Dynamic graph metrics: Tutorial, toolbox, and tale

Temporal brain network analysis of cognitive reappraisal and expressive suppression based on dynamic functional connectivity

Functional brain networks must undergo dynamic reorganization within brief time intervals to effectively process and respond to affective stimuli. The traditional static network method only could reflect the whole brain activity on an independent time scale. Based on the emerging temporal brain network analysis framework, the current study explored the difference between cognitive reappraisal and expressive suppression in the reorganization of dynamic functional connectivity. Temporal brain network in the gamma band was estimated using the sliding window method and the phase lag index to quantitatively compare the differences between cognitive reappraisal and expressive suppression. The results showed that the regulative effect of cognitive reappraisal was better than that of negative viewing and expressive suppression. In the global temporal brain networks, temporal clustering coefficients of cognitive reappraisal was increased compared with expressive suppression. The frontal and parietal lobes were essential for the process of emotion regulation, and the difference of nodal temporal betweenness centrality between the two strategies was mainly concentrated in the frontal and parietal lobes. The spatiotemporal topological network of dynamic functional connectivity for cognitive reappraisal was significantly segregated, and the frontal and parietal lobes region revealed the different performance of the two strategies at the nodal level.

NaDyNet: A toolbox for dynamic network analysis of naturalistic stimuli

Experiments with naturalistic stimuli (e.g., listening to stories or watching movies) are emerging paradigms in brain function research. The content of naturalistic stimuli is rich and continuous. The fMRI signals of naturalistic stimuli are complex and include different components. A major challenge is isolate the stimuli-induced signals while simultaneously tracking the brain's responses to these stimuli in real-time. To this end, we have developed a user-friendly graphical interface toolbox called NaDyNet (Naturalistic Dynamic Network Toolbox), which integrates existing dynamic brain network analysis methods and their improved versions. The main features of NaDyNet are: 1) extracting signals of interest from naturalistic fMRI signals; 2) incorporating six commonly used dynamic analysis methods and three static analysis methods; 3) improved versions of these dynamic methods by adopting inter-subject analysis to eliminate the effects of non-interest signals; 4) performing K-means clustering analysis to identify temporally reoccurring states along with their temporal and spatial attributes; 5) Visualization of spatiotemporal results. We then introduced the rationale for incorporating inter-subject analysis to improve existing dynamic brain network analysis methods and presented examples by analyzing naturalistic fMRI data. We hope that this toolbox will promote the development of naturalistic neuroscience. The toolbox is available at https://github.com/yuanbinke/Naturalistic-Dynamic-Network-Toolbox.

Dynamic analysis of frequency specificity in multilayer brain networks

The brain is a highly complex and delicate system, and its internal neural processes are manifested as the interweaving and superposition of multi-frequency neural signals. However, traditional brain network studies are often limited to the whole frequency band or a specific frequency band, ignoring the potentially profound impact of the diversity of information within the frequency on the dynamics of brain networks. To comprehensively and deeply analyze this phenomenon, the present study is devoted to exploring the specific performance of brain networks at different frequencies. We used the maximum overlap discrete wavelet transform technique to finely divide the time series data into the following frequency bands: scale 1 (0.125-0.25 Hz), scale 2 (0.06-0.125 Hz), scale 3 (0.03-0.06 Hz) and scale 4 (0.015-0.03 Hz). Based on these frequency bands, we constructed multilayer networks from both dynamic and static perspectives, respectively. From the dynamic perspective, we quantitatively evaluated the dynamic differences among different frequency bands using metrics such as flexibility, promiscuity, integration, and recruitment, and found that scale 3 and scale 4 bands performed particularly well. In contrast, from a static perspective, we measured the cross-frequency interaction capability between different frequency bands through metrics such as multilayer clustering coefficient and entropy of multiplexing degree, and the results show that scale 2, scale 3, and scale 4 band networks have enhanced global integration capability and local capability. In addition, we explored the correlation of gender and age with the properties of brain networks in different frequency bands. In the scale 1 frequency band, the organization of brain functions showed significant gender differences, while in the scale 2 frequency band, there was a significant correlation between age and global efficiency. By integrating the dual perspectives of time and frequency domains, this study not only reveals the critical role of frequency specificity in the brain's information processing and functional organization but also provides new perspectives for understanding the complex working mechanisms of the brain as well as gender- and age-related cognitive differences.

Resting-state dynamic functional connectivity in major depressive disorder: A systematic review

As a novel measure, dynamic functional connectivity (dFC) provides insight into the dynamic nature of brain networks and their interactions in resting-state, surpassing traditional static functional connectivity in pathological conditions such as depression. Since a comprehensive review is still lacking, we then reviewed forty-five eligible papers to explore pathological mechanisms of major depressive disorder (MDD) from perspectives including abnormal brain regions and functional networks, brain state, topological properties, relevant recognition, along with longitudinal studies. Though inconsistencies could be found, common findings are: (1) From different perspectives based on dFC, default-mode network (DMN) with its subregions exhibited a close relation to the pathological mechanism of MDD. (2) With a corrupted integrity within large-scale functional networks and imbalance between them, longer fraction time in a relatively weakly-connected state may be a possible property of MDD concerning its relation with DMN. Abnormal transition frequencies between states were correlated to the severity of MDD. (3) Including dynamic properties in topological network metrics enhanced recognition effect. In all, this review summarized its use for clinical diagnosis and treatment, elucidating the non-stationary of MDD patients' aberrant brain activity in the absence of stimuli and bringing new views into its underlying neuro mechanism.

Higher-order connectomics of human brain function reveals local topological signatures of task decoding, individual identification, and behavior

Traditional models of human brain activity often represent it as a network of pairwise interactions between brain regions. Going beyond this limitation, recent approaches have been proposed to infer higher-order interactions from temporal brain signals involving three or more regions. However, to this day it remains unclear whether methods based on inferred higher-order interactions outperform traditional pairwise ones for the analysis of fMRI data. To address this question, we conducted a comprehensive analysis using fMRI time series of 100 unrelated subjects from the Human Connectome Project. We show that higher-order approaches greatly enhance our ability to decode dynamically between various tasks, to improve the individual identification of unimodal and transmodal functional subsystems, and to strengthen significantly the associations between brain activity and behavior. Overall, our approach sheds new light on the higher-order organization of fMRI time series, improving the characterization of dynamic group dependencies in rest and tasks, and revealing a vast space of unexplored structures within human functional brain data, which may remain hidden when using traditional pairwise approaches.

Alterations in spatiotemporal characteristics of dynamic networks in juvenile myoclonic epilepsy

BACKGROUND

Juvenile myoclonic epilepsy (JME) is characterized by altered patterns of brain functional connectivity (FC). However, the nature and extent of alterations in the spatiotemporal characteristics of dynamic FC in JME patients remain elusive. Dynamic networks effectively encapsulate temporal variations in brain imaging data, offering insights into brain network abnormalities and contributing to our understanding of the seizure mechanisms and origins.

METHODS

Resting-state functional magnetic resonance imaging (rs-fMRI) data were procured from 37 JME patients and 37 healthy counterparts. Forty-seven network nodes were identified by group-independent component analysis (ICA) to construct the dynamic network. Ultimately, patients' and controls' spatiotemporal characteristics, encompassing temporal clustering and variability, were contrasted at the whole-brain, large-scale network, and regional levels.

RESULTS

Our findings reveal a marked reduction in temporal clustering and an elevation in temporal variability in JME patients at the whole-brain echelon. Perturbations were notably pronounced in the default mode network (DMN) and visual network (VN) at the large-scale level. Nodes exhibiting anomalous were predominantly situated within the DMN and VN. Additionally, there was a significant correlation between the severity of JME symptoms and the temporal clustering of the VN.

CONCLUSIONS

Our findings suggest that excessive temporal changes in brain FC may affect the temporal structure of dynamic brain networks, leading to disturbances in brain function in patients with JME. The DMN and VN play an important role in the dynamics of brain networks in patients, and their abnormal spatiotemporal properties may underlie abnormal brain function in patients with JME in the early stages of the disease.

