The human cortex possesses a reconfigurable dynamic network architecture that is disrupted in psychosis

The distinct functional brain network and its association with psychotic symptom severity in men with methamphetamine-associated psychosis

BACKGROUND

Individuals using methamphetamine (METH) may experience psychosis, which usually requires aggressive treatment. Studies of the neural correlates of METH-associated psychosis (MAP) have focused predominantly on the default mode network (DMN) and cognitive control networks. We hypothesize that METH use alters global functional connections in resting-state brain networks and that certain cross-network connections could be associated with psychosis.

METHODS

We recruited 24 healthy controls (CRL) and 54 men with METH use disorder (MUD) who were then divided into 25 without psychosis (MNP) and 29 with MAP. Psychotic symptom severity was assessed using the Positive and Negative Syndrome Scale (PANSS), evaluating (1) large-scale alterations in regional-wise resting-state functional connectivity (rsFC) across 11 brain networks and (2) associations between rsFC and psychotic symptom severity.

RESULTS

The MUD group exhibited greater rsFC between the salience network (SN)-DMN, and subcortical network (SCN)-DMN compared to the CRL group. The MAP group exhibited decreased rsFC in the sensory/somatomotor network (SMN)-dorsal attention network (DAN), SMN-ventral attention network (VAN), SMN-SN, and SMN-auditory network (AN), whereas the MNP group exhibited increased rsFC in the SMN-DMN and the frontoparietal network (FPN)-DMN compared to CRL. Additionally, the MAP group exhibited decreased rsFC strength between the SMN-DMN, SMN-AN, SMN-FPN, and DMN-VAN compared to the MNP group. Furthermore, across the entire MUD group, the PANSS-Positive subscale was negatively correlated with the DMN-FPN and FPN-SMN, while the PANSS-Negative subscale was negatively correlated with the DMN-AN and SMN-SMN.

CONCLUSION

MUD is associated with altered global functional connectivity. In addition, the MAP group exhibits a different brain functional network compared to the MNP group.

Multilayer network analysis reveals instability of brain dynamics in untreated first-episode schizophrenia

Although aberrant static functional brain network activity has been reported in schizophrenia, little is known about how the dynamics of neural function are altered in first-episode schizophrenia and are modulated by antipsychotic treatment. The baseline resting-state functional magnetic resonance imaging data were acquired from 122 first-episode drug-naïve schizophrenia patients and 128 healthy controls (HCs), and 44 patients were rescanned after 1-year of antipsychotic treatment. Multilayer network analysis was applied to calculate the network switching rates between brain states. Compared to HCs, schizophrenia patients at baseline showed significantly increased network switching rates. This effect was observed mainly in the sensorimotor (SMN) and dorsal attention networks (DAN), and in temporal and parietal regions at the nodal level. Switching rates were reduced after 1-year of antipsychotic treatment at the global level and in DAN. Switching rates at baseline at the global level and in the inferior parietal lobule were correlated with the treatment-related reduction of negative symptoms. These findings suggest that instability of functional network activity plays an important role in the pathophysiology of acute psychosis in early-stage schizophrenia. The normalization of network stability after antipsychotic medication suggests that this effect may represent a systems-level mechanism for their therapeutic efficacy.

A survey of brain functional network extraction methods using fMRI data

Functional network (FN) analyses play a pivotal role in uncovering insights into brain function and understanding the pathophysiology of various brain disorders. This paper focuses on classical and advanced methods for deriving brain FNs from functional magnetic resonance imaging (fMRI) data. We systematically review their foundational principles, advantages, shortcomings, and interrelations, encompassing both static and dynamic FN extraction approaches. In the context of static FN extraction, we present hypothesis-driven methods such as region of interest (ROI)-based approaches as well as data-driven methods including matrix decomposition, clustering, and deep learning. For dynamic FN extraction, both window-based and windowless methods are surveyed with respect to the estimation of time-varying FN and the subsequent computation of FN states. We also discuss the scope of application of the various methods and avenues for future improvements.

Neuroimage Analysis Methods and Artificial Intelligence Techniques for Reliable Biomarkers and Accurate Diagnosis of Schizophrenia: Achievements Made by Chinese Scholars Around the Past Decade

BACKGROUND AND HYPOTHESIS

Schizophrenia (SZ) is characterized by significant cognitive and behavioral disruptions. Neuroimaging techniques, particularly magnetic resonance imaging (MRI), have been widely utilized to investigate biomarkers of SZ, distinguish SZ from healthy conditions or other mental disorders, and explore biotypes within SZ or across SZ and other mental disorders, which aim to promote the accurate diagnosis of SZ. In China, research on SZ using MRI has grown considerably in recent years.

STUDY DESIGN

The article reviews advanced neuroimaging and artificial intelligence (AI) methods using single-modal or multimodal MRI to reveal the mechanism of SZ and promote accurate diagnosis of SZ, with a particular emphasis on the achievements made by Chinese scholars around the past decade.

STUDY RESULTS

Our article focuses on the methods for capturing subtle brain functional and structural properties from the high-dimensional MRI data, the multimodal fusion and feature selection methods for obtaining important and sparse neuroimaging features, the supervised statistical analysis and classification for distinguishing disorders, and the unsupervised clustering and semi-supervised learning methods for identifying neuroimage-based biotypes. Crucially, our article highlights the characteristics of each method and underscores the interconnections among various approaches regarding biomarker extraction and neuroimage-based diagnosis, which is beneficial not only for comprehending SZ but also for exploring other mental disorders.

CONCLUSIONS

We offer a valuable review of advanced neuroimage analysis and AI methods primarily focused on SZ research by Chinese scholars, aiming to promote the diagnosis, treatment, and prevention of SZ, as well as other mental disorders, both within China and internationally.

The Transdiagnostic Connectome Project: a richly phenotyped open dataset for advancing the study of brain-behavior relationships in psychiatry

An important aim in psychiatry is the establishment of valid and reliable associations linking profiles of brain functioning to clinically relevant symptoms and behaviors across patient populations. To advance progress in this area, we introduce an open dataset containing behavioral and neuroimaging data from 241 individuals aged 18 to 70, comprising 148 individuals meeting diagnostic criteria for a broad range of psychiatric illnesses and a healthy comparison group of 93 individuals. These data include high-resolution anatomical scans, multiple resting-state, and task-based functional MRI runs. Additionally, participants completed over 50 psychological and cognitive assessments. Here, we detail available behavioral data as well as raw and processed MRI derivatives. Associations between data processing and quality metrics, such as head motion, are reported. Processed data exhibit classic task activation effects and canonical functional network organization. Overall, we provide a comprehensive and analysis-ready transdiagnostic dataset, which we hope will accelerate the identification of illness-relevant features of brain functioning, enabling future discoveries in basic and clinical neuroscience.

Dynamic structure-function coupling across three major psychiatric disorders

BACKGROUND

Convergent evidence has suggested atypical relationships between brain structure and function in major psychiatric disorders, yet how the abnormal patterns coincide and/or differ across different disorders remains largely unknown. Here, we aim to investigate the common and/or unique dynamic structure-function coupling patterns across major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SZ).

METHODS

We quantified the dynamic structure-function coupling in 452 patients with psychiatric disorders (MDD/BD/SZ = 166/168/118) and 205 unaffected controls at three distinct brain network levels, such as global, meso-, and local levels. We also correlated dynamic structure-function coupling with the topological features of functional networks to examine how the structure-function relationship facilitates brain information communication over time.

RESULTS

The dynamic structure-function coupling is preserved for the three disorders at the global network level. Similar abnormalities in the rich-club organization are found in two distinct functional configuration states at the meso-level and are associated with the disease severity of MDD, BD, and SZ. At the local level, shared and unique alterations are observed in the brain regions involving the visual, cognitive control, and default mode networks. In addition, the relationships between structure-function coupling and the topological features of functional networks are altered in a manner indicative of state specificity.

