Structure and function of complex brain networks

Alterations of individual thalamic nuclei volumes in patients with migraine

Background

The aim of this study is to investigate the alterations of thalamic nuclei volumes and the intrinsic thalamic network in patients with migraine.

Methods

We enrolled 35 patients with migraine without aura and 40 healthy controls. All subjects underwent three-dimensional T1-weighted imaging. The thalamic nuclei were segmented using the FreeSurfer program. We investigated volume changes of individual thalamic nuclei and analyzed the alterations of the intrinsic thalamic network based on volumes in the patients with migraine.

Results

Right and left thalamic volumes as a whole were not different between the patients with migraine and healthy controls. However, we found that right anteroventral and right and left medial geniculate nuclei volumes were significantly increased (0.00985% vs. 0.00864%, p = 0.0002; 0.00929% vs. 0.00823%, p = 0.0005; 0.00939% vs. 0.00769%, p < 0.0001; respectively) whereas right and left parafascicular nuclei volumes were decreased in the patients with migraine (0.00359% vs. 0.00435%, p < 0.0001; 0.00360% vs. 0.00438%, p < 0.0001; respectively) compared with healthy controls. The network measures of the intrinsic thalamic network were not different between the groups.

Conclusions

We found significant alterations of thalamic nuclei volumes in patients with migraine compared with healthy controls. These findings might contribute to the underlying pathogenesis of the migraine.

Trial registration

None.

Machine learning: assessing neurovascular signals in the prefrontal cortex with non-invasive bimodal electro-optical neuroimaging in opiate addiction

Chronic and recurrent opiate use injuries brain tissue and cause serious pathophysiological changes in hemodynamic and subsequent inflammatory responses. Prefrontal cortex (PFC) has been implicated in drug addiction. However, the mechanism underlying systems-level neuroadaptations in PFC during abstinence has not been fully characterized. The objective of our study was to determine what neural oscillatory activity contributes to the chronic effect of opiate exposure and whether the activity could be coupled to neurovascular information in the PFC. We employed resting-state functional connectivity to explore alterations in 8 patients with heroin dependency who stayed abstinent (>3 months; HD) compared with 11 control subjects. A non-invasive neuroimaging strategy was applied to combine electrophysiological signals through electroencephalography (EEG) with hemodynamic signals through functional near-infrared spectroscopy (fNIRS). The electrophysiological signals indicate neural synchrony and the oscillatory activity, and the hemodynamic signals indicate blood oxygenation in small vessels in the PFC. A supervised machine learning method was used to obtain associations between EEG and fNIRS modalities to improve precision and localization. HD patients demonstrated desynchronized lower alpha rhythms and decreased connectivity in PFC networks. Asymmetric excitability and cerebrovascular injury were also observed. This pilot study suggests that cerebrovascular injury in PFC may result from chronic opiate intake.

Spiritual experiences are related to engagement of a ventral frontotemporal functional brain network: Implications for prevention and treatment of behavioral and substance addictions

BACKGROUND AND AIMS

Spirituality is an important component of 12-step programs for behavioral and substance addictions and has been linked to recovery processes. Understanding the neural correlates of spiritual experiences may help to promote efforts to enhance recovery processes in behavioral addictions. We recently used general linear model (GLM) analyses of functional magnetic resonance imaging data to examine neural correlates of spiritual experiences, with findings implicating cortical and subcortical brain regions. Although informative, the GLM-based approach does not provide insight into brain circuits that may underlie spiritual experiences.

METHODS

Spatial independent component analysis (sICA) was used to identify functional brain networks specifically linked to spiritual (vs. stressful or neutral-relaxing) conditions using a previously validated guided imagery task in 27 young adults.

RESULTS

Using sICA, engagement of a ventral frontotemporal network was identified that was engaged at the onset and conclusion of the spiritual condition in a manner distinct from engagement during the stress or neutral-relaxing conditions. Degree of engagement correlated with subjective reports of spirituality in the scanner (r = .71, p < .001) and an out-of-the-magnet measure of spirituality (r = .48, p < .018).

DISCUSSION AND CONCLUSION

The current findings suggest a distributed functional neural network associated with spiritual experiences and provide a foundation for investigating brain mechanisms underlying the role of spirituality in recovery from behavioral addictions.