Abnormal Dynamic Reconfiguration of Multilayer Temporal Networks in Patients with Bipolar Disorder

BACKGROUND

Multilayer networks have been used to identify abnormal dynamic reconfiguration in bipolar disorder (BD). However, these studies ignore the differences in information interactions between adjacent layers when constructing multilayer networks, and the analysis of dynamic reconfiguration is not comprehensive enough; Methods: Resting-state functional magnetic resonance imaging data were collected from 46 BD patients and 54 normal controls. A multilayer temporal network was constructed for each subject, and inter-layer coupling of different nodes was considered using network similarity. The promiscuity, recruitment, and integration coefficients were calculated to quantify the different dynamic reconfigurations between the two groups; Results: The global inter-layer coupling, recruitment, and integration coefficients were significantly lower in BD patients. These results were further observed in the attention network and the limbic/paralimbic and subcortical network, reflecting reduced temporal stability, intra- and inter-subnetwork communication abilities in BD patients. The whole-brain promiscuity was increased in BD patients. The same results were observed in the somatosensory/motor and auditory network, reflecting more functional interactions; Conclusions: This study discovered abnormal dynamic interactions of BD from the perspective of dynamic reconfiguration, which can help to understand the pathological mechanisms of BD.

Aberrant Flexibility of Dynamic Brain Network in Patients with Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a collection of neurodevelopmental disorders whose pathobiology remains elusive. This study aimed to investigate the possible neural mechanisms underlying ASD using a dynamic brain network model and a relatively large-sample, multi-site dataset. Resting-state functional magnetic resonance imaging data were acquired from 208 ASD patients and 227 typical development (TD) controls, who were drawn from the multi-site Autism Brain Imaging Data Exchange (ABIDE) database. Brain network flexibilities were estimated and compared between the ASD and TD groups at both global and local levels, after adjusting for sex, age, head motion, and site effects. The results revealed significantly increased brain network flexibilities (indicating a decreased stability) at the global level, as well as at the local level within the default mode and sensorimotor areas in ASD patients than TD participants. Additionally, significant ASD-related decreases in flexibilities were also observed in several occipital regions at the nodal level. Most of these changes were significantly correlated with the Autism Diagnostic Observation Schedule (ADOS) total score in the entire sample. These results suggested that ASD is characterized by significant changes in temporal stabilities of the functional brain network, which can further strengthen our understanding of the pathobiology of ASD.

Sex differences in human brain networks in normal and psychiatric populations from the perspective of small-world properties

Females and males are known to be different in the prevalences of multiple psychiatric disorders, while the underlying neural mechanisms are unclear. Based on non-invasive neuroimaging techniques and graph theory, many researchers have tried to use a small-world network model to elucidate sex differences in the brain. This manuscript aims to compile the related research findings from the past few years and summarize the sex differences in human brain networks in both normal and psychiatric populations from the perspective of small-world properties. We reviewed published reports examining altered small-world properties in both the functional and structural brain networks between males and females. Based on four patterns of altered small-world properties proposed: randomization, regularization, stronger small-worldization, and weaker small-worldization, we found that current results point to a significant trend toward more regularization in normal females and more randomization in normal males in functional brain networks. On the other hand, there seems to be no consensus to date on the sex differences in small-world properties of the structural brain networks in normal populations. Nevertheless, we noticed that the sample sizes in many published studies are small, and future studies with larger samples are warranted to obtain more reliable results. Moreover, the number of related studies conducted in psychiatric populations is still limited and more investigations might be needed. We anticipate that these conclusions will contribute to a deeper understanding of the sex differences in the brain, which may be also valuable for developing new methods in the treatment of psychiatric disorders.

Controllability in attention deficit hyperactivity disorder brains

The role of network metrics in exploring brain networks of mental illness is crucial. This study focuses on quantifying a node controllability index (CA-scores) and developing a novel framework for studying the dysfunction of attention deficit hyperactivity disorder (ADHD) brains. By analyzing fMRI data from 143 healthy controls and 102 ADHD patients, the controllability metric reveals distinct differences in nodes (brain regions) and subsystems (functional modules). There are significantly atypical CA-scores in the Rolandic operculum, superior medial orbitofrontal cortex, insula, posterior cingulate gyrus, supramarginal gyrus, angular gyrus, precuneus, heschl gyrus, and superior temporal gyrus of ADHD patients. A comparison with measures of connection strength, eigenvector centrality, and topology entropy suggests that the controllability index may be more effective in identifying abnormal regions in ADHD brains. Furthermore, our controllability index could be extended to investigate functional networks associated with other psychiatric disorders.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11571-023-10063-z.

Aberrant brain dynamics in major depressive disorder during working memory task

Working memory (WM) is a distributed and dynamic process, and WM deficits are recognized as one of the top-ranked endophenotype candidates for major depressive disorders (MDD). However, there is a lack of knowledge of brain temporal-spatial profile of WM deficits in MDD. We used the dynamical degree centrality (dDC) to investigate the whole-brain temporal-spatial profile in 40 MDD and 40 controls during an n-back task with 2 conditions (i.e., '0back' and '2back'). We explored the dDC temporal variability and clustered meta-stable states in 2 groups during different WM conditions. Pearson's correlation analysis was used to evaluate the relationship between the altered dynamics with clinical symptoms and WM performance. Compared with controls, under '2back vs. 0back' contrast, patients showed an elevated dDC variability in wide range of brain regions, including the middle frontal gyrus, orbital part of inferior frontal gyrus (IFGorb), hippocampus, and middle temporal gyrus. Furthermore, the increased dDC variability in the hippocampus and IFGorb correlated with worse WM performance. However, there were no significant group-related differences in the meta-stable states were observed. This study demonstrated the increased WM-related instability (i.e., the elevated dDC variability) was represented in MDD, and enhancing stability may help patients achieve better WM performance.

On null models for temporal small-worldness in brain dynamics

Brain dynamics can be modeled as a temporal brain network starting from the activity of different brain regions in functional magnetic resonance imaging (fMRI) signals. When validating hypotheses about temporal networks, it is important to use an appropriate statistical null model that shares some features with the treated empirical data. The purpose of this work is to contribute to the theory of temporal null models for brain networks by introducing the random temporal hyperbolic (RTH) graph model, an extension of the random hyperbolic (RH) graph, known in the study of complex networks for its ability to reproduce crucial properties of real-world networks. We focus on temporal small-worldness which, in the static case, has been extensively studied in real-world complex networks and has been linked to the ability of brain networks to efficiently exchange information. We compare the RTH graph model with standard null models for temporal networks and show it is the null model that best reproduces the small-worldness of resting brain activity. This ability to reproduce fundamental features of real brain networks, while adding only a single parameter compared with classical models, suggests that the RTH graph model is a promising tool for validating hypotheses about temporal brain networks.

Dynamic reconfigurations of brain networks in depressive and anxiety disorders: The influence of antidepressants

Major Depressive Disorder (MDD) and anxiety disorders are highly comorbid recurrent psychiatric disorders. Reduced dynamic reconfiguration of brain regions across subnetworks may play a critical role underlying these deficits, with indications of normalization after treatment with antidepressants. This study investigated dynamic reconfigurations in controls and individuals with a current MDD and/or anxiety disorder including antidepressant users and non-users in a large sample (N = 207) of adults. We quantified the number of subnetworks a region switched to (promiscuity) as well as the total number of switches (flexibility). Average whole-brain (i.e., global) values and subnetwork-specific values were compared between diagnosis and antidepressant groups. No differences in reconfiguration dynamics were found between individuals with a current MDD (N = 49), anxiety disorder (N = 46), comorbid MDD and anxiety disorder (N = 55), or controls (N = 57). Global and sensorimotor network (SMN) promiscuity and flexibility were higher in antidepressant users (N = 49, regardless of diagnosis) compared to non-users (N = 101) and controls. Dynamic reconfigurations were considerably higher in antidepressant users relative to non-users and controls, but not significantly altered in individuals with a MDD and/or anxiety disorder. The increase in antidepressant users was apparent across the whole brain and in the SMN when investigating subnetworks. These findings help disentangle how antidepressants improve symptoms.