CONCLUSIONS

These findings suggest both transdiagnostic and illness-specific alterations in the dynamic structure-function relationship of large-scale brain networks across MDD, BD, and SZ, providing new insights and potential biomarkers into the neurodevelopmental basis underlying the behavioral and cognitive deficits observed in these disorders.

Brain states as wave-like motifs

There is ample evidence of wave-like activity in the brain at multiple scales and levels. This emerging literature supports the broader adoption of a wave perspective of brain activity. Specifically, a brain state can be described as a set of recurring, sequential patterns of propagating brain activity, namely a wave. We examine a collective body of experimental work investigating wave-like properties. Based on these works, we consider brain states as waves using a scale-agnostic framework across time and space. Emphasis is placed on the sequentiality and periodicity associated with brain activity. We conclude by discussing the implications, prospects, and experimental opportunities of this framework.

Dynamical models reveal anatomically reliable attractor landscapes embedded in resting state brain networks

Analyses of functional connectivity (FC) in resting-state brain networks (RSNs) have generated many insights into cognition. However, the mechanistic underpinnings of FC and RSNs are still not well-understood. It remains debated whether resting state activity is best characterized as noise-driven fluctuations around a single stable state, or instead, as a nonlinear dynamical system with nontrivial attractors embedded in the RSNs. Here, we provide evidence for the latter, by constructing whole-brain dynamical systems models from individual resting-state fMRI (rfMRI) recordings, using the Mesoscale Individualized NeuroDynamic (MINDy) platform. The MINDy models consist of hundreds of neural masses representing brain parcels, connected by fully trainable, individualized weights. We found that our models manifested a diverse taxonomy of nontrivial attractor landscapes including multiple equilibria and limit cycles. However, when projected into anatomical space, these attractors mapped onto a limited set of canonical RSNs, including the default mode network (DMN) and frontoparietal control network (FPN), which were reliable at the individual level. Further, by creating convex combinations of models, bifurcations were induced that recapitulated the full spectrum of dynamics found via fitting. These findings suggest that the resting brain traverses a diverse set of dynamics, which generates several distinct but anatomically overlapping attractor landscapes. Treating rfMRI as a unimodal stationary process (i.e., conventional FC) may miss critical attractor properties and structure within the resting brain. Instead, these may be better captured through neural dynamical modeling and analytic approaches. The results provide new insights into the generative mechanisms and intrinsic spatiotemporal organization of brain networks.

Robust hierarchically organized whole-brain patterns of dysconnectivity in schizophrenia spectrum disorders observed after personalized intrinsic network topography

BACKGROUND

Spatial patterns of brain functional connectivity can vary substantially at the individual level. Applying cortical surface-based approaches with individualized rather than group templates may accelerate the discovery of biological markers related to psychiatric disorders. We investigated cortico-subcortical networks from multi-cohort data in people with schizophrenia spectrum disorders (SSDs) and healthy controls (HC) using individualized connectivity profiles.

METHODS

We utilized resting-state and anatomical MRI data from n = 406 participants (n = 203 SSD, n = 203 HC) from four cohorts. Functional timeseries were extracted from previously defined intrinsic network subregions of the striatum, thalamus, and cerebellum as well as 80 cortical regions of interest, representing six intrinsic networks using (1) volume-based approaches, (2) a surface-based group atlas approaches, and (3) Personalized Intrinsic Network Topography (PINT).

RESULTS

The correlations between all cortical networks and the expected subregions of the striatum, cerebellum, and thalamus were increased using a surface-based approach (Cohen's D volume vs. surface 0.27-1.00, all p < 10-6 ) and further increased after PINT (Cohen's D surface vs. PINT 0.18-0.96, all p < 10-4 ). In SSD versus HC comparisons, we observed robust patterns of dysconnectivity that were strengthened using a surface-based approach and PINT (Number of differing pairwise-correlations: volume: 404, surface: 570, PINT: 628, FDR corrected).

CONCLUSION

Surface-based and individualized approaches can more sensitively delineate cortical network dysconnectivity differences in people with SSDs. These robust patterns of dysconnectivity were visibly organized in accordance with the cortical hierarchy, as predicted by computational models.

Altered Brain Dynamics Across Bipolar Disorder and Schizophrenia During Rest and Task Switching Revealed by Overlapping Brain States

BACKGROUND

Individuals with bipolar disorder (BD) and schizophrenia (SCZ) show aberrant brain dynamics (i.e., altered recruitment or traversal through different brain states over time). Existing investigations of brain dynamics typically assume that one dominant brain state characterizes each time point. However, as multiple brain states likely are engaged at any given moment, this approach can obscure alterations in less prominent but critical brain states. Here, we examined brain dynamics in BD and SCZ by implementing a novel framework that simultaneously assessed the engagement of multiple brain states.

METHODS

Four recurring brain states were identified by applying nonlinear manifold learning and k-means clustering to the Human Connectome Project task-based functional magnetic resonance imaging data. We then assessed moment-to-moment state engagement in 2 independent samples of healthy control participants and patients with BD or SCZ using resting-state (N = 336) or task-based (N = 217) functional magnetic resonance imaging data. Relative state engagement and state engagement variability were extracted and compared across groups using multivariate analysis of covariance, controlling for site, medication, age, and sex.

RESULTS

Our framework identified dynamic alterations in BD and SCZ, while a state discretization approach revealed no significant group differences. Participants with BD or SCZ showed reduced state engagement variability, but not relative state engagement, across multiple brain states during resting-state and task-based functional magnetic resonance imaging. We found decreased state engagement variability in older participants and preliminary evidence suggesting an association with avolition.

CONCLUSIONS

Assessing multiple brain states simultaneously can reflect the complexity of aberrant brain dynamics in BD and SCZ, providing a more comprehensive understanding of the neural mechanisms underpinning these conditions.

Low-frequency repetitive transcranial magnetic stimulation alters the individual functional dynamical landscape

Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive approach to modulate brain activity and behavior in humans. Still, how individual resting-state brain dynamics after rTMS evolves across different functional configurations is rarely studied. Here, using resting state fMRI data from healthy subjects, we aimed to examine the effects of rTMS to individual large-scale brain dynamics. Using Topological Data Analysis based Mapper approach, we construct the precise dynamic mapping (PDM) for each participant. To reveal the relationship between PDM and canonical functional representation of the resting brain, we annotated the graph using relative activation proportion of a set of large-scale resting-state networks (RSNs) and assigned the single brain volume to corresponding RSN-dominant or a hub state (not any RSN was dominant). Our results show that (i) low-frequency rTMS could induce changed temporal evolution of brain states; (ii) rTMS didn't alter the hub-periphery configurations underlined resting-state brain dynamics; and (iii) the rTMS effects on brain dynamics differ across the left frontal and occipital lobe. In conclusion, low-frequency rTMS significantly alters the individual temporo-spatial dynamics, and our finding further suggested a potential target-dependent alteration of brain dynamics. This work provides a new perspective to comprehend the heterogeneous effect of rTMS.

Topological data analysis for revealing dynamic brain reconfiguration in MEG data

In recent years, the focus of the functional connectivity community has shifted from stationary approaches to the ones that include temporal dynamics. Especially, non-invasive electrophysiological data (magnetoencephalography/electroencephalography (MEG/EEG)) with high temporal resolution and good spatial coverage have made it possible to measure the fast alterations in the neural activity in the brain during ongoing cognition. In this article, we analyze dynamic brain reconfiguration using MEG images collected from subjects during the rest and the cognitive tasks. Our proposed topological data analysis method, called Mapper, produces biomarkers that differentiate cognitive tasks without prior spatial and temporal collapse of the data. The suggested method provides an interactive visualization of the rapid fluctuations in electrophysiological data during motor and cognitive tasks; hence, it has the potential to extract clinically relevant information at an individual level without temporal and spatial collapse.