A network-based response feature matrix as a brain injury metric

Conventional brain injury metrics are scalars that treat the whole head/brain as a single unit but do not characterize the distribution of brain responses. Here, we establish a network-based "response feature matrix" to characterize the magnitude and distribution of impact-induced brain strains. The network nodes and edges encode injury risks to the gray matter regions and their white matter interconnections, respectively. The utility of the metric is illustrated in injury prediction using three independent, real-world datasets: two reconstructed impact datasets from the National Football League (NFL) and Virginia Tech, respectively, and measured concussive and non-injury impacts from Stanford University. Injury predictions with leave-one-out cross-validation are conducted using the two reconstructed datasets separately, and then by combining all datasets into one. Using support vector machine, the network-based injury predictor consistently outperforms four baseline scalar metrics including peak maximum principal strain of the whole brain (MPS), peak linear/rotational acceleration, and peak rotational velocity across all five selected performance measures (e.g., maximized accuracy of 0.887 vs. 0.774 and 0.849 for MPS and rotational acceleration with corresponding positive predictive values of 0.938, 0.772, and 0.800, respectively, using the reconstructed NFL dataset). With sufficient training data, real-world injury prediction is similar to leave-one-out in-sample evaluation, suggesting the potential advantage of the network-based injury metric over conventional scalar metrics. The network-based response feature matrix significantly extends scalar metrics by sampling the brain strains more completely, which may serve as a useful framework potentially allowing for other applications such as characterizing injury patterns or facilitating targeted multi-scale modeling in the future.

Inferring correlations associated to causal interactions in brain signals using autoregressive models

The specific connectivity of a neuronal network is reflected in the dynamics of the signals recorded on its nodes. The analysis of how the activity in one node predicts the behaviour of another gives the directionality in their relationship. However, each node is composed of many different elements which define the properties of the links. For instance, excitatory and inhibitory neuronal subtypes determine the functionality of the connection. Classic indexes such as the Granger causality (GC) quantifies these interactions, but they do not infer into the mechanism behind them. Here, we introduce an extension of the well-known GC that analyses the correlation associated to the specific influence that a transmitter node has over the receiver. This way, the G-causal link has a positive or negative effect if the predicted activity follows directly or inversely, respectively, the dynamics of the sender. The method is validated in a neuronal population model, testing the paradigm that excitatory and inhibitory neurons have a differential effect in the connectivity. Our approach correctly infers the positive or negative coupling produced by different types of neurons. Our results suggest that the proposed approach provides additional information on the characterization of G-causal connections, which is potentially relevant when it comes to understanding interactions in the brain circuits.

Network curvature as a hallmark of brain structural connectivity

Although brain functionality is often remarkably robust to lesions and other insults, it may be fragile when these take place in specific locations. Previous attempts to quantify robustness and fragility sought to understand how the functional connectivity of brain networks is affected by structural changes, using either model-based predictions or empirical studies of the effects of lesions. We advance a geometric viewpoint relying on a notion of network curvature, the so-called Ollivier-Ricci curvature. This approach has been proposed to assess financial market robustness and to differentiate biological networks of cancer cells from healthy ones. Here, we apply curvature-based measures to brain structural networks to identify robust and fragile brain regions in healthy subjects. We show that curvature can also be used to track changes in brain connectivity related to age and autism spectrum disorder (ASD), and we obtain results that are in agreement with previous MRI studies.

The brain can often continue to function despite lesions in many areas, but damage to particular locations may have serious effects. Here, the authors use the concept of Ollivier-Ricci curvature to investigate the robustness of brain networks.

Neural Activity and Decoding of Action Observation Using Combined EEG and fNIRS Measurement

In a social world, observing the actions of others is fundamental to understanding what they are doing, as well as their intentions and feelings. Studies of the neural basis and decoding of action observation are important for understanding action-related processes and have implications for cognitive, social neuroscience, and human-machine interaction (HMI). In the current study, we first investigated temporal-spatial dynamics during action observation using a combined 64-channel electroencephalography (EEG) and 48-channel functional near-infrared spectroscopy (fNIRS) system. We measured brain activation while 16 healthy participants observed three action tasks: (1) grasping a cup with the intention of drinking; (2) grasping a cup with the intention of moving it; and (3) touching a cup with an unclear intention. The EEG and fNIRS source analysis results revealed the dynamic involvement of both the mirror neuron system (MNS) and the theory of mind (ToM)/mentalizing network during action observation. The source analysis results suggested that the extent to which these two systems were engaged was determined by the clarity of the intention of the observed action. Based on the difference in neural activity observed among different action-observation tasks in the first experiment, we conducted a second experiment to classify the neural processes underlying action observation using a feature classification method. We constructed complex brain networks based on the EEG and fNIRS data. Fusing features from both EEG and fNIRS complex brain networks resulted in a classification accuracy of 72.7% for the three action observation tasks. This study provides a theoretical and empirical basis for elucidating the neural mechanisms of action observation and intention understanding, and a feasible method for decoding the underlying neural processes.

Collective dynamics of rate neurons for supervised learning in a reservoir computing system

In this paper, we study collective dynamics of the network of rate neurons which constitute a central element of a reservoir computing system. The main objective of the paper is to identify the dynamic behaviors inside the reservoir underlying the performance of basic machine learning tasks, such as generating patterns with specified characteristics. We build a reservoir computing system which includes a reservoir-a network of interacting rate neurons-and an output element that generates a target signal. We study individual activities of interacting rate neurons, while implementing the task and analyze the impact of the dynamic parameter-a time constant-on the quality of implementation.