Modeling brain network flexibility in networks of coupled oscillators: a feasibility study

Modeling the functionality of the human brain is a major goal in neuroscience for which many powerful methodologies have been developed over the last decade. The impact of working memory and the associated brain regions on the brain dynamics is of particular interest due to their connection with many functions and malfunctions in the brain. In this context, the concept of brain flexibility has been developed for the characterization of brain functionality. We discuss emergence of brain flexibility that is commonly measured by the identification of changes in the cluster structure of co-active brain regions. We provide evidence that brain flexibility can be modeled by a system of coupled FitzHugh-Nagumo oscillators where the network structure is obtained from human brain Diffusion Tensor Imaging (DTI). Additionally, we propose a straightforward and computationally efficient alternative macroscopic measure, which is derived from the Pearson distance of functional brain matrices. This metric exhibits similarities to the established patterns of brain template flexibility that have been observed in prior investigations. Furthermore, we explore the significance of the brain's network structure and the strength of connections between network nodes or brain regions associated with working memory in the observation of patterns in networks flexibility. This work enriches our understanding of the interplay between the structure and function of dynamic brain networks and proposes a modeling strategy to study brain flexibility.

Statistical Brain Network Analysis

The recent fusion of network science and neuroscience has catalyzed a paradigm shift in how we study the brain and led to the field of brain network analysis. Brain network analyses hold great potential in helping us understand normal and abnormal brain function by providing profound clinical insight into links between system-level properties and health and behavioral outcomes. Nonetheless, methods for statistically analyzing networks at the group and individual levels have lagged behind. We have attempted to address this need by developing three complementary statistical frameworks-a mixed modeling framework, a distance regression framework, and a hidden semi-Markov modeling framework. These tools serve as synergistic fusions of statistical approaches with network science methods, providing needed analytic foundations for whole-brain network data. Here we delineate these approaches, briefly survey related tools, and discuss potential future avenues of research. We hope this review catalyzes further statistical interest and methodological development in the field.

Childhood trauma is linked to abnormal static-dynamic brain topology in adolescents with major depressive disorder

Childhood trauma is a leading risk factor for adolescents developing major depressive disorder (MDD); however, the underlying neuroimaging mechanisms remain unclear. This study aimed to investigate the association among childhood trauma, MDD and brain dysfunctions by combining static and dynamic brain network models. We recruited 46 first-episode drug-naïve adolescent MDD patients with childhood trauma (MDD-CT), 53 MDD patients without childhood trauma (MDD-nCT), and 90 healthy controls (HCs) for resting-state functional magnetic resonance imaging (fMRI) scans; all participants were aged 13-18 years. Compared to the HCs and MDD-nCT groups, the MDD-CT group exhibited significantly higher global and local efficiency in static brain networks and significantly higher temporal correlation coefficients in dynamic brain network models at the whole-brain level, and altered the local efficiency of default mode network (DMN) and temporal correlation coefficients of DMN, salience (SAN), and attention (ATN) networks at the local perspective. Correlation analysis indicated that altered brain network features and clinical symptoms, childhood trauma, and particularly emotional neglect were highly correlated in adolescents with MDD. This study may provide new evidence for the dysconnectivity hypothesis regarding the associations between childhood trauma and MDD in adolescents from the perspectives of both static and dynamic brain topology.

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.

Dynamic flexibility and controllability of network communities in juvenile myoclonic epilepsy

Juvenile myoclonic epilepsy (JME) is the most common syndrome within the idiopathic generalized epilepsy spectrum, manifested by myoclonic and generalized tonic-clonic seizures and spike-and-wave discharges (SWDs) on electroencephalography (EEG). Currently, the pathophysiological concepts addressing SWD generation in JME are still incomplete. In this work, we characterize the temporal and spatial organization of functional networks and their dynamic properties as derived from high-density EEG (hdEEG) recordings and MRI in 40 JME patients (25.4 ± 7.6 years, 25 females). The adopted approach allows for the construction of a precise dynamic model of ictal transformation in JME at the cortical and deep brain nuclei source levels. We implement Louvain algorithm to attribute brain regions with similar topological properties to modules during separate time windows before and during SWD generation. Afterwards, we quantify how modular assignments evolve and steer through different states towards the ictal state by measuring characteristics of flexibility and controllability. We find antagonistic dynamics of flexibility and controllability within network modules as they evolve towards and undergo ictal transformation. Prior to SWD generation, we observe concomitantly increasing flexibility (F(1,39) = 25.3, corrected p < 0.001) and decreasing controllability (F(1,39) = 55.3, p < 0.001) within the fronto-parietal module in γ-band. On a step further, during interictal SWDs as compared to preceding time windows, we notice decreasing flexibility (F(1,39) = 11.9, p < 0.001) and increasing controllability (F(1,39) = 10.1, p < 0.001) within the fronto-temporal module in γ-band. During ictal SWDs as compared to prior time windows, we demonstrate significantly decreasing flexibility (F(1,14) = 31.6; p < 0.001) and increasing controllability (F(1,14) = 44.7, p < 0.001) within the basal ganglia module. Furthermore, we show that flexibility and controllability within the fronto-temporal module of the interictal SWDs relate to seizure frequency and cognitive performance in JME patients. Our results demonstrate that detection of network modules and quantification of their dynamic properties is relevant to track the generation of SWDs. The observed flexibility and controllability dynamics reflect the reorganization of de-/synchronized connections and the ability of evolving network modules to reach a seizure-free state, respectively. These findings may advance the elaboration of network-based biomarkers and more targeted therapeutic neuromodulatory approaches in JME.

Temporal Stability of the Dynamic Resting-State Functional Brain Network: Current Measures, Clinical Research Progress, and Future Perspectives

Based on functional magnetic resonance imaging and multilayer dynamic network model, the brain network's quantified temporal stability has shown potential in predicting altered brain functions. This manuscript aims to summarize current knowledge, clinical research progress, and future perspectives on brain network's temporal stability. There are a variety of widely used measures of temporal stability such as the variance/standard deviation of dynamic functional connectivity strengths, the temporal variability, the flexibility (switching rate), and the temporal clustering coefficient, while there is no consensus to date which measure is the best. The temporal stability of brain networks may be associated with several factors such as sex, age, cognitive functions, head motion, circadian rhythm, and data preprocessing/analyzing strategies, which should be considered in clinical studies. Multiple common psychiatric disorders such as schizophrenia, major depressive disorder, and bipolar disorder have been found to be related to altered temporal stability, especially during the resting state; generally, both excessively decreased and increased temporal stabilities were thought to reflect disorder-related brain dysfunctions. However, the measures of temporal stability are still far from applications in clinical diagnoses for neuropsychiatric disorders partly because of the divergent results. Further studies with larger samples and in transdiagnostic (including schizoaffective disorder) subjects are warranted.

Mindful attention promotes control of brain network dynamics for self-regulation and discontinues the past from the present

Mindful attention is characterized by acknowledging the present experience as a transient mental event. Early stages of mindfulness practice may require greater neural effort for later efficiency. Early effort may self-regulate behavior and focalize the present, but this understanding lacks a computational explanation. Here we used network control theory as a model of how external control inputs-operationalizing effort-distribute changes in neural activity evoked during mindful attention across the white matter network. We hypothesized that individuals with greater network controllability, thereby efficiently distributing control inputs, effectively self-regulate behavior. We further hypothesized that brain regions that utilize greater control input exhibit shorter intrinsic timescales of neural activity. Shorter timescales characterize quickly discontinuing past processing to focalize the present. We tested these hypotheses in a randomized controlled study that primed participants to either mindfully respond or naturally react to alcohol cues during fMRI and administered text reminders and measurements of alcohol consumption during 4 wk postscan. We found that participants with greater network controllability moderated alcohol consumption. Mindful regulation of alcohol cues, compared to one's own natural reactions, reduced craving, but craving did not differ from the baseline group. Mindful regulation of alcohol cues, compared to the natural reactions of the baseline group, involved more-effortful control of neural dynamics across cognitive control and attention subnetworks. This effort persisted in the natural reactions of the mindful group compared to the baseline group. More-effortful neural states had shorter timescales than less effortful states, offering an explanation for how mindful attention promotes being present.

