagnetic perturbation. Yet many obstacles remain between the ability to accurately predict how and where best to perturb to force a transition from one brain state to another. The foremost challenge is a commonly agreed definition of a given brain state. Recent progress in computational neuroscience has made it possible to robustly define brain states and force transitions between them. Here, we review the state of the art and propose a framework for determining the functional hierarchical organization describing any given brain state. We describe the latest advances in creating sophisticated whole-brain computational models with interacting neuronal and neurotransmitter systems that can be studied fully in silico to predict and design novel pharmacological and electromagnetic interventions to rebalance them in disease.

Bayesian estimation of maximum entropy model for individualized energy landscape analysis of brain state dynamics

The pairwise maximum entropy model (MEM) for resting state functional MRI (rsfMRI) has been used to generate energy landscape of brain states and to explore nonlinear brain state dynamics. Researches using MEM, however, has mostly been restricted to fixed‐effect group‐level analyses, using concatenated time series across individuals, due to the need for large samples in the parameter estimation of MEM. To mitigate the small sample problem in analyzing energy landscapes for individuals, we propose a Bayesian estimation of individual MEM using variational Bayes approximation (BMEM). We evaluated the performances of BMEM with respect to sample sizes and prior information using simulation. BMEM showed advantages over conventional maximum likelihood estimation in reliably estimating model parameters for individuals with small sample data, particularly utilizing the empirical priors derived from group data. We then analyzed individual rsfMRI of the Human Connectome Project to show the usefulness of MEM in differentiating individuals and in exploring neural correlates for human behavior. MEM and its energy landscape properties showed high subject specificity comparable to that of functional connectivity. Canonical correlation analysis identified canonical variables for MEM highly associated with cognitive scores. Inter‐individual variations of cognitive scores were also reflected in energy landscape properties such as energies, occupation times, and basin sizes at local minima. We conclude that BMEM provides an efficient method to characterize dynamic properties of individuals using energy landscape analysis of individual brain states.

A Computational Framework for Controlling the Self-Restorative Brain Based on the Free Energy and Degeneracy Principles

The brain is a non-linear dynamical system with a self-restoration process, which protects itself from external damage but is often a bottleneck for clinical treatment. To treat the brain to induce the desired functionality, formulation of a self-restoration process is necessary for optimal brain control. This study proposes a computational model for the brain's self-restoration process following the free-energy and degeneracy principles. Based on this model, a computational framework for brain control is established. We posited that the pre-treatment brain circuit has long been configured in response to the environmental (the other neural populations') demands on the circuit. Since the demands persist even after treatment, the treated circuit's response to the demand may gradually approximate the pre-treatment functionality. In this framework, an energy landscape of regional activities, estimated from resting-state endogenous activities by a pairwise maximum entropy model, is used to represent the pre-treatment functionality. The approximation of the pre-treatment functionality occurs via reconfiguration of interactions among neural populations within the treated circuit. To establish the current framework's construct validity, we conducted various simulations. The simulations suggested that brain control should include the self-restoration process, without which the treatment was not optimal. We also presented simulations for optimizing repetitive treatments and optimal timing of the treatment. These results suggest a plausibility of the current framework in controlling the non-linear dynamical brain with a self-restoration process.

Parcels and particles: Markov blankets in the brain

At the inception of human brain mapping, two principles of functional anatomy underwrote most conceptions-and analyses-of distributed brain responses: namely, functional segregation and integration. There are currently two main approaches to characterizing functional integration. The first is a mechanistic modeling of connectomics in terms of directed effective connectivity that mediates neuronal message passing and dynamics on neuronal circuits. The second phenomenological approach usually characterizes undirected functional connectivity (i.e., measurable correlations), in terms of intrinsic brain networks, self-organized criticality, dynamical instability, and so on. This paper describes a treatment of effective connectivity that speaks to the emergence of intrinsic brain networks and critical dynamics. It is predicated on the notion of Markov blankets that play a fundamental role in the self-organization of far from equilibrium systems. Using the apparatus of the renormalization group, we show that much of the phenomenology found in network neuroscience is an emergent property of a particular partition of neuronal states, over progressively coarser scales. As such, it offers a way of linking dynamics on directed graphs to the phenomenology of intrinsic brain networks.