Altered Functional Brain Network Integration, Segregation, and Modularity in Infants Born Very Preterm at Term-Equivalent Age

OBJECTIVES

To determine the functional network organization of the brain in infants born very preterm at term-equivalent age and to relate network alterations to known clinical risk factors for poor neurologic outcomes in prematurity.

STUDY DESIGN

Resting-state functional magnetic resonance imaging data from 66 infants born very preterm (gestational age <32 weeks and birth weight <1500 g) and 66 healthy neonates born at full term, acquired as part of a prospective, cross-sectional study, were compared at term age using graph theory. Features of resting-state networks, including integration, segregation, and modularity, were derived from correlated hemodynamic activity arising from 93 cortical and subcortical regions of interest and compared between groups.

RESULTS

Despite preserved small-world topology and modular organization, resting-state networks of infants born very preterm at term-equivalent age were less segregated and less integrated than those of infants born full term. Chronic respiratory illness (ie, bronchopulmonary dysplasia and the length of oxygen support) was associated with decreased global efficiency and increased path lengths (P < .05). In both cohorts, 4 functional modules with similar composition were observed (parietal/temporal, frontal, subcortical/limbic, and occipital). The density of connections in 3 of the 4 modules was decreased in the very preterm network (P < .01); however, in the occipital/visual cortex module, connectivity was increased in infants born very preterm relative to control infants (P < .0001).

CONCLUSIONS

Early exposure to the ex utero environment is associated with altered resting-state network functional organization in infants born very preterm at term-equivalent age, likely reflecting disrupted brain maturational processes.

Inward versus reward: white matter pathways in extraversion

The trait of extraversion is one of the longest-standing domains that captures the social dimension of personality and can potentially explain the covariation of a wide variety of behaviors. To date, there is a growing recognition that human behavior should be specified not only through the psychological mechanisms underlying each trait but also through their underlying neurobehavioral systems. While imaging studies have revealed important initial insights into the structural and functional neural correlates of extraversion, current knowledge about the relationships between extraversion and brain structures is still rather limited, especially with regard to the relationship between extraversion and white matter (WM). In this study, we aimed to investigate WM microstructure in extraversion in greater depth. Thirty-five healthy volunteers (21 women; mean age 35) underwent magnetic resonance imaging, as a part of a larger project aimed at investigating the longitudinal effect of motor training. WM integrity was assessed using the diffusion tensor imaging technique combining multiple diffusion tensor measures. Extraversion was assessed by the Eysenck Personality Questionnaire-Revised. Voxelwise correlation analyses between fractional anisotropy, axial diffusivities, and radial diffusivities maps and extraversion score showed decreased connectivity in the right inferior fronto-occipital fasciculus and forceps major among individuals who had high extraversion ratings. In conclusion, individual differences in extraversion may reflect differential organization of the WM tracts connecting frontal cortex, temporal, and occipital areas, which are related to socioemotional and control functions.

Role of brain imaging in disorders of brain-gut interaction: a Rome Working Team Report

Imaging of the living human brain is a powerful tool to probe the interactions between brain, gut and microbiome in health and in disorders of brain-gut interactions, in particular IBS. While altered signals from the viscera contribute to clinical symptoms, the brain integrates these interoceptive signals with emotional, cognitive and memory related inputs in a non-linear fashion to produce symptoms. Tremendous progress has occurred in the development of new imaging techniques that look at structural, functional and metabolic properties of brain regions and networks. Standardisation in image acquisition and advances in computational approaches has made it possible to study large data sets of imaging studies, identify network properties and integrate them with non-imaging data. These approaches are beginning to generate brain signatures in IBS that share some features with those obtained in other often overlapping chronic pain disorders such as urological pelvic pain syndromes and vulvodynia, suggesting shared mechanisms. Despite this progress, the identification of preclinical vulnerability factors and outcome predictors has been slow. To overcome current obstacles, the creation of consortia and the generation of standardised multisite repositories for brain imaging and metadata from multisite studies are required.

Unified analysis of global and focal aspects of absence epilepsy via neural field theory of the corticothalamic system

Absence epilepsy is characterized by a sudden paroxysmal loss of consciousness accompanied by oscillatory activity propagating over many brain areas. Although primary generalized absence seizures are supported by the global corticothalamic system, converging experimental evidence supports a focal theory of absence epilepsy. Here a physiology-based corticothalamic model is investigated with spatial heterogeneity due to focal epilepsy to unify global and focal aspects of absence epilepsy. Numeric and analytic calculations are employed to investigate the emergent spatiotemporal dynamics as well as their underlying dynamical mechanisms. They can be categorized into three scenarios: suppressed epilepsy, focal seizures, or generalized seizures, as summarized from a phase diagram vs focal width and characteristic axon range. The corresponding temporal frequencies and spatial extents of cortical waves in generalized seizures and focal seizures agree well with experimental observations of global and focal aspects of absence epilepsy, respectively. The emergence of the spatiotemporal dynamics corresponding to focal seizures provides a biophysical explanation of the temporally higher frequency but spatially more localized cortical waves observed in genetic rat models that display characteristics of human absence epilepsy. Predictions are also presented for further experimental test.