CaMKIIα neurons in the anterior insular cortex regulate attention behavior in mice

Introduction

The insular cortex is involved in multiple physiological processes including working memory, pain, emotion, and interoceptive functions. Previous studies have indicated that the anterior insular cortex (aIC) also mediates interoceptive attention in humans. However, the exact cellular and physiological function of the aIC in the regulation of this process is still elusive.

Methods

In this study, using the 5-choice serial reaction time task (5-CSRTT) testing paradigm, we assessed the role of the aIC in visuospatial attention and impulsiveness in mice.

Results

The results showed a dramatic activation of c-Fos in the aIC CaMKIIα neurons after the 5-CSRTT procedure. In vivo fiber photometry revealed enhanced calcium signaling in aIC CaMKIIα neurons when the mice responded correctly. In addition, chemogenetic suppression of aIC CaMKIIα neurons led to increased incorrect responses within the appropriate time. Importantly, pharmacological activation of aIC CaMKIIα neurons enhanced their performance in the 5-CSRTT test.

Discussion

These results provide compelling evidence that aIC CaMKIIα neurons are essential for the modulation of attentional processing in mice.

Alterations of insular dynamic functional connectivity and psychological characteristics in unmedicated bipolar depression patients with a recent suicide attempt

BACKGROUND

Mounting evidence showed that insula contributed to the neurobiological mechanism of suicidal behaviors in bipolar disorder (BD). However, no studies have analyzed the dynamic functional connectivity (dFC) of insular Mubregions and its association with personality traits in BD with suicidal behaviors. Therefore, we investigated the alterations of dFC variability in insular subregions and personality characteristics in BD patients with a recent suicide attempt (SA).

METHODS

Thirty unmedicated BD patients with SA, 38 patients without SA (NSA) and 35 demographically matched healthy controls (HCs) were included. The sliding-window analysis was used to evaluate whole-brain dFC for each insular subregion seed. We assessed between-group differences of psychological characteristics on the Minnesota Multiphasic Personality Inventory-2. Finally, a multivariate regression model was adopted to predict the severity of suicidality.

RESULTS

Compared to NSA and HCs, the SA group exhibited decreased dFC variability values between the left dorsal anterior insula and the left anterior cerebellum. These dFC variability values could also be utilized to predict the severity of suicidality (r = 0.456, p = 0.031), while static functional connectivity values were not appropriate for this prediction. Besides, the SA group scored significantly higher on the schizophrenia clinical scales (p < 0.001) compared with the NSA group.

CONCLUSIONS

Our findings indicated that the dysfunction of insula-cerebellum connectivity may underlie the neural basis of SA in BD patients, and highlighted the dFC variability values could be considered a neuromarker for predictive models of the severity of suicidality. Moreover, the psychiatric features may increase the vulnerability of suicidal behavior.

Evaluating methods for measuring background connectivity in slow event-related functional magnetic resonance imaging designs

INTRODUCTION

Resting-state functional magnetic resonance imaging (fMRI) is widely used for measuring functional interactions between brain regions, significantly contributing to our understanding of large-scale brain networks and brain-behavior relationships. Furthermore, idiosyncratic patterns of resting-state connections can be leveraged to identify individuals and predict individual differences in clinical symptoms, cognitive abilities, and other individual factors. Idiosyncratic connectivity patterns are thought to persist across task states, suggesting task-based fMRI can be similarly leveraged for individual differences analyses.

METHOD

Here, we tested the degree to which functional interactions occurring in the background of a task during slow event-related fMRI parallel or differ from those captured during resting-state fMRI. We compared two approaches for removing task-evoked activity from task-based fMRI: (1) applying a low-pass filter to remove task-related frequencies in the signal, or (2) extracting residuals from a general linear model (GLM) that accounts for task-evoked responses.

RESULT

We found that the organization of large-scale cortical networks and individual's idiosyncratic connectivity patterns are preserved during task-based fMRI. In contrast, individual differences in connection strength can vary more substantially between rest and task. Compared to low-pass filtering, background connectivity obtained from GLM residuals produced idiosyncratic connectivity patterns and individual differences in connection strength that more resembled rest. However, all background connectivity measures were highly similar when derived from the low-pass-filtered signal or GLM residuals, indicating that both methods are suitable for measuring background connectivity.

CONCLUSION

Together, our results highlight new avenues for the analysis of task-based fMRI datasets and the utility of each background connectivity method.

Abnormal dynamic functional connectivity of hippocampal subregions associated with working memory impairment in melancholic depression

BACKGROUND

Previous studies have demonstrated structural and functional changes of the hippocampus in patients with major depressive disorder (MDD). However, no studies have analyzed the dynamic functional connectivity (dFC) of hippocampal subregions in melancholic MDD. We aimed to reveal the patterns for dFC variability in hippocampus subregions - including the bilateral rostral and caudal areas and its associations with cognitive impairment in melancholic MDD.

METHODS

Forty-two treatment-naive MDD patients with melancholic features and 55 demographically matched healthy controls were included. The sliding-window analysis was used to evaluate whole-brain dFC for each hippocampal subregions seed. We assessed between-group differences in the dFC variability values of each hippocampal subregion in the whole brain and cognitive performance on the MATRICS Consensus Cognitive Battery (MCCB). Finally, association analysis was conducted to investigate their relationships.

RESULTS

Patients with melancholic MDD showed decreased dFC variability between the left rostral hippocampus and left anterior lobe of cerebellum compared with healthy controls (voxel p < 0.005, cluster p < 0.0125, GRF corrected), and poorer cognitive scores in working memory, verbal learning, visual learning, and social cognition (all p < 0.05). Association analysis showed that working memory was positively correlated with the dFC variability values of the left rostral hippocampus-left anterior lobe of the cerebellum (r = 0.338, p = 0.029) in melancholic MDD.

CONCLUSIONS

These findings confirmed the distinct dynamic functional pathway of hippocampal subregions in patients with melancholic MDD, and suggested that the dysfunction of hippocampus-cerebellum connectivity may be underlying the neural substrate of working memory impairment in melancholic MDD.

Evaluating test-retest reliability and sex-/age-related effects on temporal clustering coefficient of dynamic functional brain networks

The multilayer dynamic network model has been proposed as an effective method to understand the brain function. In particular, derived from the definition of clustering coefficient in static networks, the temporal clustering coefficient provides a direct measure of the topological stability of dynamic brain networks and shows potential in predicting altered brain functions. However, test-retest reliability and demographic-related effects on this measure remain to be evaluated. Using a data set from the Human Connectome Project (157 male and 180 female healthy adults; 22-37 years old), the present study investigated: (1) the test-retest reliability of temporal clustering coefficient across four repeated resting-state functional magnetic resonance imaging scans as measured by intraclass correlation coefficient (ICC); and (2) sex- and age-related effects on temporal clustering coefficient. The results showed that (1) the temporal clustering coefficient had overall moderate test-retest reliability (ICC > 0.40 over a wide range of densities) at both global and subnetwork levels, (2) female subjects showed significantly higher temporal clustering coefficient than males at both global and subnetwork levels, particularly within the default-mode and subcortical regions, and (3) temporal clustering coefficient of the subcortical subnetwork was positively correlated with age in young adults. The results of sex effects were robustly replicated in an independent REST-meta-MDD data set, while the results of age effects were not. Our findings suggest that the temporal clustering coefficient is a relatively reliable and reproducible approach for identifying individual differences in brain function, and provide evidence for demographically related effects on the human brain dynamic connectomes.

Anhedonia and dysregulation of an angular gyrus-centred and dynamic functional network in adolescent-onset depression

BACKGROUND

Anhedonia is an important aspect of adolescent-onset major depressive disorder (MDD) and is associated with increased risk of suicidal behaviors and poor treatment outcomes. However, the neural circuitry underlying this deficit has not been well defined. This study aims to identify the relationships between anhedonia and changes in static and dynamic functional connectivity (FC) in adolescent-onset MDD patients compared with healthy control subjects (HCs) and adult-onset MDD patients.