Pairwise maximum entropy model explains the role of white matter structure in shaping emergent co-activation states

A major challenge in neuroscience is determining a quantitative relationship between the brain's white matter structural connectivity and emergent activity. We seek to uncover the intrinsic relationship among brain regions fundamental to their functional activity by constructing a pairwise maximum entropy model (MEM) of the inter-ictal activation patterns of five patients with medically refractory epilepsy over an average of ~14 hours of band-passed intracranial EEG (iEEG) recordings per patient. We find that the pairwise MEM accurately predicts iEEG electrodes' activation patterns' probability and their pairwise correlations. We demonstrate that the estimated pairwise MEM's interaction weights predict structural connectivity and its strength over several frequencies significantly beyond what is expected based solely on sampled regions' distance in most patients. Together, the pairwise MEM offers a framework for explaining iEEG functional connectivity and provides insight into how the brain's structural connectome gives rise to large-scale activation patterns by promoting co-activation between connected structures.

A Complex Systems Perspective on Neuroimaging Studies of Behavior and Its Disorders

The study of complex systems deals with emergent behavior that arises as a result of nonlinear spatiotemporal interactions between a large number of components both within the system, as well as between the system and its environment. There is a strong case to be made that neural systems as well as their emergent behavior and disorders can be studied within the framework of complexity science. In particular, the field of neuroimaging has begun to apply both theoretical and experimental procedures originating in complexity science—usually in parallel with traditional methodologies. Here, we illustrate the basic properties that characterize complex systems and evaluate how they relate to what we have learned about brain structure and function from neuroimaging experiments. We then argue in favor of adopting a complex systems-based methodology in the study of neuroimaging, alongside appropriate experimental paradigms, and with minimal influences from noncomplex system approaches. Our exposition includes a review of the fundamental mathematical concepts, combined with practical examples and a compilation of results from the literature.

Topological impact of negative links on the stability of resting-state brain network

Stability is a physical attribute that stands opposite the change. However, it is still unclear how the arrangement of links called topology affects network stability. In this study, we tackled this issue in the resting-state brain network using structural balance. Structural balance theory employs the quality of triadic associations between signed links to determine the network stability. In this study, we showed that negative links of the resting-state network make hubs to reduce balance-energy and push the network into a more stable state compared to null-networks with trivial topologies. In this regard, we created a global measure entitled 'tendency to make hub' to assess the hubness of the network. Besides, we revealed nodal degrees of negative links have an exponential distribution that confirms the existence of negative hubs. Our findings indicate that the arrangement of negative links plays an important role in the balance (stability) of the resting-state brain network.

Modeling Heterogeneous Brain Dynamics of Depression and Melancholia Using Energy Landscape Analysis

Our current understanding of melancholic depression is shaped by its position in the depression spectrum. The lack of consensus on how it should be treated-whether as a subtype of depression, or as a distinct disorder altogethe-interferes with the recovery of suffering patients. In this study, we analyzed brain state energy landscape models of melancholic depression, in contrast to healthy and non-melancholic energy landscapes. Our analyses showed significant group differences on basin energy, basin frequency, and transition dynamics in several functional brain networks such as basal ganglia, dorsal default mode, and left executive control networks. Furthermore, we found evidences suggesting the connection between energy landscape characteristics (basin characteristics) and depressive symptom scores (BDI-II and SHAPS). These results indicate that melancholic depression is distinguishable from its non-melancholic counterpart, not only in terms of depression severity, but also in brain dynamics.