rTMS combined with motor training changed the inter-hemispheric lateralization

Repetitive transcranial magnetic stimulation combined with motor training (rTMS-MT) can be an effective method for enhancing motor function. However, the effects of rTMS-MT on inter-hemispheric lateralization remain unclear. Nineteen healthy volunteers were recruited. The volunteers were randomized to receive 2 weeks of rTMS-MT or MT to improve the motor function of the nondominant hand. Hand dexterity was tested by the Nine-Hole Peg Test. Resting motor threshold (RMT), motor evoked potentials (MEP) and electroencephalography (EEG) in the resting state with eyes closed were recorded, to calculate inter-hemispheric lateralization before and after rTMS-MT or MT. rTMS-MT and MT improved the dexterity and MEP amplitude of the nondominant hand. Furthermore, there were significant changes in the lateralization of not only power spectral density, but also information transmission efficiency between regions following rTMS-MT, especially between the central cortices of both hemispheres. However, although the lateralization change of the power spectral density between the central cortices was observed following MT, there was no such change for information transmission efficiency between any cortices. These results suggested that rTMS-MT could modulate inter-hemispheric lateralization. Changes in inter-hemispheric lateralization might be an important neural mechanism by which rTMS-MT improves motor function. These results could be helpful for understanding the brain mechanism of rTMS-MT.

The lateral neocortex is critical for contextual fear memory reconsolidation

Memories are a product of the concerted activity of many brain areas. Deregulation of consolidation and reprocessing of mnemonic traces that encode fearful experiences might result in fear-related psychopathologies. Here, we assessed how pre-established memories change with experience, particularly the labilization/reconsolidation of memory, using the whole-brain analysis technique of positron emission tomography in male mice. We found differences in glucose consumption in the lateral neocortex, hippocampus and amygdala in mice that underwent labilization/reconsolidation processes compared to animals that did not reactivate a fear memory. We used chemogenetics to obtain insight into the role of cortical areas in these phases of memory and found that the lateral neocortex is necessary for fear memory reconsolidation. Inhibition of lateral neocortex during reconsolidation altered glucose consumption levels in the amygdala. Using an optogenetic/neuronal recording-based strategy we observed that the lateral neocortex is functionally connected with the amygdala, which, along with retrograde labeling using fluorophore-conjugated cholera toxin subunit B, support a monosynaptic connection between these areas and poses this connection as a hot-spot in the circuits involved in reactivation of fear memories.

Functional Geometry of Human Connectomes

Mapping the brain imaging data to networks, where nodes represent anatomical brain regions and edges indicate the occurrence of fiber tracts between them, has enabled an objective graph-theoretic analysis of human connectomes. However, the latent structure on higher-order interactions remains unexplored, where many brain regions act in synergy to perform complex functions. Here we use the simplicial complexes description of human connectome, where the shared simplexes encode higher-order relationships between groups of nodes. We study consensus connectome of 100 female (F-connectome) and of 100 male (M-connectome) subjects that we generated from the Budapest Reference Connectome Server v3.0 based on data from the Human Connectome Project. Our analysis reveals that the functional geometry of the common F&M-connectome coincides with the M-connectome and is characterized by a complex architecture of simplexes to the 14th order, which is built in six anatomical communities, and linked by short cycles. The F-connectome has additional edges that involve different brain regions, thereby increasing the size of simplexes and introducing new cycles. Both connectomes contain characteristic subjacent graphs that make them 3/2-hyperbolic. These results shed new light on the functional architecture of the brain, suggesting that insightful differences among connectomes are hidden in their higher-order connectivity.

Chimera state in complex networks of bistable Hodgkin-Huxley neurons

In this paper we study a chimera state in complex networks of bistable Hodgkin-Huxley neurons with excitatory coupling, which manifests as a termination of spiking activity of a part of interacting neurons. We provide a detailed investigation of this phenomenon in scale-free, small-world, and random networks and show that the chimera state is robust to the network topology. Nevertheless, network topological properties determine the stability of spatiotemporal states and therefore affect the excitability of the chimera state in the whole network. In particular, the scale-free network whose higher degree nodes are more stable to small perturbations is least exposed to chimera formation and exhibits an abrupt transition from a spiking to a silent regime. On the other hand, small-world and random networks are more likely to provide transitions to the chimera state.