METHODS

A total of 157 participants completed the Snaith-Hamilton Pleasure Scale (SHAPS) to assess hedonic capacity. Resting-state functional imaging scans were analysed using graph theoretical analysis, network-based statistics (NBS) and sliding window correlation analysis to explore the potential patterns of neural network brain disruptions in adolescent-onset MDD. Pearson correlations and support vector machines regression (SVR) were used to explore correlations and predict network measures with SHAPS scores.

RESULTS

Compared with those with adult-onset MDD, adolescent-onset MDD patients showed decreased FC in 7 nodes and 6 connections, with the right angular gyrus (AG), left AG and left paracentral lobule having the largest number of connected edges (P = 0.0396, NBS-corrected). Their average FC and SHAPS scores were positively correlated (r = 0.309, P = 0.035). Regarding dynamic FC, compared with HCs, adolescent-onset MDD patients showed a tendency towards a decreased frequency in moderate-intensity brain FC states (P = 0.014), which was significantly and positively correlated with SHAPS scores (r = 0.425, P = 0.003). SVR also revealed AG-centred FC and dynamic FC could predict SHAPS scores (MSE = 27.233, P = 0.001).

CONCLUSIONS

These findings provide distinct evidence on the physiological mechanisms of adolescent-onset MDD and anhedonia.

Impaired dynamic functional brain properties and their relationship to symptoms in never treated first-episode patients with schizophrenia

Studies of dynamic functional connectivity (dFC) and topology can provide novel insights into the neurophysiology of brain dysfunction in schizophrenia and its relation to core symptoms of psychosis. Limited investigations of these disturbances have been conducted with never-treated first-episode patients to avoid the confounds of treatment or chronic illness. Therefore, we recruited 95 acutely ill, first-episode, never-treated patients with schizophrenia and examined brain dFC patterns relative to healthy controls using resting-state functional magnetic resonance imaging and a sliding-window approach. We compared the dynamic attributes at the group level and found patients spent more time in a hypoconnected state and correspondingly less time in a hyperconnected state. Patients demonstrated decreased dynamics of nodal efficiency and eigenvector centrality (EC) in the right medial prefrontal cortex, which was associated with psychosis severity reflected in Positive and Negative Syndrome Scale ratings. We also observed increased dynamics of EC in temporal and sensorimotor regions. These findings were supported by validation analysis. To supplement the group comparison analyses, a support vector classifier was used to identify the dynamic attributes that best distinguished patients from controls at the individual level. Selected features for case-control classification were highly coincident with the properties having significant between-group differences. Our findings provide novel neuroimaging evidence about dynamic characteristics of brain physiology in acute schizophrenia. The clinically relevant atypical pattern of dynamic shifting between brain states in schizophrenia may represent a critical aspect of illness pathophysiology underpinning its defining cognitive, behavioral, and affective features.

Precision dynamical mapping using topological data analysis reveals a hub-like transition state at rest

In the absence of external stimuli, neural activity continuously evolves from one configuration to another. Whether these transitions or explorations follow some underlying arrangement or lack a predictable ordered plan remains to be determined. Here, using fMRI data from highly sampled individuals (~5 hours of resting-state data per individual), we aimed to reveal the rules that govern transitions in brain activity at rest. Our Topological Data Analysis based Mapper approach characterized a highly visited transition state of the brain that acts as a switch between different neural configurations to organize the spontaneous brain activity. Further, while the transition state was characterized by a uniform representation of canonical resting-state networks (RSNs), the periphery of the landscape was dominated by a subject-specific combination of RSNs. Altogether, we revealed rules or principles that organize spontaneous brain activity using a precision dynamics approach.

Behavioral Studies Using Large-Scale Brain Networks – Methods and Validations

Mapping human behaviors to brain activity has become a key focus in modern cognitive neuroscience. As methods such as functional MRI (fMRI) advance cognitive scientists show an increasing interest in investigating neural activity in terms of functional connectivity and brain networks, rather than activation in a single brain region. Due to the noisy nature of neural activity, determining how behaviors are associated with specific neural signals is not well-established. Previous research has suggested graph theory techniques as a solution. Graph theory provides an opportunity to interpret human behaviors in terms of the topological organization of brain network architecture. Graph theory-based approaches, however, only scratch the surface of what neural connections relate to human behavior. Recently, the development of data-driven methods, e.g., machine learning and deep learning approaches, provide a new perspective to study the relationship between brain networks and human behaviors across the whole brain, expanding upon past literatures. In this review, we sought to revisit these data-driven approaches to facilitate our understanding of neural mechanisms and build models of human behaviors. We start with the popular graph theory approach and then discuss other data-driven approaches such as connectome-based predictive modeling, multivariate pattern analysis, network dynamic modeling, and deep learning techniques that quantify meaningful networks and connectivity related to cognition and behaviors. Importantly, for each topic, we discuss the pros and cons of the methods in addition to providing examples using our own data for each technique to describe how these methods can be applied to real-world neuroimaging data.

Thyroid hormones disturbances, cognitive deficits and abnormal dynamic functional connectivity variability of the amygdala in unmedicated bipolar disorder

OBJECTIVE

Accumulating evidence suggests that hypothalamus-pituitary-thyroid (HPT) axis dysfunction is relevant to the neuropsychological and pathophysiology functions of bipolar disorder (BD). However, no research has investigated the inter-relationships among thyroid hormones disturbance, neurocognitive deficits, and aberrant brain function (particularly in the amygdala) in patients with BD.

MATERIALS AND METHODS

Data of dynamic resting-state functional connectivity (rs-dFC) were gathered from 59 patients with unmedicated BD II during depressive episodes and 52 healthy controls (HCs). Four seeds were selected (the bilateral lateral amygdala and the bilateral medial amygdala). The sliding-window analysis was applied to investigate dynamic functional connectivity (dFC). Additionally, the serum thyroid hormone (free tri-iodothyronine (FT3), total tri-iodothyronine (TT3), free thyroxin (FT4), total thyroxin (TT4) and thyroid-stimulating hormone (TSH)) levels, and cognitive scores on the MATRICS Consensus Cognitive Battery (MCCB) in patients and HCs were detected.

RESULTS

The BD group exhibited increased dFC variability between the left medial amygdala and right medial prefrontal cortex (mPFC) when compared with the HC group. Additionally, the BD group showed lower FT3, TT3, and TSH level, higher FT4 level, and poorer cognitive score. Moreover, a significant negative correlation was observed between the dFC variability of the left medial amygdala-right mPFC and TSH level, or reasoning and problem solving of MCCB score in BD group. Multiple regression analysis showed that the TSH level × dFC variability of the medial amygdala-mPFC was an independent predictor for cognitive processing speed in BD group.

CONCLUSIONS

This study revealed patients with BD II depression had excessive variability in dFC between the medial amygdala and mPFC. Moreover, both HPT axis dysfunction and abnormal dFC of the amygdala-mPFC might be implicated in cognitive impairment in the early stages of BD.

Meta-matching as a simple framework to translate phenotypic predictive models from big to small data

We propose a simple framework-meta-matching-to translate predictive models from large-scale datasets to new unseen non-brain-imaging phenotypes in small-scale studies. The key consideration is that a unique phenotype from a boutique study likely correlates with (but is not the same as) related phenotypes in some large-scale dataset. Meta-matching exploits these correlations to boost prediction in the boutique study. We apply meta-matching to predict non-brain-imaging phenotypes from resting-state functional connectivity. Using the UK Biobank (N = 36,848) and Human Connectome Project (HCP) (N = 1,019) datasets, we demonstrate that meta-matching can greatly boost the prediction of new phenotypes in small independent datasets in many scenarios. For example, translating a UK Biobank model to 100 HCP participants yields an eight-fold improvement in variance explained with an average absolute gain of 4.0% (minimum = -0.2%, maximum = 16.0%) across 35 phenotypes. With a growing number of large-scale datasets collecting increasingly diverse phenotypes, our results represent a lower bound on the potential of meta-matching.