Increased flexibility of brain dynamics in patients with multiple sclerosis

Patients with multiple sclerosis consistently show widespread changes in functional connectivity. Yet, alterations are heterogeneous across studies, underscoring the complexity of functional reorganization in multiple sclerosis. Here, we aim to provide new insights by applying a time-resolved graph-analytical framework to identify a clinically relevant pattern of dynamic functional connectivity reconfigurations in multiple sclerosis. Resting-state data from 75 patients with multiple sclerosis (N = 75, female:male ratio of 3:2, median age: 42.0 ± 11.0 years, median disease duration: 6 ± 11.4 years) and 75 age- and sex-matched controls (N = 75, female:male ratio of 3:2, median age: 40.2 ± 11.8 years) were analysed using multilayer community detection. Local, resting-state functional system and global levels of dynamic functional connectivity reconfiguration were characterized using graph-theoretical measures including flexibility, promiscuity, cohesion, disjointedness and entropy. Moreover, we quantified hypo- and hyper-flexibility of brain regions and derived the flexibility reorganization index as a summary measure of whole-brain reorganization. Lastly, we explored the relationship between clinical disability and altered functional dynamics. Significant increases in global flexibility (t = 2.38, P_FDR = 0.024), promiscuity (t = 1.94, P_FDR = 0.038), entropy (t = 2.17, P_FDR = 0.027) and cohesion (t = 2.45, P_FDR = 0.024) were observed in patients and were driven by pericentral, limbic and subcortical regions. Importantly, these graph metrics were correlated with clinical disability such that greater reconfiguration dynamics tracked greater disability. Moreover, patients demonstrate a systematic shift in flexibility from sensorimotor areas to transmodal areas, with the most pronounced increases located in regions with generally low dynamics in controls. Together, these findings reveal a hyperflexible reorganization of brain activity in multiple sclerosis that clusters in pericentral, subcortical and limbic areas. This functional reorganization was linked to clinical disability, providing new evidence that alterations of multilayer temporal dynamics play a role in the manifestation of multiple sclerosis.

Temporal Stability of Dynamic Default Mode Network Connectivity Negatively Correlates with Suicidality in Major Depressive Disorder

Previous studies have demonstrated that the suicidality in patients with major depressive disorder (MDD) is related to abnormal brain functional connectivity (FC) patterns. However, little is known about its relationship with dynamic functional connectivity (dFC) based on the assumption that brain FCs fluctuate over time. Temporal stabilities of dFCs within the whole brain and nine key networks were compared between 52 MDD patients and 21 age, sex-matched healthy controls (HCs) using resting-state functional magnetic resonance imaging and temporal correlation coefficients. The alterations in MDD were further correlated with the scores of suicidality item in the Hamilton Rating Scale for Depression (HAMD). Compared with HCs, the MDD patients showed a decreased temporal stability of dFC as indicated by a significantly decreased temporal correlation coefficient at the global level, as well as within the default mode network (DMN) and subcortical network. In addition, temporal correlation coefficients of the DMN were found to be significantly negatively correlated with the HAMD suicidality item scores in MDD patients. These results suggest that MDD may be characterized by excessive temporal fluctuations of dFCs within the DMN and subcortical network, and that decreased stability of DMN connectivity may be particularly associated with the suicidality in MDD.

Temporal Dynamics of Resting-state Functional Networks and Cognitive Functioning following Systemic Treatment for Breast Cancer

Many women with breast cancer suffer from a decline in memory and executive function, particularly after treatment with chemotherapy. Recent neuroimaging studies suggest that changes in network dynamics are fundamental in decline in these cognitive functions. This has, however, not yet been investigated in breast cancer patients. Using resting state functional magnetic resonance imaging, we prospectively investigated whether changes in dynamic functional connectivity were associated with changes in memory and executive function. We examined 34 breast cancer patients that received chemotherapy, 32 patients that did not receive chemotherapy, and 35 no-cancer controls. All participants were assessed prior to treatment and six months after completion of chemotherapy, or at similar intervals for the other groups. To assess memory and executive function, we used the Hopkins Verbal Learning Test – Immediate Recall and the Trail Making Test B, respectively. Using a sliding window approach, we then evaluated dynamic functional connectivity of resting state networks supporting memory and executive function, i.e. the default mode network and frontoparietal network, respectively. Next, we directly investigated the association between cognitive performance and dynamic functional connectivity. We found no group differences in cognitive performance or connectivity measures. The association between dynamic functional connectivity of the default mode network and memory differed significantly across groups. This was not the case for the frontoparietal network and executive function. This suggests that cancer and chemotherapy alter the role of dynamic functional connectivity in memory function. Further implications of these findings are discussed.

Probabilistically Weighted Multilayer Networks disclose the link between default mode network instability and psychosis-like experiences in healthy adults

The brain is a complex system in which the functional interactions among its subunits vary over time. The trajectories of this dynamic variation contribute to inter-individual behavioral differences and psychopathologic phenotypes. Despite many methodological advancements, the study of dynamic brain networks still relies on biased assumptions in the temporal domain. The current paper has two goals. First, we present a novel method to study multilayer networks: by modelling intra-nodal connections in a probabilistic, biologically driven way, we introduce a temporal resolution of the multilayer network based on signal similarity across time series. This new method is tested on synthetic networks by varying the number of modules and the sources of noise in the simulation. Secondly, we implement these probabilistically weighted (PW) multilayer networks to study the association between network dynamics and subclinical, psychosis-relevant personality traits in healthy adults. We show that the PW method for multilayer networks outperforms the standard procedure in modular detection and is less affected by increasing noise levels. Additionally, the PW method highlighted associations between the temporal instability of default mode network connections and psychosis-like experiences in healthy adults. PW multilayer networks allow an unbiased study of dynamic brain functioning and its behavioral correlates.

A more unstable resting-state functional network in cognitively declining multiple sclerosis

Cognitive impairment is common in people with multiple sclerosis and strongly affects their daily functioning. Reports have linked disturbed cognitive functioning in multiple sclerosis to changes in the organization of the functional network. In a healthy brain, communication between brain regions and which network a region belongs to is continuously and dynamically adapted to enable adequate cognitive function. However, this dynamic network adaptation has not been investigated in multiple sclerosis, and longitudinal network data remain particularly rare. Therefore, the aim of this study was to longitudinally identify patterns of dynamic network reconfigurations that are related to the worsening of cognitive decline in multiple sclerosis. Resting-state functional MRI and cognitive scores (expanded Brief Repeatable Battery of Neuropsychological tests) were acquired in 230 patients with multiple sclerosis and 59 matched healthy controls, at baseline (mean disease duration: 15 years) and at 5-year follow-up. A sliding-window approach was used for functional MRI analyses, where brain regions were dynamically assigned to one of seven literature-based subnetworks. Dynamic reconfigurations of subnetworks were characterized using measures of promiscuity (number of subnetworks switched to), flexibility (number of switches), cohesion (mutual switches) and disjointedness (independent switches). Cross-sectional differences between cognitive groups and longitudinal changes were assessed, as well as relations with structural damage and performance on specific cognitive domains. At baseline, 23% of patients were cognitively impaired (≥2/7 domains Z < −2) and 18% were mildly impaired (≥2/7 domains Z < −1.5). Longitudinally, 28% of patients declined over time (0.25 yearly change on ≥2/7 domains based on reliable change index). Cognitively impaired patients displayed more dynamic network reconfigurations across the whole brain compared with cognitively preserved patients and controls, i.e. showing higher promiscuity (P = 0.047), flexibility (P = 0.008) and cohesion (P = 0.008). Over time, cognitively declining patients showed a further increase in cohesion (P = 0.004), which was not seen in stable patients (P = 0.544). More cohesion was related to more severe structural damage (average r = 0.166, P = 0.015) and worse verbal memory (r = −0.156, P = 0.022), information processing speed (r = −0.202, P = 0.003) and working memory (r = −0.163, P = 0.017). Cognitively impaired multiple sclerosis patients exhibited a more unstable network reconfiguration compared to preserved patients, i.e. brain regions switched between subnetworks more often, which was related to structural damage. This shift to more unstable network reconfigurations was also demonstrated longitudinally in patients that showed cognitive decline only. These results indicate the potential relevance of a progressive destabilization of network topology for understanding cognitive decline in multiple sclerosis.