Sensorimotor Connectivity after Motor Exercise with Neurofeedback in Post-Stroke Patients with Hemiplegia

Impaired finger motor function in post-stroke hemiplegia is a debilitating condition with no evidence-based or accessible treatments. Here, we evaluated the neurophysiological effectiveness of direct brain control of robotic exoskeleton that provides movement support contingent with brain activity. To elucidate the mechanisms underlying the neurofeedback intervention, we assessed resting-state functional connectivity with functional magnetic resonance imaging (rsfcMRI) between the ipsilesional sensory and motor cortices before and after a single 1-h intervention. Eighteen stroke patients were randomly assigned to crossover interventions in a double-blind and sham-controlled design. One patient dropped out midway through the study, and 17 patients were included in this analysis. Interventions involved motor imagery, robotic assistance, and neuromuscular electrical stimulation administered to a paretic finger. The neurofeedback intervention delivered stimulations contingent on desynchronized ipsilesional electroencephalographic (EEG) oscillations during imagined movement, and the control intervention delivered sensorimotor stimulations that were independent of EEG oscillations. There was a significant time × intervention interaction in rsfcMRI in the ipsilesional sensorimotor cortex. Post-hoc analysis showed a larger gain in increased functional connectivity during the neurofeedback intervention. Although the neurofeedback intervention delivered fewer total sensorimotor stimulations compared to the sham-control, rsfcMRI in the ipsilesional sensorimotor cortices was increased during the neurofeedback intervention compared to the sham-control. Higher coactivation of the sensory and motor cortices during neurofeedback intervention enhanced rsfcMRI in the ipsilesional sensorimotor cortices. This study showed neurophysiological evidence that EEG-contingent neurofeedback is a promising strategy to induce intrinsic ipsilesional sensorimotor reorganization, supporting the importance of integrating closed-loop sensorimotor processing at a neurophysiological level.

How the Brain Transitions from Conscious to Subliminal Perception

We study the transition in the functional networks that characterize the human brains' conscious-state to an unconscious subliminal state of perception by using k-core percolation. We find that the most inner core (i.e., the most connected kernel) of the conscious-state functional network corresponds to areas which remain functionally active when the brain transitions from the conscious-state to the subliminal-state. That is, the inner core of the conscious network coincides with the subliminal-state. Mathematical modeling allows to interpret the conscious to subliminal transition as driven by k-core percolation, through which the conscious state is lost by the inactivation of the peripheral k-shells of the conscious functional network. Thus, the inner core and most robust component of the conscious brain corresponds to the unconscious subliminal state. This finding imposes constraints to theoretical models of consciousness, in that the location of the core of the functional brain network is in the unconscious part of the brain rather than in the conscious state as previously thought.

Low-Level Primary Blast Induces Neuroinflammation and Neurodegeneration in Rats

OBJECTIVE

Mild blast traumatic brain injury is commonly prevalent in modern combat casualty care and has been associated with the development of neurodegenerative conditions. However, whether primary lower level blast overpressure (LBOP) causes neurodegeneration and neuroinflammation remains largely unknown. The aim of our present study was to determine whether LBOP can cause neuroinflammation and neurodegeneration.

METHODS

Anesthetized rats were randomly assigned to LBOP group (70 kPa, n = 5) or sham group (without blast, n = 5). Histopathological and cytokine changes in brain tissue at 5 days post-injury were evaluated by hematoxylin-eosin staining and Bioplex assay, respectively.

RESULTS

Histopathological assessment revealed neuronal degeneration and increased density of inflammatory cells in frontal and parietal cortex, hippocampus and thalamus in rats exposed to LBOP. LBOP exposure significantly elevated levels of pro-inflammatory cytokines (EPO, IL-1β, IL-6, IL-12, IL-18, and TNF-α) and chemokines (GRO and RANTES) as well as of an anti-inflammatory cytokine (IL-13) in the frontal cortex.

CONCLUSIONS

This study reveals a role of neuroinflammation in neurodegeneration after mild blast traumatic brain injury. Therapies that target this process might in warfighters might function either by attenuating the development of post-traumatic stress disorder, chronic traumatic encephalopathy and Alzheimer's disease, or by slowing their progression.

Increased segregation of functional networks in developing brains

A growing literature conceptualises typical brain development from a network perspective. However, largely due to technical and methodological challenges inherent in paediatric functional neuroimaging, there remains an important gap in our knowledge regarding the typical development of functional brain networks in "preschool" childhood (i.e., children younger than 6 years of age). In this study, we recorded brain oscillatory activity using age-appropriate magnetoencephalography in 24 children, including 14 preschool children aged from 4 to 6 years and 10 school children aged from 7 to 12 years. We compared the topology of the resting-state brain networks in these children, estimated using minimum spanning tree (MST) constructed from phase synchrony between beamformer-reconstructed time-series, with that of 24 adults. Our results show that during childhood the MST topology shifts from a star-like (centralised) toward a more line-like (de-centralised) configuration, indicating the functional brain networks become increasingly segregated. In addition, the increasing global network segregation is frequency-independent and accompanied by decreases in centrality (or connectedness) of cortical regions with age, especially in areas of the default mode network. We propose a heuristic MST model of "network space", which posits a clear developmental trajectory for the emergence of complex brain networks. Our results not only revealed topological reorganisation of functional networks across multiple temporal and spatial scales in childhood, but also fill a gap in the literature regarding neurophysiological mechanisms of functional brain maturation during the preschool years of childhood.