Frequency-specific coactivation patterns in resting-state and their alterations in schizophrenia: An fMRI study

The resting‐state human brain is a dynamic system that shows frequency‐dependent characteristics. Recent studies demonstrate that coactivation pattern (CAP) analysis can identify recurring brain states with similar coactivation configurations. However, it is unclear whether and how CAPs depend on the frequency bands. The current study investigated the spatial and temporal characteristics of CAPs in the four frequency sub‐bands from slow‐5 (0.01–0.027 Hz), slow‐4 (0.027–0.073 Hz), slow‐3 (0.073–0.198 Hz), to slow‐2 (0.198–0.25 Hz), in addition to the typical low‐frequency range (0.01–0.08 Hz). In the healthy subjects, six CAP states were obtained at each frequency band in line with our prior study. Similar spatial patterns with the typical range were observed in slow‐5, 4, and 3, but not in slow‐2. While the frequency increased, all CAP states displayed shorter persistence, which caused more between‐state transitions. Specifically, from slow‐5 to slow‐4, the coactivation not only changed significantly in distributed cortical networks, but also increased in the basal ganglia as well as the amygdala. Schizophrenia patients showed significant alteration in the persistence of CAPs of slow‐5. Using leave‐one‐pair‐out, hold‐out and resampling validations, the highest classification accuracy (84%) was achieved by slow‐4 among different frequency bands. In conclusion, our findings provide novel information about spatial and temporal characteristics of CAP states at different frequency bands, which contributes to a better understanding of the frequency aspect of biomarkers for schizophrenia and other disorders.

Shared and specific patterns of dynamic functional connectivity variability of striato-cortical circuitry in unmedicated bipolar and major depressive disorders

BACKGROUND

Accumulating studies have found structural and functional abnormalities of the striatum in bipolar disorder (BD) and major depressive disorder (MDD). However, changes in intrinsic brain functional connectivity dynamics of striato-cortical circuitry have not been investigated in BD and MDD. This study aimed to investigate the shared and specific patterns of dynamic functional connectivity (dFC) variability of striato-cortical circuitry in BD and MDD.

METHODS

Brain resting-state functional magnetic resonance imaging data were acquired from 128 patients with unmedicated BD II (current episode depressed), 140 patients with unmedicated MDD, and 132 healthy controls (HCs). Six pairs of striatum seed regions were selected: the ventral striatum inferior (VSi) and the ventral striatum superior (VSs), the dorsal-caudal putamen (DCP), the dorsal-rostral putamen (DRP), and the dorsal caudate and the ventral-rostral putamen (VRP). The sliding-window analysis was used to evaluate dFC for each seed.

RESULTS

Both BD II and MDD exhibited increased dFC variability between the left DRP and the left supplementary motor area, and between the right VRP and the right inferior parietal lobule. The BD II had specific increased dFC variability between the right DCP and the left precentral gyrus compared with MDD and HCs. The MDD had increased dFC variability between the left VSi and the left medial prefrontal cortex compared with BD II and HCs.

CONCLUSIONS

The patients with BD and MDD shared common dFC alteration in the dorsal striatal-sensorimotor and ventral striatal-cognitive circuitries. The patients with MDD had specific dFC alteration in the ventral striatal-affective circuitry.

Hippocampus-Based Dynamic Functional Connectivity Mapping in the Early Stages of Alzheimer's Disease

BACKGROUND

The hippocampus with varying degrees of atrophy was a crucial neuroimaging feature resulting in the declining memory and cognitive function in Alzheimer's disease (AD). However, the abnormal dynamic functional connectivity (DFC) in both white matter (WM) and gray matter (GM) from the left and right hippocampus remains unclear.

OBJECTIVE

To explore the abnormal DFC within WM and GM from the left and right hippocampus across the different stages of AD.

METHODS

Current study employed the OASIS-3 dataset including 43 mild cognitive impairment (MCI), 71 pre-mild cognitive impairment (pre-MCI), and matched 87 normal cognitive (NC). Adopting the FMRIB's Integrated Registration and Segmentation Tool, we obtained the left and right hippocampus mask. Based on above hippocampus mask as seed point, we calculated the DFC between left/right hippocampus and all voxel time series within whole brain. One-way ANOVA analysis was performed to estimate the abnormal DFC among MCI, pre-MCI, and NC groups.

RESULTS

We found that MCI and pre-MCI groups showed the common abnormalities of DFC in the Temporal_Mid_L, Cingulum_Mid_L, and Thalamus_L. Specific abnormalities were found in the Cerebelum_9_L and Precuneus of MCI group and Vermis_8 and Caudate_L of pre-MCI group. In addition, we found that DFC within WM regions also showed the common low DFC for the Cerebellum anterior lobe-WM, Corpus callosum, and Frontal lobe-WM in MCI and pre-MCI group.

CONCLUSION

Our findings provided a novel information for discover the pathophysiological mechanisms of AD and indicate WM lesions were also an important cause of cognitive decline in AD.

Predictive processing models and affective neuroscience

The neural bases of affective experience remain elusive. Early neuroscience models of affect searched for specific brain regions that uniquely carried out the computations that underlie dimensions of valence and arousal. However, a growing body of work has failed to identify these circuits. Research turned to multivariate analyses, but these strategies, too, have made limited progress. Predictive processing models offer exciting new directions to address this problem. Here, we use predictive processing models as a lens to critique prevailing functional neuroimaging research practices in affective neuroscience. Our review highlights how much work relies on rigid assumptions that are inconsistent with a predictive processing approach. We outline the central aspects of a predictive processing model and draw out their implications for research in affective and cognitive neuroscience. Predictive models motivate a reformulation of "reverse inference" in cognitive neuroscience, and placing a greater emphasis on external validity in experimental design.

White Matter Functional Connectivity in Resting-State fMRI: Robustness, Reliability, and Relationships to Gray Matter

A comprehensive characterization of the spatiotemporal organization in the whole brain is critical to understand both the function and dysfunction of the human brain. Resting-state functional connectivity (FC) of gray matter (GM) has helped in uncovering the inherent baseline networks of brain. However, the white matter (WM), which composes almost half of brain, has been largely ignored in this characterization despite studies indicating that FC in WM does change during task and rest functional magnetic resonance imaging (fMRI). In this study, we identify 9 white matter functional networks (WM-FNs) and 9 gray matter functional networks (GM-FNs) of resting fMRI. Intraclass correlation coefficient (ICC) was calculated on multirun fMRI data to estimate the reliability of static functional connectivity (SFC) and dynamic functional connectivity (DFC). Associations between SFC, DFC, and their respective ICCs are estimated for GM-FNs, WM-FNs, and GM-WM-FNs. SFC of GM-FNs were stronger than that of WM-FNs, but the corresponding DFC of GM-FNs was lower, indicating that WM-FNs were more dynamic. Associations between SFC, DFC, and their ICCs were similar in both GM- and WM-FNs. These findings suggest that WM fMRI signal contains rich spatiotemporal information similar to that of GM and may hold important cues to better establish the functional organization of the whole brain.

Sensory-motor cortices shape functional connectivity dynamics in the human brain

Large-scale biophysical circuit models provide mechanistic insights into the micro-scale and macro-scale properties of brain organization that shape complex patterns of spontaneous brain activity. We developed a spatially heterogeneous large-scale dynamical circuit model that allowed for variation in local synaptic properties across the human cortex. Here we show that parameterizing local circuit properties with both anatomical and functional gradients generates more realistic static and dynamic resting-state functional connectivity (FC). Furthermore, empirical and simulated FC dynamics demonstrates remarkably similar sharp transitions in FC patterns, suggesting the existence of multiple attractors. Time-varying regional fMRI amplitude may track multi-stability in FC dynamics. Causal manipulation of the large-scale circuit model suggests that sensory-motor regions are a driver of FC dynamics. Finally, the spatial distribution of sensory-motor drivers matches the principal gradient of gene expression that encompasses certain interneuron classes, suggesting that heterogeneity in excitation-inhibition balance might shape multi-stability in FC dynamics.

