Standardizing a method for functional assessment of neural networks in brain organoids.

During the last decade brain organoids have emerged as an attractive model system, allowing stem cells to be differentiated into complex 3D models, recapitulating many aspects of human brain development. Whilst many studies have analysed anatomical and cytoarchitectural characteristics of organoids, their functional characterisation has been limited, and highly variable between studies. Standardised, consistent methods for recording functional activity are critical to providing a functional understanding of neuronal networks at the synaptic and network level that can yield useful information about functional network phenotypes in disease and healthy states. In this study we outline a detailed methodology for calcium imaging and Multi-Electrode Array (MEA) recordings in brain organoids. To illustrate the utility of these functional interrogation techniques in uncovering induced differences in neural network activity we applied various stimulating media protocols. We demonstrate overlapping information from the two modalities, with comparable numbers of active cells in the four treatment groups and an increase in synchronous behaviour in BrainPhys treated groups. Further development of analysis pipelines to reveal network level changes in brain organoids will enrich our understanding of network formation and perturbation in these structures, and aid in the future development of drugs that target neurological disorders at the network level.

Fast connectivity gradient approximation: maintaining spatially fine-grained connectivity gradients while reducing computational costs.

Brain connectome analysis suffers from the high dimensionality of connectivity data, often forcing a reduced representation of the brain at a lower spatial resolution or parcellation. This is particularly true for graph-based representations, which are increasingly used to characterize connectivity gradients, capturing patterns of systematic spatial variation in the functional connectivity structure. However, maintaining a high spatial resolution is crucial for enabling fine-grained topographical analysis and preserving subtle individual differences that might otherwise be lost. Here we introduce a computationally efficient approach to establish spatially fine-grained connectivity gradients. At its core, it leverages a set of landmarks to approximate the underlying connectivity structure at the full spatial resolution without requiring a full-scale vertex-by-vertex connectivity matrix. We show that this approach reduces computational time and memory usage while preserving informative individual features and demonstrate its application in improving brain-behavior predictions. Overall, its efficiency can remove computational barriers and enable the widespread application of connectivity gradients to capture spatial signatures of the connectome. Importantly, maintaining a spatially fine-grained resolution facilitates to characterize the spatial transitions inherent in the core concept of gradients of brain organization.

Simple model to incorporate statistical noise based on a modified hodgkin-huxley approach for external electrical field driven neural responses.

Noise activity is known to affect neural networks, enhance the system response to weak external signals, and lead to stochastic resonance phenomenon that can effectively amplify signals in nonlinear systems. In most treatments, channel noise has been modeled based on multi-state Markov descriptions or the use stochastic differential equation models. Here we probe a computationally simple approach based on a minor modification of the traditional Hodgkin-Huxley approach to embed noise in neural response. Results obtained from numerous simulations with different excitation frequencies and noise amplitudes for the action potential firing show very good agreement with output obtained from well-established models. Furthermore, results from the Mann-Whitney U Test reveal a statistically insignificant difference. The distribution of the time interval between successive potential spikes obtained from this simple approach compared very well with the results of complicated Fox and Lu type methods at much reduced computational cost. This present method could also possibly be applied to the analysis of spatial variations and/or differences in characteristics of random incident electromagnetic signals.

A predictor-informed multi-subject bayesian approach for dynamic functional connectivity.

Dynamic functional connectivity investigates how the interactions among brain regions vary over the course of an fMRI experiment. Such transitions between different individual connectivity states can be modulated by changes in underlying physiological mechanisms that drive functional network dynamics, e.g., changes in attention or cognitive effort. In this paper, we develop a multi-subject Bayesian framework where the estimation of dynamic functional networks is informed by time-varying exogenous physiological covariates that are simultaneously recorded in each subject during the fMRI experiment. More specifically, we consider a dynamic Gaussian graphical model approach where a non-homogeneous hidden Markov model is employed to classify the fMRI time series into latent neurological states. We assume the state-transition probabilities to vary over time and across subjects as a function of the underlying covariates, allowing for the estimation of recurrent connectivity patterns and the sharing of networks among the subjects. We further assume sparsity in the network structures via shrinkage priors, and achieve edge selection in the estimated graph structures by introducing a multi-comparison procedure for shrinkage-based inferences with Bayesian false discovery rate control. We evaluate the performances of our method vs alternative approaches on synthetic data. We apply our modeling framework on a resting-state experiment where fMRI data have been collected concurrently with pupillometry measurements, as a proxy of cognitive processing, and assess the heterogeneity of the effects of changes in pupil dilation on the subjects' propensity to change connectivity states. The heterogeneity of state occupancy across subjects provides an understanding of the relationship between increased pupil dilation and transitions toward different cognitive states.