Topological gene expression networks recapitulate brain anatomy and function

Understanding how gene expression translates to and affects human behavior is one of the ultimate goals of neuroscience. In this paper, we present a pipeline based on Mapper, a topological simplification tool, to analyze gene co-expression data. We first validate the method by reproducing key results from the literature on the Allen Human Brain Atlas and the correlations between resting-state fMRI and gene co-expression maps. We then analyze a dopamine-related gene set and find that co-expression networks produced by Mapper return a structure that matches the well-known anatomy of the dopaminergic pathway. Our results suggest that network based descriptions can be a powerful tool to explore the relationships between genetic pathways and their association with brain function and its perturbation due to illness and/or pharmacological challenges.

Functional Connectivity of Attention, Visual, and Language Networks During Audio, Illustrated, and Animated Stories in Preschool-Age Children

The American Academy of Pediatrics recommends that parents read with their children early and often and limits on screen-based media. While book sharing may benefit attention in children, effects of animated content are controversial, and the influence of either on attention networks has not previously been studied. This study involved functional magnetic resonance imaging (fMRI) of three separate active-task scans composed of similar 5-min stories presented in the same order for each child (audio → illustrated → animated), followed by assessment of comprehension. Five functional brain networks were defined a priori through literature review: dorsal attention network (DAN), ventral attention network (VAN), language (L), visual imagery (VI), and visual perception (VP). Analyses involved comparison of functional connectivity (FC) within- and between networks across formats, applying false discovery rate correction. Twenty-seven of 33 children completed fMRI (82%; 15 boys, 12 girls; mean 58 ± 8 months old). Comprehension of audio and illustrated stories was equivalent and lower for animation (p < 0.05). For illustration relative to audio, FC within DAN and VAN and between each of these and all other networks was similar, lower within-L, and higher between VI-VP, suggesting reduced strain on the language network using illustrations and imagery. For animation relative to illustration, FC was lower between DAN-L, VAN-VP, VAN-VI, L-VI, and L-VP, suggesting less focus on narrative, reorienting to imagery, and visual-language integration. These findings suggest that illustrated storybooks may be optimal at this age to encourage integration of attention, visual, and language networks, while animation may bias attention toward VP.

Impact of early adverse life events and sex on functional brain networks in patients with urological chronic pelvic pain syndrome (UCPPS): A MAPP Research Network study

Pain is a highly complex and individualized experience with biopsychosocial components. Neuroimaging research has shown evidence of the involvement of the central nervous system in the development and maintenance of chronic pain conditions, including urological chronic pelvic pain syndrome (UCPPS). Furthermore, a history of early adverse life events (EALs) has been shown to adversely impact symptoms throughout childhood and into adulthood. However, to date, the role of EAL's in the central processes of chronic pain have not been adequately investigated. We studied 85 patients (56 females) with UCPPS along with 86 healthy controls (HCs) who had resting-state magnetic resonance imaging scans (59 females), and data on EALs as a part of the Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) Research Network Study. We used graph theory methods in order to investigate the impact of EALs on measures of centrality, which characterize information flow, communication, influence, and integration in a priori selected regions of interest. Patients with UCPPS exhibited lower centrality in the right anterior insula compared to HCs, a key node in the salience network. Males with UCPPS exhibited lower centrality in the right anterior insula compared the HC males. Females with UCPPS exhibited greater centrality in the right caudate nucleus and left angular gyrus compared to HC females. Males with UCPPS exhibited lower centrality in the left posterior cingulate, angular gyrus, middle temporal gyrus, and superior temporal sulcus, but greater centrality in the precuneus and anterior mid-cingulate cortex (aMCC) compared to females with UCPPS. Higher reports of EALs was associated with greater centrality in the left precuneus and left aMCC in females with UCPPS. This study provides evidence for disease and sex-related alterations in the default mode, salience, and basal ganglia networks in patients with UCPPS, which are moderated by EALs, and associated with clinical symptoms and quality of life (QoL).

Neural correlates of emotional valence processing in Parkinson's disease: dysfunction in the subcortex

Parkinson's disease (PD) is frequently accompanied by cognitive and neuropsychiatric symptoms including impairments in affective processing. Despite this, mechanisms underlying vulnerability to deficits in affective processing remain unclear. In this study, we utilized functional Magnetic Resonance Imaging (fMRI) and an Affective Go-NoGo paradigm, to examine the neural correlates of emotional valence processing in PD. Results suggest that PD is associated with aberrant processing of emotional valence in subcortical limbic structures. Specifically, we found significant group-by-valence interactions in the ventral striatum and amygdala in response to words of differing emotional valence. Our findings contribute to a broader understanding of affective processing in PD and may provide insights into the mechanisms underlying vulnerability to mood disorders in PD.