Frequency-specific altered global signal topography in drug-naïve first-episode patients with adolescent-onset schizophrenia

Adolescent-onset schizophrenia (AOS) is a severe neuropsychiatric disease associated with frequency-specific abnormalities across distributed neural systems in a slow rhythm. Recently, functional magnetic resonance imaging (fMRI) studies have determined that the global signal. (GS) is an important source of the local neuronal activity in 0.01-0.1 Hz frequency band. However, it remains unknown whether the effects follow a specific spatially preferential pattern in different frequency bands in schizophrenia. To address this issue, resting-state fMRI data from 39 drug-naïve AOS patients and 31 healthy controls (HCs) were used to assess the changes in GS topography patterns in the slow-4 (0.027-0.073 Hz) and slow-5 bands (0.01-0.027 Hz). Results revealed that GS mainly affects the default mode network (DMN) in slow-4 and sensory regions in the slow-5 band respectively, and GS has a stronger driving effect in the slow-5 band. Moreover, significant frequency-by-group interaction was observed in the frontoparietal network. Compared with HCs, patients with AOS exhibited altered GS topography mainly located in the DMN. Our findings demonstrated that the influence of the GS on brain networks altered in a frequency-specific way in schizophrenia.

Quantum computing at the frontiers of biological sciences

Computing plays a critical role in the biological sciences but faces increasing challenges of scale and complexity. Quantum computing, a computational paradigm exploiting the unique properties of quantum mechanical analogs of classical bits, seeks to address many of these challenges. We discuss the potential for quantum computing to aid in the merging of insights across different areas of biological sciences.

Sensory, somatomotor and internal mentation networks emerge dynamically in the resting brain with internal mentation predominating in older age

Age-related changes in the brain are associated with a decline in functional flexibility. Intrinsic functional flexibility is evident in the brain's dynamic ability to switch between alternative spatiotemporal states during resting state. However, the relationship between brain connectivity states, associated psychological functions during resting state, and the changes in normal aging remain poorly understood. In this study, we analyzed resting-state functional magnetic resonance imaging (rsfMRI) data from the Human Connectome Project (HCP; N = 812) and the UK Biobank (UKB; N = 6,716). Using signed community clustering to identify distinct states of dynamic functional connectivity, and text-mining of a large existing literature for functional annotation of each state, our findings from the HCP dataset indicated that the resting brain spontaneously transitions between three functionally specialized states: sensory, somatomotor, and internal mentation networks. The occurrence, transition-rate, and persistence-time parameters for each state were correlated with behavioural scores using canonical correlation analysis. We estimated the same brain states and parameters in the UKB dataset, subdivided into three distinct age ranges: 50-55, 56-67, and 68-78 years. We found that the internal mentation network was more frequently expressed in people aged 71 and older, whereas people younger than 55 more frequently expressed sensory and somatomotor networks. Furthermore, analysis of the functional entropy - a measure of uncertainty of functional connectivity - also supported this finding across the three age ranges. Our study demonstrates that dynamic functional connectivity analysis can expose the time-varying patterns of transition between functionally specialized brain states, which are strongly tied to increasing age.

Heritability of individualized cortical network topography

Human cortex is patterned by a complex and interdigitated web of large-scale functional networks. Recent methodological breakthroughs reveal variation in the size, shape, and spatial topography of cortical networks across individuals. While spatial network organization emerges across development, is stable over time, and is predictive of behavior, it is not yet clear to what extent genetic factors underlie interindividual differences in network topography. Here, leveraging a nonlinear multidimensional estimation of heritability, we provide evidence that individual variability in the size and topographic organization of cortical networks are under genetic control. Using twin and family data from the Human Connectome Project (n = 1,023), we find increased variability and reduced heritability in the size of heteromodal association networks (h2 : M = 0.34, SD = 0.070), relative to unimodal sensory/motor cortex (h2 : M = 0.40, SD = 0.097). We then demonstrate that the spatial layout of cortical networks is influenced by genetics, using our multidimensional estimation of heritability (h2-multi; M = 0.14, SD = 0.015). However, topographic heritability did not differ between heteromodal and unimodal networks. Genetic factors had a regionally variable influence on brain organization, such that the heritability of network topography was greatest in prefrontal, precuneus, and posterior parietal cortex. Taken together, these data are consistent with relaxed genetic control of association cortices relative to primary sensory/motor regions and have implications for understanding population-level variability in brain functioning, guiding both individualized prediction and the interpretation of analyses that integrate genetics and neuroimaging.

Dynamic functional connectome predicts individual working memory performance across diagnostic categories

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We created transdiagnostic predictive working memory models using connectome-based predictive modeling (CPM).

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Dynamic functional connectivity-based CPM models successfully predicted working memory.

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Static functional connectivity-based CPM models fell short in prediction.

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Frontoparietal, somato-motor, default mode and visual networks contributed most to prediction.

Working memory impairment is a common feature of psychiatric disorders. Although its neural mechanisms have been extensively examined in healthy subjects or individuals with a certain clinical condition, studies investigating neural predictors of working memory in a transdiagnostic sample are scarce. The objective of this study was to create a transdiagnostic predictive working memory model from whole-brain functional connectivity using connectome-based predictive modeling (CPM), a recently developed machine learning approach. Resting-state functional MRI data from 242 subjects across 4 diagnostic categories (healthy controls and individuals with schizophrenia, bipolar disorder, and attention deficit/hyperactivity) were used to construct dynamic and static functional connectomes. Spatial working memory was assessed by the spatial capacity task. CPM was conducted to predict individual working memory from dynamic and static functional connectivity patterns. Results showed that dynamic connectivity-based CPM models successfully predicted overall working memory capacity and accuracy as well as mean reaction time, yet their static counterparts fell short in the prediction. At the neural level, we found that dynamic connectivity of the frontoparietal and somato-motor networks were negatively correlated with working memory capacity and accuracy, and those of the default mode and visual networks were positively associated with mean reaction time. Moreover, different feature selection thresholds, parcellation strategies and model validation methods as well as diagnostic categories did not significantly influence the prediction results. Our findings not only are coherent with prior reports that dynamic functional connectivity encodes more behavioral information than static connectivity, but also help advance the translation of cognitive “connectome fingerprinting” into real-world application.

Unraveling reproducible dynamic states of individual brain functional parcellation

Data-driven parcellations are widely used for exploring the functional organization of the brain, and also for reducing the high dimensionality of fMRI data. Despite the flurry of methods proposed in the literature, functional brain parcellations are not highly reproducible at the level of individual subjects, even with very long acquisitions. Some brain areas are also more difficult to parcellate than others, with association heteromodal cortices being the most challenging. An important limitation of classical parcellations is that they are static, that is, they neglect dynamic reconfigurations of brain networks. In this paper, we proposed a new method to identify dynamic states of parcellations, which we hypothesized would improve reproducibility over static parcellation approaches. For a series of seed voxels in the brain, we applied a cluster analysis to regroup short (3 min) time windows into "states" with highly similar seed parcels. We split individual time series of the Midnight scan club sample into two independent sets of 2.5 hr (test and retest). We found that average within-state parcellations, called stability maps, were highly reproducible (over 0.9 test-retest spatial correlation in many instances) and subject specific (fingerprinting accuracy over 70% on average) between test and retest. Consistent with our hypothesis, seeds in heteromodal cortices (posterior and anterior cingulate) showed a richer repertoire of states than unimodal (visual) cortex. Taken together, our results indicate that static functional parcellations are incorrectly averaging well-defined and distinct dynamic states of brain parcellations. This work calls to revisit previous methods based on static parcellations, which includes the majority of published network analyses of fMRI data. Our method may, thus, impact how researchers model the rich interactions between brain networks in health and disease.