SARS-CoV-2, Trait Anxiety, and the Microbiome

During the COVID-19 pandemic, research on the relationships between the virus and its human host has become fundamental to understand this pathology and its effects. Attaining this profound understanding is critical for the effective containment and treatment of infections caused by the virus. In this review, we present some possible mechanisms by which psychopathological symptoms emerge following viral infections of the central nervous system (CNS). These proposed mechanisms are based on microbial communication and the induced priming of microglial antibody activation within the CNS through Toll-like receptor signaling. In this process, chronic microglial activation causes increased glutamate release in virally-altered, high-density neuronal structures, thereby modulating cognitive networks and information integration processes. This modulation, in turn, we suggest, affects the accuracy of sensory integration and connectivity of major control networks, such as the default mode network. The chronic activation of immunological responses and neurochemical shifts toward an elevated glutamate/gamma-aminobutyric acid ratio lead to negative reinforcement learning and suboptimal organismic functioning, for example, maintaining the body in an anxious state, which can later become internalized as trait anxiety. Therefore, we hypothesize that the homeostatic relationship between host, microbiome, and virome, would be decisive in determining the efficiency of subsequent immunological responses, disease susceptibility, and long-term psychopathological effects of diseases that impact the CNS, such as the COVID-19.

A proof of concept 'phase zero' study of neurodevelopment using brain organoid models with Vis/near-infrared spectroscopy and electrophysiology

Homeostatic control of neuronal excitability by modulation of synaptic inhibition (I) and excitation (E) of the principal neurons is important during brain maturation. The fundamental features of in-utero brain development, including local synaptic E-I ratio and bioenergetics, can be modeled by cerebral organoids (CO) that have exhibited highly regular nested oscillatory network events. Therefore, we evaluated a 'Phase Zero' clinical study platform combining broadband Vis/near-infrared(NIR) spectroscopy and electrophysiology with studying E-I ratio based on the spectral exponent of local field potentials and bioenergetics based on the activity of mitochondrial Cytochrome-C Oxidase (CCO). We found a significant effect of the age of the healthy controls iPSC CO from 23 days to 3 months on the CCO activity (chi-square (2, N = 10) = 20, p = 4.5400e-05), and spectral exponent between 30-50 Hz (chi-square (2, N = 16) = 13.88, p = 0.001). Also, a significant effect of drugs, choline (CHO), idebenone (IDB), R-alpha-lipoic acid plus acetyl-L-carnitine (LCLA), was found on the CCO activity (chi-square (3, N = 10) = 25.44, p = 1.2492e-05), spectral exponent between 1 and 20 Hz (chi-square (3, N = 16) = 43.5, p = 1.9273e-09) and 30-50 Hz (chi-square (3, N = 16) = 23.47, p = 3.2148e-05) in 34 days old CO from schizophrenia (SCZ) patients iPSC. We present the feasibility of a multimodal approach, combining electrophysiology and broadband Vis-NIR spectroscopy, to monitor neurodevelopment in brain organoid models that can complement traditional drug design approaches to test clinically meaningful hypotheses.

Topological analysis reveals state transitions in human gut and marine bacterial communities

Microbiome dynamics influence the health and functioning of human physiology and the environment and are driven in part by interactions between large numbers of microbial taxa, making large-scale prediction and modeling a challenge. Here, using topological data analysis, we identify states and dynamical features relevant to macroscopic processes. We show that gut disease processes and marine geochemical events are associated with transitions between community states, defined as topological features of the data density. We find a reproducible two-state succession during recovery from cholera in the gut microbiomes of multiple patients, evidence of dynamic stability in the gut microbiome of a healthy human after experiencing diarrhea during travel, and periodic state transitions in a marine Prochlorococcus community driven by water column cycling. Our approach bridges small-scale fluctuations in microbiome composition and large-scale changes in phenotype without details of underlying mechanisms, and provides an assessment of microbiome stability and its relation to human and environmental health.