Network Neuroscience: A Framework for Developing Biomarkers in Psychiatry

Psychiatric disorders are disturbances of cognitive and behavioral processes mediated by the brain. Emerging evidence suggests that accurate biomarkers for psychiatric disorders might benefit from incorporating information regarding multiple brain regions and their interactions with one another, rather than considering local perturbations in brain structure and function alone. Recent advances in the field of applied mathematics generally - and network science specifically - provide a language to capture the complexity of interacting brain regions, and the application of this language to fundamental questions in neuroscience forms the emerging field of network neuroscience. This chapter provides an overview of the use and utility of network neuroscience for building biomarkers in psychiatry. The chapter begins with an overview of the theoretical frameworks and tools that encompass network neuroscience before describing applications of network neuroscience to the study of schizophrenia and major depressive disorder. With reference to work on genetic, molecular, and environmental correlates of network neuroscience features, the promises and challenges of network neuroscience for providing tools that aid in the diagnosis and the evaluation of treatment response in psychiatric disorders are discussed.

Application of Graph Theory for Identifying Connectivity Patterns in Human Brain Networks: A Systematic Review

Background: Analysis of the human connectome using functional magnetic resonance imaging (fMRI) started in the mid-1990s and attracted increasing attention in attempts to discover the neural underpinnings of human cognition and neurological disorders. In general, brain connectivity patterns from fMRI data are classified as statistical dependencies (functional connectivity) or causal interactions (effective connectivity) among various neural units. Computational methods, especially graph theory-based methods, have recently played a significant role in understanding brain connectivity architecture. Objectives: Thanks to the emergence of graph theoretical analysis, the main purpose of the current paper is to systematically review how brain properties can emerge through the interactions of distinct neuronal units in various cognitive and neurological applications using fMRI. Moreover, this article provides an overview of the existing functional and effective connectivity methods used to construct the brain network, along with their advantages and pitfalls. Methods: In this systematic review, the databases Science Direct, Scopus, arXiv, Google Scholar, IEEE Xplore, PsycINFO, PubMed, and SpringerLink are employed for exploring the evolution of computational methods in human brain connectivity from 1990 to the present, focusing on graph theory. The Cochrane Collaboration's tool was used to assess the risk of bias in individual studies. Results: Our results show that graph theory and its implications in cognitive neuroscience have attracted the attention of researchers since 2009 (as the Human Connectome Project launched), because of their prominent capability in characterizing the behavior of complex brain systems. Although graph theoretical approach can be generally applied to either functional or effective connectivity patterns during rest or task performance, to date, most articles have focused on the resting-state functional connectivity. Conclusions: This review provides an insight into how to utilize graph theoretical measures to make neurobiological inferences regarding the mechanisms underlying human cognition and behavior as well as different brain disorders.

A Paradigm for Longitudinal Complex Network Analysis over Patient Cohorts in Neuroscience

The study of complex brain networks, where structural or functional connections are evaluated to create an interconnected representation of the brain, has grown tremendously over the past decade. Much of the statistical network science tools for analyzing brain networks have been developed for cross-sectional studies and for the analysis of static networks. However, with both an increase in longitudinal study designs, as well as an increased interest in the neurological network changes that occur during the progression of a disease, sophisticated methods for longitudinal brain network analysis are needed. We propose a paradigm for longitudinal brain network analysis over patient cohorts, with the key challenge being the adaptation of Stochastic Actor-Oriented Models (SAOMs) to the neuroscience setting. SAOMs are designed to capture network dynamics representing a variety of influences on network change in a continuous-time Markov chain framework. Network dynamics are characterized through both endogenous (i.e., network related) and exogenous effects, where the latter include mechanisms conjectured in the literature. We outline an application to the resting-state fMRI setting with data from the Alzheimers Disease Neuroimaging Initiative (ADNI) study. We draw illustrative conclusions at the subject level and make a comparison between elderly controls and individuals with AD.

Network neurobiology of electroconvulsive therapy in patients with depression

Graph theory, a popular analytic tool for resting state fMRI (rsfMRI) has provided important insights in the neurobiology of depression. We aimed to analyze the changes in the network measures of segregation and integration associated with the administration of ECT in patients with depression and to correlate with both clinical response and cognitive deficits. Changes in normalised clustering coefficient (γ), path length (λ) and small-world (σ) index were explored in 17 patients with depressive episode before 1st and after 6th brief-pulse bifrontal ECT (BFECT) sessions. Significant brain regions were then correlated with differences in clinical and cognitive scales. There was significantly increased γ and σ despite significant increase in λ in several brain regions after ECT in patients with depression. The brain areas revealing significant differences in γ before and after ECT were medial left superior frontal gyrus, left paracentral lobule, right pallidum and left inferior frontal operculum; correlating with changes in verbal fluency, HAM-D scores and delayed verbal memory (last two regions) respectively. BFECT reorganized the brain network topology in patients with depression and made it more segregated and less integrated; these correlated with clinical improvement and associated cognitive deficits.