Altered temporal, but intact spatial, features of transient network dynamics in psychosis

Contemporary models of psychosis suggest that a continuum of severity of psychotic symptoms exists, with subthreshold psychotic experiences (PEs) potentially reflecting some genetic and environmental risk factors shared with clinical psychosis. Thus, identifying abnormalities in brain activity that manifest across this continuum can shed new light on the pathophysiology of psychosis. Here, we investigated the moment-to-moment engagement of brain networks ("states") in individuals with schizophrenia (SCZ) and PEs and identified features of these states that are associated with psychosis-spectrum symptoms. Transient brain states were defined by clustering "single snapshots" of blood oxygen level-dependent images, based on spatial similarity of the images. We found that individuals with SCZ (n = 35) demonstrated reduced recruitment of three brain states compared to demographically matched healthy controls (n = 35). Of these three illness-related states, one specific state, involving primarily the visual and salience networks, also occurred at a lower rate in individuals with persistent PEs (n = 22), compared to demographically matched healthy youth (n = 22). Moreover, the occurrence rate of this marker brain state was negatively correlated with the severity of PEs (r = -0.26, p = 0.003, n = 130). In contrast, the spatial map of this state appeared to be unaffected in the SCZ or PE groups. Thus, reduced engagement of a brain state involving the visual and salience networks was demonstrated across the psychosis continuum, suggesting that early disruptions of perceptual and affective function may underlie some of the core symptoms of the illness.

Transdiagnostic time-varying dysconnectivity across major psychiatric disorders

Dynamic functional connectivity (DFC) analysis can capture time‐varying properties of connectivity. However, studies on large samples using DFC to investigate transdiagnostic dysconnectivity across schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD) are rare. In this study, we used resting‐state functional magnetic resonance imaging and a sliding‐window method to study DFC in a total of 610 individuals (150 with SZ, 100 with BD, 150 with MDD, and 210 healthy controls [HC]) at a single site. Using k‐means clustering, DFCs were clustered into three functional connectivity states: one was a more frequent state with moderate positive and negative connectivity (State 1), and the other two were less frequent states with stronger positive and negative connectivity (State 2 and State 3). Significant 4‐group differences (SZ, BD, MDD, and HC groups; q < .05, false‐discovery rate [FDR]‐corrected) in DFC were nearly only in State 1. Post hoc analyses (q < .05, FDR‐corrected) in State 1 showed that transdiagnostic dysconnectivity patterns among SZ, BD and MDD featured consistently decreased connectivity within most networks (the visual, somatomotor, salience and frontoparietal networks), which was most obvious in both range and extent for SZ. Our findings suggest that there is more common dysconnectivity across SZ, BD and MDD than we previously expected and that such dysconnectivity is state‐dependent, which provides new insights into the pathophysiological mechanism of major psychiatric disorders.

Cortical electrophysiological evidence for individual-specific temporal organization of brain functional networks

The human brain has been demonstrated to rapidly and continuously form and dissolve networks on a subsecond timescale, offering effective and essential substrates for cognitive processes. Understanding how the dynamic organization of brain functional networks on a subsecond level varies across individuals is, therefore, of great interest for personalized neuroscience. However, it remains unclear whether features of such rapid network organization are reliably unique and stable in single subjects and, therefore, can be used in characterizing individual networks. Here, we used two sets of 5‐min magnetoencephalography (MEG) resting data from 39 healthy subjects over two consecutive days and modeled the spontaneous brain activity as recurring networks fast shifting between each other in a coordinated manner. MEG cortical maps were obtained through source reconstruction using the beamformer method and subjects' temporal structure of recurring networks was obtained via the Hidden Markov Model. Individual organization of dynamic brain activity was quantified with the features of the network‐switching pattern (i.e., transition probability and mean interval time) and the time‐allocation mode (i.e., fractional occupancy and mean lifetime). Using these features, we were able to identify subjects from the group with significant accuracies (~40% on average in 0.5–48 Hz). Notably, the default mode network displayed a distinguishable pattern, being the least frequently visited network with the longest duration for each visit. Together, we provide initial evidence suggesting that the rapid dynamic temporal organization of brain networks achieved in electrophysiology is intrinsic and subject specific.

Revisiting the Functional Anatomy of the Human Brain: Toward a Meta-Networking Theory of Cerebral Functions

For more than one century, brain processing was mainly thought in a localizationist framework, in which one given function was underpinned by a discrete, isolated cortical area, and with a similar cerebral organization across individuals. However, advances in brain mapping techniques in humans have provided new insights into the organizational principles of anatomo-functional architecture. Here, we review recent findings gained from neuroimaging, electrophysiological, as well as lesion studies. Based on these recent data on brain connectome, we challenge the traditional, outdated localizationist view and propose an alternative meta-networking theory. This model holds that complex cognitions and behaviors arise from the spatiotemporal integration of distributed but relatively specialized networks underlying conation and cognition (e.g., language, spatial cognition). Dynamic interactions between such circuits result in a perpetual succession of new equilibrium states, opening the door to considerable interindividual behavioral variability and to neuroplastic phenomena. Indeed, a meta-networking organization underlies the uniquely human propensity to learn complex abilities, and also explains how postlesional reshaping can lead to some degrees of functional compensation in brain-damaged patients. We discuss the major implications of this approach in fundamental neurosciences as well as for clinical developments, especially in neurology, psychiatry, neurorehabilitation, and restorative neurosurgery.

Deep neural networks and kernel regression achieve comparable accuracies for functional connectivity prediction of behavior and demographics

There is significant interest in the development and application of deep neural networks (DNNs) to neuroimaging data. A growing literature suggests that DNNs outperform their classical counterparts in a variety of neuroimaging applications, yet there are few direct comparisons of relative utility. Here, we compared the performance of three DNN architectures and a classical machine learning algorithm (kernel regression) in predicting individual phenotypes from whole-brain resting-state functional connectivity (RSFC) patterns. One of the DNNs was a generic fully-connected feedforward neural network, while the other two DNNs were recently published approaches specifically designed to exploit the structure of connectome data. By using a combined sample of almost 10,000 participants from the Human Connectome Project (HCP) and UK Biobank, we showed that the three DNNs and kernel regression achieved similar performance across a wide range of behavioral and demographic measures. Furthermore, the generic feedforward neural network exhibited similar performance to the two state-of-the-art connectome-specific DNNs. When predicting fluid intelligence in the UK Biobank, performance of all algorithms dramatically improved when sample size increased from 100 to 1000 subjects. Improvement was smaller, but still significant, when sample size increased from 1000 to 5000 subjects. Importantly, kernel regression was competitive across all sample sizes. Overall, our study suggests that kernel regression is as effective as DNNs for RSFC-based behavioral prediction, while incurring significantly lower computational costs. Therefore, kernel regression might serve as a useful baseline algorithm for future studies.

Altered resting-state dynamic functional brain networks in major depressive disorder: Findings from the REST-meta-MDD consortium

BACKGROUND

Major depressive disorder (MDD) is known to be characterized by altered brain functional connectivity (FC) patterns. However, whether and how the features of dynamic FC would change in patients with MDD are unclear. In this study, we aimed to characterize dynamic FC in MDD using a large multi-site sample and a novel dynamic network-based approach.

METHODS

Resting-state functional magnetic resonance imaging (fMRI) data were acquired from a total of 460 MDD patients and 473 healthy controls, as a part of the REST-meta-MDD consortium. Resting-state dynamic functional brain networks were constructed for each subject by a sliding-window approach. Multiple spatio-temporal features of dynamic brain networks, including temporal variability, temporal clustering and temporal efficiency, were then compared between patients and healthy subjects at both global and local levels.