The DIRECT consortium and the REST-meta-MDD project: towards neuroimaging biomarkers of major depressive disorder

Despite a growing neuroimaging literature on the pathophysiology of major depressive disorder (MDD), reproducible findings are lacking, probably reflecting mostly small sample sizes and heterogeneity in analytic approaches. To address these issues, the Depression Imaging REsearch ConsorTium (DIRECT) was launched. The REST-meta-MDD project, pooling 2428 functional brain images processed with a standardized pipeline across all participating sites, has been the first effort from DIRECT. In this review, we present an overview of the motivations, rationale, and principal findings of the studies so far from the REST-meta-MDD project. Findings from the first round of analyses of the pooled repository have included alterations in functional connectivity within the default mode network, in whole-brain topological properties, in dynamic features, and in functional lateralization. These well-powered exploratory observations have also provided the basis for future longitudinal hypothesis-driven research. Following these fruitful explorations, DIRECT has proceeded to its second stage of data sharing that seeks to examine ethnicity in brain alterations in MDD by extending the exclusive Chinese original sample to other ethnic groups through international collaborations. A state-of-the-art, surface-based preprocessing pipeline has also been introduced to improve sensitivity. Functional images from patients with bipolar disorder and schizophrenia will be included to identify shared and unique abnormalities across diagnosis boundaries. In addition, large-scale longitudinal studies targeting brain network alterations following antidepressant treatment, aggregation of diffusion tensor images, and the development of functional magnetic resonance imaging-guided neuromodulation approaches are underway. Through these endeavours, we hope to accelerate the translation of functional neuroimaging findings to clinical use, such as evaluating longitudinal effects of antidepressant medications and developing individualized neuromodulation targets, while building an open repository for the scientific community.

Dynamics of Functional Network Organization Through Graph Mixture Learning

Understanding the organizational principles of human brain activity at the systems level remains a major challenge in network neuroscience. Here, we introduce a fully data-driven approach based on graph learning to extract meaningful repeating network patterns from regionally-averaged timecourses. We use the Graph Laplacian Mixture Model (GLMM), a generative model that treats functional data as a collection of signals expressed on multiple underlying graphs. By exploiting covariance between activity of brain regions, these graphs can be learned without resorting to structural information. To validate the proposed technique, we first apply it to task fMRI with a known experimental paradigm. The probability of each graph to occur at each time-point is found to be consistent with the task timing, while the spatial patterns associated to each epoch of the task are in line with previously established activation patterns using classical regression analysis. We further on apply the technique to resting state data, which leads to extracted graphs that correspond to well-known brain functional activation patterns. The GLMM allows to learn graphs entirely from the functional activity that, in practice, turn out to reveal high degrees of similarity to the structural connectome. The Default Mode Network (DMN) is always captured by the algorithm in the different tasks and resting state data. Therefore, we compare the states corresponding to this network within themselves and with structure. Overall, this method allows us to infer relevant functional brain networks without the need of structural connectome information. Moreover, we overcome the limitations of windowing the time sequences by feeding the GLMM with the whole functional signal and neglecting the focus on sub-portions of the signals.

A mixed-modeling framework for whole-brain dynamic network analysis

The emerging area of dynamic brain network analysis has gained considerable attention in recent years. However, development of multivariate statistical frameworks that allow for examining the associations between phenotypic traits and dynamic patterns of system-level properties of the brain, and drawing statistical inference about such associations, has largely lagged behind. To address this need we developed a mixed-modeling framework that allows for assessing the relationship between any desired phenotype and dynamic patterns of whole-brain connectivity and topology. This novel framework also allows for simulating dynamic brain networks with respect to desired covariates. Unlike current tools, which largely use data-driven methods, our model-based method enables aligning neuroscientific hypotheses with the analytic approach. We demonstrate the utility of this model in identifying the relationship between fluid intelligence and dynamic brain networks by using resting-state fMRI (rfMRI) data from 200 participants in the Human Connectome Project (HCP) study. We also demonstrate the utility of this model to simulate dynamic brain networks at both group and individual levels. To our knowledge, this approach provides the first model-based statistical method for examining dynamic patterns of system-level properties of the brain and their relationships to phenotypic traits as well as simulating dynamic brain networks.

In recent years, a growing body of studies have aimed at analyzing the brain as a complex dynamic system by using various neuroimaging data. This has opened new avenues to answer compelling questions about the brain function in health and disease. However, methods that allow for providing statistical inference about how the complex interactions of the brain are associated with desired phenotypes are to be developed for a more profound insight. This study introduces a promising regression-based model to relate dynamic brain networks to desired phenotypes and provide statistical inference. Moreover, it can be used for simulating dynamic brain networks with respect to desired phenotypes at the group and individual levels.

Dynamic reconfiguration of human brain networks across altered states of consciousness

Consciousness is supported by rich neuronal dynamics to orchestrate behaviors and conscious processing can be disrupted by general anesthetics. Previous studies suggested that dynamic reconfiguration of large-scale functional network is critical for learning and higher-order cognitive function. During altered states of consciousness, how brain functional networks are dynamically changed and reconfigured at the whole-brain level is still unclear. To fill this gap, using multilayer network approach and functional magnetic resonance imaging (fMRI) data of 21 healthy subjects, we investigated the dynamic network reconfiguration in three different states of consciousness: wakefulness, dexmedetomidine-induced sedation, and recovery. Applying time-varying community detection algorithm, we constructed multilayer modularity networks to track and quantify dynamic interactions among brain areas that span time and space. We compared four high-level network features (i.e., switching, promiscuity, integration, and recruitment) derived from multilayer modularity across the three conditions. We found that sedation state is primarily characterized by increased switching rates as well as decreased integration, representing a whole-brain pattern with higher modular dynamics and more fragmented communication; such alteration can be mostly reversed after the recovery of consciousness. Thus, our work can provide additional insights to understand the modular network reconfiguration across different states of consciousness and may provide some clinical implications for disorders of consciousness.

A survey of brain network analysis by electroencephalographic signals

Brain network analysis is one efficient tool in exploring human brain diseases and can differentiate the alterations from comparative networks. The alterations account for time, mental states, tasks, individuals, and so forth. Furthermore, the changes determine the segregation and integration of functional networks that lead to network reorganization (or reconfiguration) to extend the neuroplasticity of the brain. Exploring related brain networks should be of interest that may provide roadmaps for brain research and clinical diagnosis. Recent electroencephalogram (EEG) studies have revealed the secrets of the brain networks and diseases (or disorders) within and between subjects and have provided instructive and promising suggestions and methods. This review summarized the corresponding algorithms that had been used to construct functional or effective networks on the scalp and cerebral cortex. We reviewed EEG network analysis that unveils more cognitive functions and neural disorders of the human and then explored the relationship between brain science and artificial intelligence which may fuel each other to accelerate their advances, and also discussed some innovations and future challenges in the end.