Social functioning predicts individual changes in EEG microstates following intranasal oxytocin administration: A double-blind, cross-over randomized clinical trial.

Oxytocin (OXT) modulates social behaviors. However, the administration of exogenous OXT in humans produces inconsistent behavioral changes, affecting future consideration of OXT as a treatment for autism and other disorders with social symptoms. Inter-individual variability in social functioning traits might play a key role in how OXT changes brain activity and, therefore, behavior. Here, we investigated if inter-individual variability might dictate how single-dose intranasal OXT administration (IN-OXT) changes spontaneous neural activity during the eyes-open resting state. We used a double-blinded, randomized, placebo-controlled, cross-over design on 30 typically developing young adult men to investigate the dynamics of EEG microstates corresponding to activity in defined neural networks. We confirmed previous reports that, at the group level, IN-OXT increases the representation of the attention and salience microstates. Furthermore, we identified a decreased representation of microstates associated with the default mode network. Using multivariate partial least square statistical analysis, we found that social functioning traits associated with IN-OXT-induced changes in microstate dynamics in specific spectral bands. Correlation analysis further revealed that the higher the social functioning, the more IN-OXT increased the appearance of the visual network-associated microstate, and suppressed the appearance of a default mode network-related microstate. The lower the social functioning, the more IN-OXT increases the appearance of the salience microstate. The effects we report on the salience microstate support the hypothesis that OXT regulates behavior by enhancing social salience. Moreover, our findings indicate that social functioning traits modulate responses to IN-OXT and could partially explain the inconsistent reports on IN-OXT effects.

The Determining Role of Covariances in Large Networks of Stochastic Neurons.

Biological neural networks are notoriously hard to model due to their stochastic behavior and high dimensionality. We tackle this problem by constructing a dynamical model of both the expectations and covariances of the fractions of active and refractory neurons in the network's populations. We do so by describing the evolution of the states of individual neurons with a continuous-time Markov chain, from which we formally derive a low-dimensional dynamical system. This is done by solving a moment closure problem in a way that is compatible with the nonlinearity and boundedness of the activation function. Our dynamical system captures the behavior of the high-dimensional stochastic model even in cases where the mean-field approximation fails to do so. Taking into account the second-order moments modifies the solutions that would be obtained with the mean-field approximation and can lead to the appearance or disappearance of fixed points and limit cycles. We moreover perform numerical experiments where the mean-field approximation leads to periodically oscillating solutions, while the solutions of the second-order model can be interpreted as an average taken over many realizations of the stochastic model. Altogether, our results highlight the importance of including higher moments when studying stochastic networks and deepen our understanding of correlated neuronal activity.

Functional Brain Networks of Minor and Well-Structured Major Hallucinations in Parkinson's Disease.

BACKGROUND: Minor hallucinations (mHs) and well-structured major hallucinations (MHs) are common symptoms of Parkinson's disease (PD) psychosis. OBJECTIVES: To investigate the resting-state networks (RSNs) in patients with PD without hallucinations (PD-nH), with mH (PD-mH), and with MH (PD-MH). METHODS: A total of 73 patients with PD were enrolled (27 PD-nH, 23 PD-mH, and 23 PD-MH). Using seed-based functional connectivity analyses, we investigated the RSNs supposedly related to hallucinations in PD: the default mode network (DMN), executive control network (ECN), dorsal attention network (DAN), ventral attention network (VAN), and visual network (VN). We compared the cognitive function and RSN connectivity among the three groups. In addition, we performed a seed-to-seed analysis to examine the inter-network connectivity within each group using the corresponding RSN seeds. RESULTS: PD-MH group had lower test scores for attention and visuospatial functions compared with those in the other groups. The connectivity of the right intracalcarine cortex within the DAN was lower in the PD-MH group than in the others. The PD-mH and PD-MH groups showed higher connectivity in the left orbitofrontal cortex within DMN compared with the PD-nH group, whereas the connectivity was lower in the right middle frontal gyrus (MFG) within ECN, precuneus cortex within VAN, right middle temporal gyrus and precuneus cortex within DAN, and left MFG within VN. The PD-mH and PD-MH groups showed different inter-network connectivity between the five RSNs, especially regarding DAN connectivity. CONCLUSIONS: DAN dysfunction may be a key factor in the progression from mH to MH in patients with PD. © 2023 International Parkinson and Movement Disorder Society.