RESULTS

The group of MDD patients showed significantly higher temporal variability, lower temporal correlation coefficient (indicating decreased temporal clustering) and shorter characteristic temporal path length (indicating increased temporal efficiency) compared with healthy controls (corrected p < 3.14×10^-3). Corresponding local changes in MDD were mainly found in the default-mode, sensorimotor and subcortical areas. Measures of temporal variability and characteristic temporal path length were significantly correlated with depression severity in patients (corrected p < 0.05). Moreover, the observed between-group differences were robustly present in both first-episode, drug-naïve (FEDN) and non-FEDN patients.

CONCLUSIONS

Our findings suggest that excessive temporal variations of brain FC, reflecting abnormal communications between large-scale bran networks over time, may underlie the neuropathology of MDD.

Machine learning in resting-state fMRI analysis

Machine learning techniques have gained prominence for the analysis of resting-state functional Magnetic Resonance Imaging (rs-fMRI) data. Here, we present an overview of various unsupervised and supervised machine learning applications to rs-fMRI. We offer a methodical taxonomy of machine learning methods in resting-state fMRI. We identify three major divisions of unsupervised learning methods with regard to their applications to rs-fMRI, based on whether they discover principal modes of variation across space, time or population. Next, we survey the algorithms and rs-fMRI feature representations that have driven the success of supervised subject-level predictions. The goal is to provide a high-level overview of the burgeoning field of rs-fMRI from the perspective of machine learning applications.

Somatosensory-Motor Dysconnectivity Spans Multiple Transdiagnostic Dimensions of Psychopathology

BACKGROUND

There is considerable interest in a dimensional transdiagnostic approach to psychiatry. Most transdiagnostic studies have derived factors based only on clinical symptoms, which might miss possible links between psychopathology, cognitive processes, and personality traits. Furthermore, many psychiatric studies focus on higher-order association brain networks, thereby neglecting the potential influence of huge swaths of the brain.

METHODS

A multivariate data-driven approach (partial least squares) was used to identify latent components linking a large set of clinical, cognitive, and personality measures to whole-brain resting-state functional connectivity patterns across 224 participants. The participants were either healthy (n = 110) or diagnosed with bipolar disorder (n = 40), attention-deficit/hyperactivity disorder (n = 37), schizophrenia (n = 29), or schizoaffective disorder (n = 8). In contrast to traditional case-control analyses, the diagnostic categories were not used in the partial least squares analysis but were helpful for interpreting the components.

RESULTS

Our analyses revealed three latent components corresponding to general psychopathology, cognitive dysfunction, and impulsivity. Each component was associated with a unique whole-brain resting-state functional connectivity signature and was shared across all participants. The components were robust across multiple control analyses and replicated using independent task functional magnetic resonance imaging data from the same participants. Strikingly, all three components featured connectivity alterations within the somatosensory-motor network and its connectivity with subcortical structures and cortical executive networks.

CONCLUSIONS

We identified three distinct dimensions with dissociable (but overlapping) whole-brain resting-state functional connectivity signatures across healthy individuals and individuals with psychiatric illness, providing potential intermediate phenotypes that span diagnostic categories. Our results suggest expanding the focus of psychiatric neuroscience beyond higher-order brain networks.

Relationships between depressive symptoms and brain responses during emotional movie viewing emerge in adolescence

Affective disorders such as major depression are common but serious illnesses characterized by altered processing of emotional information. Although the frequency and severity of depressive symptoms increase dramatically over the course of childhood and adolescence, much of our understanding of their neurobiological bases comes from work characterizing adults' responses to static emotional information. As a consequence, relationships between depressive brain phenotypes and naturalistic emotional processing, as well as the manner in which these associations emerge over the lifespan, remain poorly understood. Here, we apply static and dynamic inter-subject correlation analyses to examine how brain function is associated with clinical and non-clinical depressive symptom severity in 112 children and adolescents (7-21 years old) who viewed an emotionally evocative clip from the film Despicable Me during functional MRI. Our results reveal that adolescents with greater depressive symptom severity exhibit atypical fMRI responses during movie viewing, and that this effect is stronger during less emotional moments of the movie. Furthermore, adolescents with more similar item-level depressive symptom profiles showed more similar brain responses during movie viewing. In contrast, children's depressive symptom severity and profiles were unrelated to their brain response typicality or similarity. Together, these results indicate a developmental change in the relationships between brain function and depressive symptoms from childhood through adolescence. Our findings suggest that depressive symptoms may shape how the brain responds to complex emotional information in a dynamic manner sensitive to both developmental stage and affective context.

Dynamic functional connectivity states characterize NREM sleep and wakefulness

According to recent neuroimaging studies, temporal fluctuations in functional connectivity patterns can be clustered into dynamic functional connectivity (DFC) states and correspond to fluctuations in vigilance. However, whether there consistently exist DFC states associated with wakefulness and sleep stages and what are the characteristics and electrophysiological origin of these states remain unclear. The aims of the current study were to investigate the properties of DFC in different sleep stages and to explore the relationship between the characteristics of DFC and slow‐wave activity. We collected both eyes‐closed wakefulness and sleep data from 48 healthy young volunteers with simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) recordings. EEG data were employed as the gold standard of sleep stage scoring, and DFC states were estimated based on fMRI data. The results demonstrated that DFC states of the fMRI signals consistently corresponded to wakefulness and nonrapid eye movement sleep stages independent of the number of clusters. Furthermore, the mean dwell time of these states significantly correlated with slow‐wave activity. The inclusion or omission of regression of the global signal and the selection of parcellation schemes exerted minimal effects on the current findings. These results provide strong evidence that DFC states underlying fMRI signals match the fluctuations of vigilance and suggest a possible electrophysiological source of DFC states corresponding to vigilance states.

The Roles of Statistics in Human Neuroscience

Statistics plays three important roles in brain studies. They are (1) the study of differences between brains in distinctive populations; (2) the study of the variability in the structure and functioning of the brain; and (3) the study of data reduction on large-scale brain data. I discuss these concepts using examples from past and ongoing research in brain connectivity, brain information flow, information extraction from large-scale neuroimaging data, and neural predictive modeling. Having dispensed with the past, I attempt to present a few areas where statistical science facilitates brain decoding and to write prospectively, in the light of present knowledge and in the quest for artificial intelligence, about questions that statistical and neurobiological communities could work closely together to address in the future.

Tracking the Main States of Dynamic Functional Connectivity in Resting State

Dynamical changes have recently been tracked in functional connectivity (FC) calculated from resting-state functional magnetic resonance imaging (R-fMRI), when a person is conscious but not carrying out a directed task during scanning. Diverse dynamical FC states (dFC) are believed to represent different internal states of the brain, in terms of brain-regional interactions. In this paper, we propose a novel protocol, the signed community clustering with the optimized modularity by two-step procedures, to track dynamical whole brain functional connectivity (dWFC) states. This protocol is assumption free without a priori threshold for the number of clusters. By applying our method on sliding window based dWFC’s with automated anatomical labeling 2 (AAL2), three main dWFC states were extracted from R-fMRI datasets in Human Connectome Project, that are independent on window size. Through extracting the FC features of these states, we found the functional links in state 1 (WFC-C₁) mainly involved visual, somatomotor, attention and cerebellar (posterior lobe) modules. State 2 (WFC-C₂) was similar to WFC-C₁, but more FC’s linking limbic, default mode, and frontoparietal modules and less linking the cerebellum, sensory and attention modules. State 3 had more FC’s linking default mode, limbic, and cerebellum, compared to WFC-C₁ and WFC-C₂. With tests of robustness and stability, our work provides a solid, hypothesis-free tool to detect dWFC states for the possibility of tracking rapid dynamical change in FCs among large data sets.