On the Importance of Being Flexible: Dynamic Brain Networks and Their Potential Functional Significances

In this theoretical review, we begin by discussing brains and minds from a dynamical systems perspective, and then go on to describe methods for characterizing the flexibility of dynamic networks. We discuss how varying degrees and kinds of flexibility may be adaptive (or maladaptive) in different contexts, specifically focusing on measures related to either more disjoint or cohesive dynamics. While disjointed flexibility may be useful for assessing neural entropy, cohesive flexibility may potentially serve as a proxy for self-organized criticality as a fundamental property enabling adaptive behavior in complex systems. Particular attention is given to recent studies in which flexibility methods have been used to investigate neurological and cognitive maturation, as well as the breakdown of conscious processing under varying levels of anesthesia. We further discuss how these findings and methods might be contextualized within the Free Energy Principle with respect to the fundamentals of brain organization and biological functioning more generally, and describe potential methodological advances from this paradigm. Finally, with relevance to computational psychiatry, we propose a research program for obtaining a better understanding of ways that dynamic networks may relate to different forms of psychological flexibility, which may be the single most important factor for ensuring human flourishing.

General principles of brain electromagnetic rhythmic oscillations and implications for neuroplasticity

Neuro-plasticity describes the ability of the brain in achieving novel functions, either by transforming its internal connectivity, or by changing the elements of which it is made, meaning that, only those changes, that affect both structural and functional aspects of the system, can be defined as "plastic." The concept of plasticity can be applied to molecular as well as to environmental events that can be recognized as the basic mechanism by which our brain reacts to the internal and external stimuli. When considering brain plasticity within a clinical context-that is the process linked with changes of brain functions following a lesion- the term "reorganization" is somewhat synonymous, referring to the specific types of structural/functional modifications observed as axonal sprouting, long-term synaptic potentiation/inhibition or to the plasticity related genomic responses. Furthermore, brain rewires during maturation, and aging thus maintaining a remarkable learning capacity, allowing it to acquire a wide range of skills, from motor actions to complex abstract reasoning, in a lifelong expression. In this review, the contribution on the "neuroplasticity" topic coming from advanced analysis of EEG rhythms is put forward.

Dynamic Reorganization of Functional Connectivity During Post-break Task Reengagement

Because of the undesired fatigue-related consequences, accumulating efforts have been made to find an effective intervention to alleviate the suboptimal cognitive function caused by mental fatigue. Nonetheless, limitations of intervention and evaluation methods may hinder the revealing of underlying neural mechanisms of fatigue recovery. Through the newly-developed dynamic functional connectivity (FC) analysis framework, this study aims to investigate the effects of two types of mid-task interventions (i.e., rest-break and moderate-intensity exercise-break) on the dynamic reorganization of FC during the execution of psychomotor vigilance test (PVT). Using a sliding window approach, temporal brain networks within each frequency band (i.e., δ, θ, α, & β) were estimated before and immediate after the intervention, and towards the end of the task to investigate the immediate and delayed effects respectively during post-break task reengagement. Behaviourally, similar beneficial effects of exercise- and rest-break on performance were observed, manifested by the immediate improvements after both interventions and a long-lasting influence towards the end of tasks. Moreover, temporal brain networks assessment showed significant immediate decreases of fluctuability, which followed by an increase of fluctuability towards the end of intervention tasks. Furthermore, the temporal nodal measure revealed the channels with significant differences across tasks were mainly resided in the fronto-parietal areas that exhibited interesting frequency-dependent distribution. The observations of immediate and delayed dynamic FC reorganizations extend previous fatigue-related intervention and static FC studies, and provide new insight into the dynamic characteristics of FC during post-break task reengagement.

Altered temporal reachability highlights the role of sensory perception systems in major depressive disorder

BACKGROUND

The latest studies have considered the time-dependent structures in dynamic brain networks. However, the effect of periphery structures on the temporal flow of information remains unexplored in patients with major depressive disorder (MDD). In this work, we aimed to explore the pattern of interactions between brain regions in MDD across space and time.

METHODS

We concentrated on the temporal reachability of nodes in temporal brain networks derived from the resting-state functional magnetic resonance imaging (rs-fMRI) of 55 MDD patients and 62 sex-, age-matched healthy controls. Specifically, temporal connectedness and temporal efficiency (TEF) were estimated based on the length of temporal paths between node pairs. Subsequently, the temporal clustering coefficient (TCC) and temporal distance were jointly employed to explore the patterns in which a node's periphery structure affects its reachability.

RESULTS

Significantly higher TEF and lower TCC were found in temporal brain networks in MDD. Besides, significant between-group differences of nodal TCC were detected in regions of sensory perception systems. Considering the temporal paths that begin or end at these regions, MDD patients showed several altered temporal distances.

CONCLUSION

Our results showed that the temporal reachability of specific brain regions in MDD could be affected as their periphery structures evolve, which may explain the dysfunction of sensory perception systems in the spatiotemporal domain.

Mixed Modeling Frameworks for Analyzing Whole-Brain Network Data

Brain network analyses have exploded in recent years and hold great potential in helping us understand normal and abnormal brain function. Network science approaches have facilitated these analyses and our understanding of how the brain is structurally and functionally organized. However, the development of statistical methods that allow relating this organization to health outcomes has lagged behind. We have attempted to address this need by developing mixed modeling frameworks that allow relating system-level properties of brain networks to outcomes of interest. These frameworks serve as a synergistic fusion of multivariate statistical approaches with network science, providing a needed analytic (modeling and inferential) foundation for whole-brain network data. In this chapter we delineate these approaches that have been developed for single-task and multitask (longitudinal) brain network data, illustrate their utility with data applications, detail their implementation with a user-friendly Matlab toolbox, and discuss ongoing work to adapt the methods to (within-task) dynamic network analysis.

Dynamic reconfiguration of macaque brain networks during natural vision

Natural vision engages a wide range of higher-level regions that integrate visual information over the large-scale brain network. How interareal connectivity reconfigures during the processing of ongoing natural visual scenes and how these dynamic functional changes relate to the underlaying anatomical links between regions is not well understood. Here, we hypothesized that macaque visual brain regions are poly-functional sharing the capacity to change their configuration state depending on the nature of visual input. To address this hypothesis, we reconstructed networks from in-vivo diffusion-weighted imaging (DWI) and functional magnetic resonance imaging (fMRI) data obtained in four alert macaque monkeys viewing naturalistic movie scenes. At first, we characterized network properties and found greater interhemispheric density and greater inter-subject variability in free-viewing networks as compared to structural networks. From the structural connectivity, we then captured modules on which we identified hubs during free-viewing that formed a widespread visuo-saccadic network across frontal (FEF, 46v), parietal (LIP, Tpt), and occipitotemporal modules (MT, V4, TEm), and that excluded primary visual cortex. Inter-subject variability of well-connected hubs reflected subject-specific configurations that largely recruited occipito-parietal and frontal modules. Across the cerebral hemispheres, free-viewing networks showed higher correlations among long-distance brain regions as compared to structural networks. From these findings, we hypothesized that long-distance interareal connectivity could reconfigure depending on the ongoing changes in visual scenes. Testing this hypothesis by applying temporally resolved functional connectivity we observed that many structurally defined areas (such as areas V4, MT/MST and LIP) were poly-functional as they were recruited as hub members of multiple network states that changed during the presentation of scenes containing objects, motion, faces, and actions. We suggest that functional flexibility in macaque macroscale brain networks is required for the efficient interareal communication during active natural vision. To further promote the use of naturalistic free-viewing paradigms and increase the development of macaque neuroimaging resources, we share our datasets in the PRIME-DE consortium.

Altered Dynamic Brain Connectivity in Individuals With Sickle Cell Disease and Chronic Pain Secondary to Hip Osteonecrosis

Individuals with sickle cell disease (SCD) exhibit changes in static brain connectivity in rest. However, little known as chronic pain associated with hip osteonecrosis affects dynamic brain connectivity during rest and the motor imagery task. The aim of this study was to investigate the characteristics of the dynamic functional brain connectivity of individuals with SCD and chronic pain secondary to hip osteonecrosis. This is a cross-sectional study comparing the dynamic brain connectivity of healthy individuals (n = 18) with the dynamic brain connectivity of individuals with SCD and chronic pain (n = 22). Individuals with SCD and chronic pain were stratified into high- or low-intensity pain groups based on pain intensity at the time of assessment. Dynamic brain connectivity was assessed through electroencephalography in 3 stages, resting state with eyes closed, and during hip (painful for the SCD individuals) and hand (control, nonpainful) motor imagery. Average weight of the edges and full synchronization time (FST)-time required for 95% of the possible edges to appear over time during a given task-were evaluated. Regarding the average weight of the edges, individuals with SCD and high-intensity pain presented higher edge weight during hip motor imagery. The average weight of the edges correlated positively with pain intensity and depression symptoms. Individuals with SCD and chronic pain complete the cerebral network at rest more quickly (lower FST). Individuals with SCD and chronic pain/hip osteonecrosis have impaired dynamic brain network with shorter FST in rest network and more pronounced diffuse connectivity in individuals with high-intensity pain. The dynamic brain network evaluated by time-varying graphs and motif synchronization was able to identify differences between groups.