Socioeconomic resources are associated with distributed alterations of the brain's intrinsic functional architecture in youth.

Little is known about how exposure to limited socioeconomic resources (SER) in childhood gets "under the skin" to shape brain development, especially using rigorous whole-brain multivariate methods in large, adequately powered samples. The present study examined resting state functional connectivity patterns from 5821 youth in the Adolescent Brain Cognitive Development (ABCD) study, employing multivariate methods across three levels: whole-brain, network-wise, and connection-wise. Across all three levels, SER was associated with widespread alterations across the connectome. However, critically, we found that parental education was the primary driver of neural associations with SER. These parental education associations with the developing connectome exhibited notable concentrations in somatosensory and subcortical regions, and they were partially accounted for by home enrichment activities, child's cognitive abilities, and child's grades, indicating interwoven links between parental education, child stimulation, and child cognitive performance. These results add a new data-driven, multivariate perspective on links between household SER and the child's developing functional connectome.

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.

Canonical neural networks perform active inference.

This work considers a class of canonical neural networks comprising rate coding models, wherein neural activity and plasticity minimise a common cost function-and plasticity is modulated with a certain delay. We show that such neural networks implicitly perform active inference and learning to minimise the risk associated with future outcomes. Mathematical analyses demonstrate that this biological optimisation can be cast as maximisation of model evidence, or equivalently minimisation of variational free energy, under the well-known form of a partially observed Markov decision process model. This equivalence indicates that the delayed modulation of Hebbian plasticity-accompanied with adaptation of firing thresholds-is a sufficient neuronal substrate to attain Bayes optimal inference and control. We corroborated this proposition using numerical analyses of maze tasks. This theory offers a universal characterisation of canonical neural networks in terms of Bayesian belief updating and provides insight into the neuronal mechanisms underlying planning and adaptive behavioural control.

Epileptogenic networks in drug-resistant epilepsy with amygdala enlargement: Assessment with stereo-EEG and 7 T MRI.

OBJECTIVE: Amygdala enlargement is increasingly described in association with temporal lobe epilepsies. Its significance, however, remains uncertain both in terms of etiology and its link with psychiatric disorders and of its involvement in the epileptogenic zone. We assessed the epileptogenic networks underlying drug-resistant epilepsy with amygdala enlargement and investigated correlations between clinical features, epileptogenicity and morphovolumetric amygdala characteristics. METHODS: We identified 12 consecutive patients suffering from drug-resistant epilepsy with visually suspected amygdala enlargement and available stereoelectroencephalographic recording. The epileptogenic zone was defined using the Connectivity Epileptogenicity Index. Morphovolumetric measurements were performed using automatic segmentation and co-registration on the 7TAMIbrain Amygdala atlas. RESULTS: The epileptogenic zone involved the enlarged amygdala in all but three cases and corresponded to distributed, temporal-insular, temporal-insular-prefrontal or prefrontal-temporal networks in ten cases, while only two were temporo-mesial networks. Morphovolumetrically, amygdala enlargement was bilateral in 75% of patients. Most patients presented psychiatric comorbidities (anxiety, depression, posttraumatic stress disorder). The level of depression defined by screening questionnaire was positively correlated with the extent of amygdala enlargement. CONCLUSIONS: Drug-resistant epilepsy with amygdala enlargement is heterogeneous; most cases implied "temporal plus" networks. SIGNIFICANCE: The enlarged amygdala could reflect an interaction of stress-mediated limbic network alterations and mechanisms of epileptogenesis.

Static and dynamic topological organizations of the costly punishment network predict individual differences in punishment propensity.

Human costly punishment plays a vital role in maintaining social norms. Recently, a brain network model is conceptually proposed indicating that the implement of costly punishment depends on a subset of nodes in three high-level networks. This model, however, has not yet been empirically examined from an integrated perspective of large-scale brain networks. Here, we conducted comprehensive graph-based network analyses of resting-state functional magnetic resonance imaging data to explore system-level characteristics of intrinsic functional connectivity among 18 regions related to costly punishment. Nontrivial organizations (small-worldness, connector hubs, and high flexibility) were found that were qualitatively stable across participants and over time but quantitatively exhibited low test-retest reliability. The organizations were predictive of individual costly punishment propensities, which was reproducible on independent samples and robust against different analytical strategies and parameter settings. Moreover, the prediction was specific to system-level network organizations (rather than interregional functional connectivity) derived from positive (rather than negative or combined) connections among the specific (rather than randomly chosen) subset of regions from the three high-order (rather than primary) networks. Collectively, these findings suggest that human costly punishment emerges from integrative behaviors among specific regions in certain functional networks, lending support to the brain network model for costly punishment.