Degeneracy and Redundancy in Active Inference

The notions of degeneracy and redundancy are important constructs in many areas, ranging from genomics through to network science. Degeneracy finds a powerful role in neuroscience, explaining key aspects of distributed processing and structure-function relationships in the brain. For example, degeneracy accounts for the superadditive effect of lesions on functional deficits in terms of a "many-to-one" structure-function mapping. In this paper, we offer a principled account of degeneracy and redundancy, when function is operationalized in terms of active inference, namely, a formulation of perception and action as belief updating under generative models of the world. In brief, "degeneracy" is quantified by the "entropy" of posterior beliefs about the causes of sensations, while "redundancy" is the "complexity" cost incurred by forming those beliefs. From this perspective, degeneracy and redundancy are complementary: Active inference tries to minimize redundancy while maintaining degeneracy. This formulation is substantiated using statistical and mathematical notions of degenerate mappings and statistical efficiency. We then illustrate changes in degeneracy and redundancy during the learning of a word repetition task. Finally, we characterize the effects of lesions-to intrinsic and extrinsic connections-using in silico disconnections. These numerical analyses highlight the fundamental difference between degeneracy and redundancy-and how they score distinct imperatives for perceptual inference and structure learning that are relevant to synthetic and biological intelligence.

Reconfigurations within resonating communities of brain regions following TMS reveal different scales of processing

An overarching goal of neuroscience research is to understand how heterogeneous neuronal ensembles cohere into networks of coordinated activity to support cognition. To investigate how local activity harmonizes with global signals, we measured electroencephalography (EEG) while single pulses of transcranial magnetic stimulation (TMS) perturbed occipital and parietal cortices. We estimate the rapid network reconfigurations in dynamic network communities within specific frequency bands of the EEG, and characterize two distinct features of network reconfiguration, flexibility and allegiance, among spatially distributed neural sources following TMS. Using distance from the stimulation site to infer local and global effects, we find that alpha activity (8–12 Hz) reflects concurrent local and global effects on network dynamics. Pairwise allegiance of brain regions to communities on average increased near the stimulation site, whereas TMS-induced changes to flexibility were generally invariant to distance and stimulation site. In contrast, communities within the beta (13–20 Hz) band demonstrated a high level of spatial specificity, particularly within a cluster comprising paracentral areas. Together, these results suggest that focal magnetic neurostimulation to distinct cortical sites can help identify both local and global effects on brain network dynamics, and highlight fundamental differences in the manifestation of network reconfigurations within alpha and beta frequency bands.

TMS may be used to probe the causal link between local regional activity and global brain dynamics. Using simultaneous TMS-EEG and dynamic community detection, we introduce what we call “resonating communities” or frequency band-specific clusters in the brain, as a way to index local and global processing. These resonating communities within the alpha and beta bands display both global (or integrating) behavior and local specificity, highlighting fundamental differences in the manifestation of network reconfigurations.

Connectome spectral analysis to track EEG task dynamics on a subsecond scale

We present an approach for tracking fast spatiotemporal cortical dynamics in which we combine white matter connectivity data with source-projected electroencephalographic (EEG) data. We employ the mathematical framework of graph signal processing in order to derive the Fourier modes of the brain structural connectivity graph, or "network harmonics". These network harmonics are naturally ordered by smoothness. Smoothness in this context can be understood as the amount of variation along the cortex, leading to a multi-scale representation of brain connectivity. We demonstrate that network harmonics provide a sparse representation of the EEG signal, where, at certain times, the smoothest 15 network harmonics capture 90% of the signal power. This suggests that network harmonics are functionally meaningful, which we demonstrate by using them as a basis for the functional EEG data recorded from a face detection task. There, only 13 network harmonics are sufficient to track the large-scale cortical activity during the processing of the stimuli with a 50 ​ms resolution, reproducing well-known activity in the fusiform face area as well as revealing co-activation patterns in somatosensory/motor and frontal cortices that an unconstrained ROI-by-ROI analysis fails to capture. The proposed approach is simple and fast, provides a means of integration of multimodal datasets, and is tied to a theoretical framework in mathematics and physics. Thus, network harmonics point towards promising research directions both theoretically - for example in exploring the relationship between structure and function in the brain - and practically - for example for network tracking in different tasks and groups of individuals, such as patients.