Network alignment and similarity reveal atlas-based topological differences in structural connectomes

The interactions between different brain regions can be modeled as a graph, called connectome, whose nodes correspond to parcels from a predefined brain atlas. The edges of the graph encode the strength of the axonal connectivity between regions of the atlas that can be estimated via diffusion magnetic resonance imaging (MRI) tractography. Herein, we aim to provide a novel perspective on the problem of choosing a suitable atlas for structural connectivity studies by assessing how robustly an atlas captures the network topology across different subjects in a homogeneous cohort. We measure this robustness by assessing the alignability of the connectomes, namely the possibility to retrieve graph matchings that provide highly similar graphs. We introduce two novel concepts. First, the graph Jaccard index (GJI), a graph similarity measure based on the well-established Jaccard index between sets; the GJI exhibits natural mathematical properties that are not satisfied by previous approaches. Second, we devise WL-align, a new technique for aligning connectomes obtained by adapting the Weisfeiler-Leman (WL) graph-isomorphism test. We validated the GJI and WL-align on data from the Human Connectome Project database, inferring a strategy for choosing a suitable parcellation for structural connectivity studies. Code and data are publicly available.

An important part of our current understanding of the structure of the human brain relies on the concept of brain network, which is obtained by looking at how different brain regions are connected with each other. In this paper we present a strategy for choosing a suitable parcellation of the brain for structural connectivity studies by making use of the concepts of network alignment and similarity. To do so, we design a novel similarity measure between weighted networks called graph Jaccard index, and a new network alignment technique called WL-align. By assessing the possibility to retrieve graph matchings that provide highly similar graphs, we show that morphology- and structure-based atlases define brain networks that are more topologically robust across a wide range of resolutions.

Nonlinear manifold learning in functional magnetic resonance imaging uncovers a low-dimensional space of brain dynamics

Large-scale brain dynamics are believed to lie in a latent, low-dimensional space. Typically, the embeddings of brain scans are derived independently from different cognitive tasks or resting-state data, ignoring a potentially large-and shared-portion of this space. Here, we establish that a shared, robust, and interpretable low-dimensional space of brain dynamics can be recovered from a rich repertoire of task-based functional magnetic resonance imaging (fMRI) data. This occurs when relying on nonlinear approaches as opposed to traditional linear methods. The embedding maintains proper temporal progression of the tasks, revealing brain states and the dynamics of network integration. We demonstrate that resting-state data embeds fully onto the same task embedding, indicating similar brain states are present in both task and resting-state data. Our findings suggest analysis of fMRI data from multiple cognitive tasks in a low-dimensional space is possible and desirable.

Childhood trauma is linked to decreased temporal stability of functional brain networks in young adults

BACKGROUND

Both childhood trauma and disruptions in brain functional networks are implicated in the development of psychiatric disorders in early adulthood. However, the relationships between these two factors remain unclear. This study aimed to investigate whether and how childhood trauma would relate to changes of functional network dynamics in young adults.

METHODS

Resting-state functional magnetic resonance imaging data were collected from 53 young healthy adults, whose childhood trauma histories were assessed by the Childhood Trauma Questionnaire (CTQ). Network switching rate, a measure of stability of dynamic brain networks over time, was calculated at both global and local levels for each participant. Switching rates at both levels were compared between participants with and without childhood trauma, and further correlated with CTQ total score.

RESULTS

In the current sample, 19 (35.8%) participants reported a history of childhood trauma. At the global level, participants with childhood trauma showed significantly higher network switching rates than those without trauma (F = 10.021, p = 0.003). A significant positive correlation was found between network switching rates and CTQ scores in the entire sample (r = 0.378, p = 0.007). At the local level, these effects were mainly observed in the default-mode, fronto-parietal, cingulo-opercular, and occipital subnetworks.

CONCLUSIONS

Our study provides preliminary evidence for a possible long-term effect of childhood trauma on brain functional dynamism. These findings may have potential contributions to psychiatric disorders during adulthood.

On the estimate of music appraisal from surface EEG: a dynamic-network approach based on cross-sensor PAC measurements

Objective.The aesthetic evaluation of music is strongly dependent on the listener and reflects manifold brain processes that go well beyond the perception of incident sound. Being a high-level cognitive reaction, it is difficult to predict merely from the acoustic features of the audio signal and this poses serious challenges to contemporary music recommendation systems. We attempted to decode music appraisal from brain activity, recorded via wearable EEG, during music listening.Approach.To comply with the dynamic nature of music stimuli, cross-frequency coupling measurements were employed in a time-evolving manner to capture the evolving interactions between distinct brain-rhythms during music listening. Brain response to music was first represented as a continuous flow of functional couplings referring to both regional and inter-regional brain dynamics and then modelled as an ensemble of time-varying (sub)networks. Dynamic graph centrality measures were derived, next, as the final feature-engineering step and, lastly, a support-vector machine was trained to decode the subjective music appraisal. A carefully designed experimental paradigm provided the labeled brain signals.Main results.Using data from 20 subjects, dynamic programming to tailor the decoder to each subject individually and cross-validation, we demonstrated highly satisfactory performance (MAE= 0.948,R²= 0.63) that can be attributed, mostly, to interactions of left frontal gamma rhythm. In addition, our music-appraisal decoder was also employed in a part of the DEAP dataset with similar success. Finally, even a generic version of the decoder (common for all subjects) was found to perform sufficiently.Significance.A novel brain signal decoding scheme was introduced and validated empirically on suitable experimental data. It requires simple operations and leaves room for real-time implementation. Both the code and the experimental data are publicly available.

Brain Connectivity Studies on Structure-Function Relationships: A Short Survey with an Emphasis on Machine Learning

This short survey reviews the recent literature on the relationship between the brain structure and its functional dynamics. Imaging techniques such as diffusion tensor imaging (DTI) make it possible to reconstruct axonal fiber tracks and describe the structural connectivity (SC) between brain regions. By measuring fluctuations in neuronal activity, functional magnetic resonance imaging (fMRI) provides insights into the dynamics within this structural network. One key for a better understanding of brain mechanisms is to investigate how these fast dynamics emerge on a relatively stable structural backbone. So far, computational simulations and methods from graph theory have been mainly used for modeling this relationship. Machine learning techniques have already been established in neuroimaging for identifying functionally independent brain networks and classifying pathological brain states. This survey focuses on methods from machine learning, which contribute to our understanding of functional interactions between brain regions and their relation to the underlying anatomical substrate.

Neural correlates of treatment effect and prediction of treatment outcome in patients with PTSD and comorbid personality disorder: study design

BACKGROUND

Neural alterations related to treatment outcome in patients with both post-traumatic stress disorder (PTSD) and comorbid personality disorder are unknown. Here we describe the protocol for a neuroimaging study of treatment of patients with PTSD and comorbid borderline (BPD) or cluster C (CPD) personality disorder traits. Our specific aims are to 1) investigate treatment-induced neural alterations, 2) predict treatment outcome using structural and functional magnetic resonance imaging (MRI) and 3) study neural alterations associated with BPD and CPD in PTSD patients. We hypothesize that 1) all treatment conditions are associated with normalization of limbic and prefrontal brain activity and hyperconnectivity in resting-state brain networks, with additional normalization of task-related activation in emotion regulation brain areas in the patients who receive trauma-focused therapy and personality disorder treatment; 2) Baseline task-related activation, together with structural brain measures and clinical variables predict treatment outcome; 3) dysfunction in task-related activation and resting-state connectivity of emotion regulation areas is comparable in PTSD patients with BPD or CPD, with a hypoconnected central executive network in patients with PTSD+BPD.