Unveiling whole-brain dynamics in normal aging through Hidden Markov Models.

During normal aging, the brain undergoes structural and functional changes. Many studies applied static functional connectivity (FC) analysis on resting state functional magnetic resonance imaging (rs-fMRI) data showing a link between aging and the increase of between-networks connectivity. However, it has been demonstrated that FC is not static but varies over time. By employing the dynamic data-driven approach of Hidden Markov Models, this study aims to investigate how aging is related to specific characteristics of dynamic brain states. Rs-fMRI data of 88 subjects, equally distributed in young and old were analyzed. The best model resulted to be with six states, which we characterized not only in terms of FC and mean BOLD activation, but also uncertainty of the estimates. We found two states were mostly occupied by young subjects, whereas three other states by old subjects. A graph-based analysis revealed a decrease in strength with the increase of age, and an overall more integrated topology of states occupied by old subjects. Indeed, while young subjects tend to cycle in a loop of states characterized by a high segregation of the networks, old subjects' loops feature high integration, with a crucial intermediary role played by the dorsal attention network. These results suggest that the employed mathematical approach captures the complex and rich brain's dynamics underpinning the aging process.

Racial Discrimination and White Matter Microstructure in Trauma-Exposed Black Women.

BACKGROUND: Experiences of racial discrimination are linked to a range of negative brain health outcomes, but little is known about how these experiences impact neural architecture, including white matter microstructure, which may partially mediate these outcomes. Our goal was to examine associations between racially discriminatory experiences and white matter structural integrity in a sample of Black American women. METHODS: We recruited 116 Black American women as part of a long-standing study of trauma. Participants completed assessments of racial discrimination, trauma exposure, and posttraumatic stress disorder and underwent diffusion tensor imaging. Fractional anisotropy and mean diffusivity values were extracted from major white matter tracts throughout the brain. RESULTS: Experiences of racial discrimination were associated with significantly lower fractional anisotropy in multiple white matter tracts, including the corpus callosum, cingulum, and superior longitudinal fasciculus (ps < .004), even after accounting for variance associated with trauma, posttraumatic stress disorder, and demographic- and scanner-related factors. CONCLUSIONS: These findings suggest that experiences of racial discrimination are independently related to decrements in white matter microarchitecture throughout the brain. In individuals who have experienced other types of adversity, racial discrimination clearly has additive and distinctive deleterious effects on white matter structure. Our findings suggest a pathway through which racial discrimination can contribute to brain health disparities in Black Americans; the deleterious contributions of racial discrimination on the microstructure of major white matter pathways may increase vulnerability for the development of neurodegenerative disorders as well as the development of mental health problems.

Hidden Markov Modeling Reveals Prolonged "Baseline" State and Shortened Antagonistic State across the Adult Lifespan.

The brain networks undergo functional reorganization across the whole lifespan, but the dynamic patterns behind the reorganization remain largely unclear. This study models the dynamics of spontaneous activity of large-scale networks using hidden Markov model (HMM), and investigates how it changes with age on two adult lifespan datasets of 176/157 subjects (aged 20-80 years). Results for both datasets showed that 1) older adults tended to spend less time on a state where default mode network (DMN) and attentional networks show antagonistic activity, 2) older adults spent more time on a "baseline" state with moderate-level activation of all networks, accompanied with lower transition probabilities from this state to the others and higher transition probabilities from the others to this state, and 3) HMM exhibited higher sensitivity in uncovering the age effects compared with temporal clustering method. Our results suggest that the aging brain is characterized by the shortening of the antagonistic instances between DMN and attention systems, as well as the prolongation of the inactive period of all networks, which might reflect the shift of the dynamical working point near criticality in older adults.

Perineuronal Nets in the Prefrontal Cortex of a Schizophrenia Mouse Model: Assessment of Neuroanatomical, Electrophysiological, and Behavioral Contributions.

Schizophrenia is a neurodevelopmental disorder whose etiopathogenesis includes changes in cellular as well as extracellular structures. Perineuronal nets (PNNs) associated with parvalbumin-positive interneurons (PVs) in the prefrontal cortex (PFC) are dysregulated in schizophrenia. However, the postnatal development of these structures along with their associated neurons in the PFC is unexplored, as is their effects on behavior and neural activity. Therefore, in this study, we employed a DISC1 (Disruption in Schizophrenia) mutation mouse model of schizophrenia to assess these developmental changes and tested whether enzymatic digestion of PNNs in the PFC affected schizophrenia-like behaviors and neural activity. Developmentally, we found that the normal formation of PNNs, PVs, and colocalization of these two in the PFC, peaked around PND 22 (postnatal day 22). However, in DISC1, mutation animals from PND 0 to PND 60, both PNNs and PVs were significantly reduced. After enzymatic digestion of PNNs with chondroitinase in adult animals, the behavioral pattern of control animals mimicked that of DISC1 mutation animals, exhibiting reduced sociability, novelty and increased ultrasonic vocalizations, while there was very little change in other behaviors, such as working memory (Y-maze task involving medial temporal lobe) or depression-like behavior (tail-suspension test involving processing via the hypothalamic pituitary adrenal (HPA) axis). Moreover, following chondroitinase treatment, electrophysiological recordings from the PFC exhibited a reduced proportion of spontaneous, high-frequency firing neurons, and an increased proportion of irregularly firing neurons, with increased spike count and reduced inter-spike intervals in control animals. These results support the proposition that the aberrant development of PNNs and PVs affects normal neural operations in the PFC and contributes to the emergence of some of the behavioral phenotypes observed in the DISC1 mutation model of schizophrenia.

A reachable probability approach for the analysis of spatio-temporal dynamics in the human functional network.

The dynamic architecture of the human brain has been consistently observed. However, there is still limited modeling work to elucidate how neuronal circuits are hierarchically and flexibly organized in functional systems. Here we proposed a reachable probability approach based on non-homogeneous Markov chains, to characterize all possible connectivity flows and the hierarchical structure of brain functional systems at the dynamic level. We proved at the theoretical level the convergence of the functional brain network system, and demonstrated that this approach is able to detect network steady states across connectivity structure, particularly in areas of the default mode network. We further explored the dynamically hierarchical functional organization centered at the primary sensory cortices. We observed smaller optimal reachable steps to their local functional regions, and differentiated patterns in larger optimal reachable steps for primary perceptual modalities. The reachable paths with the largest and second largest transition probabilities between primary sensory seeds via multisensory integration regions were also tracked to explore the flexibility and plasticity of the multisensory integration. The present work provides a novel approach to depict both the stable and flexible hierarchical connectivity organization of the human brain.

Altered network stability in progressive supranuclear palsy.

The clinical syndromes of Progressive Supranuclear Palsy (PSP) may be mediated by abnormal temporal dynamics of brain networks, due to the impact of atrophy, synapse loss and neurotransmitter deficits. We tested the hypothesis that alterations in signal complexity in neural networks influence short-latency state transitions. Ninety-four participants with PSP and 64 healthy controls were recruited from two independent cohorts. All participants underwent clinical and neuropsychological testing and resting-state functional MRI. Network dynamics were assessed using hidden Markov models and neural signal complexity measured in terms of multiscale entropy. In both cohorts, PSP increased the proportion of time in networks associated with higher cognitive functions. This effect correlated with clinical severity as measured by the PSP-rating-scale, and with reduced neural signal complexity. Regional atrophy influenced abnormal brain-state occupancy, but abnormal network topology and dynamics were not restricted to areas of atrophy. Our findings show that the pathology of PSP causes clinically relevant changes in neural temporal dynamics, leading to a greater proportion of time in inefficient brain-states.

Interpretable and parameter optimized ensemble model for knee osteoarthritis assessment using radiographs.

Knee osteoarthritis (KOA) is an orthopedic disorder with a substantial impact on mobility and quality of life. An accurate assessment of the KOA levels is imperative in prioritizing meaningful patient care. Quantifying osteoarthritis features such as osteophytes and joint space narrowing (JSN) from low-resolution images (i.e., X-ray images) are mostly subjective. We implement an objective assessment and quantification of KOA to aid practitioners. In particular, we developed an interpretable ensemble of convolutional neural network (CNN) models consisting of three modules. First, we developed a scale-invariant and aspect ratio preserving model to localize Knee joints. Second, we created multiple instances of "hyperparameter optimized" CNN models with diversity and build an ensemble scoring system to assess the severity of KOA according to the Kellgren-Lawrence grading (KL) scale. Third, we provided visual explanations of the predictions by the ensemble model. We tested our models using a collection of 37,996 Knee joints from the Osteoarthritis Initiative (OAI) dataset. Our results show a superior (13-27%) performance improvement compared to the state-of-the-art methods.