METHODS

We aim to include pre- and post-treatment 3 T-MRI scans in 40 patients with PTSD and (sub) clinical comorbid BPD or CPD. With an expected attrition rate of 50%, at least 80 patients will be scanned before treatment. MRI scans for 30 matched healthy controls will additionally be acquired. Patients with PTSD and BPD were randomized to either EMDR-only or EMDR combined with Dialectical Behaviour Therapy. Patients with PTSD and CPD were randomized to Imaginary Rescripting (ImRs) or to ImRs combined with Schema Focused Therapy. The scan protocol consists of a T1-weighted structural scan, resting state fMRI, task-based fMRI during an emotional face task and multi-shell diffusion weighted images. For data analysis, multivariate mixed-models, regression analyses and machine learning models will be used.

DISCUSSION

This study is one of the first to use neuroimaging measures to predict and better understand treatment response in patients with PTSD and comorbid personality disorders. A heterogeneous, naturalistic sample will be included, ensuring generalizability to a broad group of treatment seeking PTSD patients.

TRIAL REGISTRATION

Clinical Trials, NCT03833453 & NCT03833531 . Retrospectively registered, February 2019.

Stimulus transformation into motor action: Dynamic graph analysis reveals a posterior-to-anterior shift in brain network communication of older subjects

Cognitive performance slows down with increasing age. This includes cognitive processes that are essential for the performance of a motor act, such as the slowing down in response to an external stimulus. The objective of this study was to identify aging-associated functional changes in the brain networks that are involved in the transformation of external stimuli into motor action. To investigate this topic, we employed dynamic graphs based on phase-locking of Electroencephalography signals recorded from healthy younger and older subjects while performing a simple visually-cued finger-tapping task. The network analysis yielded specific age-related network structures varying in time in the low frequencies (2-7 Hz), which are closely connected to stimulus processing, movement initiation and execution in both age groups. The networks in older subjects, however, contained several additional, particularly interhemispheric, connections and showed an overall increased coupling density. Cluster analyses revealed reduced variability of the subnetworks in older subjects, particularly during movement preparation. In younger subjects, occipital, parietal, sensorimotor and central regions were-temporally arranged in this order-heavily involved in hub nodes. Whereas in older subjects, a hub in frontal regions preceded the noticeably delayed occurrence of sensorimotor hubs, indicating different neural information processing in older subjects. All observed changes in brain network organization, which are based on neural synchronization in the low frequencies, provide a possible neural mechanism underlying previous fMRI data, which report an overactivation, especially in the prefrontal and pre-motor areas, associated with a loss of hemispheric lateralization in older subjects.

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

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

Increased dynamic flexibility in the medial temporal lobe network following an exercise intervention mediates generalization of prior learning

Recent work has conceptualized the brain as a network comprised of groups of sub-networks or modules. "Flexibility" of brain network(s) indexes the dynamic reconfiguration of comprising modules. Using novel techniques from dynamic network neuroscience applied to high-resolution resting-state functional magnetic resonance imaging (fMRI), the present study investigated the effects of an aerobic exercise intervention on the dynamic rearrangement of modular community structure-a measure of neural flexibility-within the medial temporal lobe (MTL) network. The MTL is one of the earliest brain regions impacted by Alzheimer's disease. It is also a major site of neuroplasticity that is sensitive to the effects of exercise. In a two-group non-randomized, repeated measures and matched control design with 34 healthy older adults, we observed an exercise-related increase in flexibility within the MTL network. Furthermore, MTL network flexibility mediated the beneficial effect aerobic exercise had on mnemonic flexibility, as measured by the ability to generalize past learning to novel task demands. Our results suggest that exercise exerts a rehabilitative and protective effect on MTL function, resulting in dynamically evolving networks of regions that interact in complex communication patterns. These reconfigurations may underlie exercise-induced improvements on cognitive measures of generalization, which are sensitive to subtle changes in the MTL.

Longitudinal functional brain network reconfiguration in healthy aging

Healthy aging is associated with changes in cognitive performance and functional brain organization. In fact, cross-sectional studies imply lower modularity and significant heterogeneity in modular architecture across older subjects. Here, we used a longitudinal dataset consisting of four occasions of resting-state-fMRI and cognitive testing (spanning 4 years) in 150 healthy older adults. We applied a graph-theoretic analysis to investigate the time-evolving modular structure of the whole-brain network, by maximizing the multilayer modularity across four time points. Global flexibility, which reflects the tendency of brain nodes to switch between modules across time, was significantly higher in healthy elderly than in a temporal null model. Further, global flexibility, as well as network-specific flexibility of the default mode, frontoparietal control, and somatomotor networks, were significantly associated with age at baseline. These results indicate that older age is related to higher variability in modular organization. The temporal metrics were not associated with simultaneous changes in processing speed or learning performance in the context of memory encoding. Finally, this approach provides global indices for longitudinal change across a given time span and it may contribute to uncovering patterns of modular variability in healthy and clinical aging populations.

A methodology for structured literature network meta-analysis

Purpose

Little attention has been paid to restructuring existing massive amounts of literature data such that evidence-based meaningful inferences and networks be drawn therefrom. This paper aims to structure extant literature data into a network and demonstrate by graph visualization and manipulation tool “Gephi” how to obtain an evidence-based literature review.

Design/methodology/approach

The main objective of this paper is to propose a methodology to structure existing literature data into a network. This network is examined through certain graph theory metrics to uncover evidence-based research insights arising from existing huge amounts of literature data. From the list metrics, this study considers degree centrality, closeness centrality and betweenness centrality to comprehend the information available in the literature pool.

Findings

There is a significant amount of literature on any given research problem. Approaching this massive volume of literature data to find an appropriate research problem is a complicated process. The proposed methodology and metrics enable the extraction of appropriate and relevant information from huge quantities of literature data. The methodology is validated by three different scenarios of review questions, and results are reported.

Research limitations/implications

The proposed methodology comprises of more manual hours to structure literature data.

Practical implications

This paper enables researchers in any domain to systematically extract and visualize meaningful and evidence-based insights from existing literature.

Originality/value

The procedure for converting literature data into a network representation is not documented in the existing literature. The paper lays down the procedure to structure literature data into a network.

Dynamic functional connectivity in temporal lobe epilepsy: a graph theoretical and machine learning approach

PURPOSE

Functional magnetic resonance imaging (fMRI) in resting state can be used to evaluate the functional organization of the human brain in the absence of any task or stimulus. The functional connectivity (FC) has non-stationary nature and consented to be varying over time. By considering the dynamic characteristics of the FC and using graph theoretical analysis and a machine learning approach, we aim to identify the laterality in cases of temporal lobe epilepsy (TLE).

METHODS

Six global graph measures are extracted from static and dynamic functional connectivity matrices using fMRI data of 35 unilateral TLE subjects. Alterations in the time trend of the graph measures are quantified. The random forest (RF) method is used for the determination of feature importance and selection of dynamic graph features including mean, variance, skewness, kurtosis, and Shannon entropy. The selected features are used in the support vector machine (SVM) classifier to identify the left and right epileptogenic sides in patients with TLE.

RESULTS

Our results for the performance of SVM demonstrate that the utility of dynamic features improves the classification outcome in terms of accuracy (88.5% for dynamic features compared with 82% for static features). Selecting the best dynamic features also elevates the accuracy to 91.5%.

CONCLUSION

Accounting for the non-stationary characteristics of functional connectivity, dynamic connectivity analysis of graph measures along with machine learning approach can identify the temporal trend of some specific network features. These network features may be used as potential imaging markers in determining the epileptogenic hemisphere in patients with TLE.