System-level matching of structural and functional connectomes in the human brain

The brain can be considered as an information processing network, where complex behavior manifests as a result of communication between large-scale functional systems such as visual and default mode networks. As the communication between brain regions occurs through underlying anatomical pathways, it is important to define a "traffic pattern" that properly describes how the regions exchange information. Empirically, the choice of the traffic pattern can be made based on how well the functional connectivity between regions matches the structural pathways equipped with that traffic pattern. In this paper, we present a multimodal connectomics paradigm utilizing graph matching to measure similarity between structural and functional connectomes (derived from dMRI and fMRI data) at node, system, and connectome level. Through an investigation of the brain's structure-function relationship over a large cohort of 641 healthy developmental participants aged 8-22 years, we demonstrate that communicability as the traffic pattern describes the functional connectivity of the brain best, with large-scale systems having significant agreement between their structural and functional connectivity patterns. Notably, matching between structural and functional connectivity for the functionally specialized modular systems such as visual and motor networks are higher as compared to other more integrated systems. Additionally, we show that the negative functional connectivity between the default mode network (DMN) and motor, frontoparietal, attention, and visual networks is significantly associated with its underlying structural connectivity, highlighting the counterbalance between functional activation patterns of DMN and other systems. Finally, we investigated sex difference and developmental changes in brain and observed that similarity between structure and function changes with development.

Towards understanding neural network signatures of motor skill learning in Parkinson's disease and healthy aging

In the past decade, neurorehabilitation has been shown to be an effective therapeutic supplement for patients with Parkinson's disease (PD). However, patients still experience severe problems with the consolidation of learned motor skills. Knowledge on the neural correlates underlying this process is thus essential to optimize rehabilitation for PD. This review investigates the existing studies on neural network connectivity changes in relation to motor learning in healthy aging and PD and critically evaluates the imaging methods used from a methodological point of view. The results indicate that despite neurodegeneration there is still potential to modify connectivity within and between motor and cognitive networks in response to motor training, although these alterations largely bypass the most affected regions in PD. However, so far training-related changes are inferred and possible relationships are not substantiated by brain-behavior correlations. Furthermore, the studies included suffer from many methodological drawbacks. This review also highlights the potential for using neural network measures as predictors for the response to rehabilitation, mainly based on work in young healthy adults. We speculate that future approaches, including graph theory and multimodal neuroimaging, may be more sensitive than brain activation patterns and model-based connectivity maps to capture the effects of motor learning. Overall, this review suggests that methodological developments in neuroimaging will eventually provide more detailed knowledge on how neural networks are modified by training, thereby paving the way for optimized neurorehabilitation for patients.

Multi-scale detection of hierarchical community architecture in structural and functional brain networks

Community detection algorithms have been widely used to study the organization of complex networks like the brain. These techniques provide a partition of brain regions (or nodes) into clusters (or communities), where nodes within a community are densely interconnected with one another. In their simplest application, community detection algorithms are agnostic to the presence of community hierarchies: clusters embedded within clusters of other clusters. To address this limitation, we exercise a multi-scale extension of a common community detection technique, and we apply the tool to synthetic graphs and to graphs derived from human neuroimaging data, including structural and functional imaging data. Our multi-scale community detection algorithm links a graph to copies of itself across neighboring topological scales, thereby becoming sensitive to conserved community organization across levels of the hierarchy. We demonstrate that this method is sensitive to topological inhomogeneities of the graph's hierarchy by providing a local measure of community stability and inter-scale reliability across topological scales. We compare the brain's structural and functional network architectures, and we demonstrate that structural graphs display a more prominent hierarchical community organization than functional graphs. Finally, we build an explicitly multimodal multiplex graph that combines both structural and functional connectivity in a single model, and we identify the topological scales where resting state functional connectivity and underlying structural connectivity show similar versus unique hierarchical community architecture. Together, our results demonstrate the advantages of the multi-scale community detection algorithm in studying hierarchical community structure in brain graphs, and they illustrate its utility in modeling multimodal neuroimaging data.

Age differences in specific neural connections within the Default Mode Network underlie theory of mind

Theory of mind (i.e., the ability to infer others' mental states) - a fundamental social cognitive ability - declines with increasing age. Prior investigations have focused on identifying task-evoked differences in neural activation that underlie these performance declines. However, these declines could also be related to dysregulation of the baseline, or 'intrinsic', functional connectivity of the brain. If so, age differences in intrinsic connectivity may provide novel insight into the mechanisms that contribute to poorer theory of mind in older adults. To examine this possibility, we assessed younger and older adults' theory of mind while they underwent task-based fMRI, as well as the intrinsic functional connectivity measured during resting-state within the (task-defined) theory of mind network. Older adults exhibited poorer theory of mind behavioral performance and weaker intrinsic connectivity within this network compared to younger adults. Intrinsic connectivity between the right temporoparietal junction and the right temporal pole mediated age differences in theory of mind. Specifically, older adults had weaker intrinsic connectivity between right temporoparietal junction and right temporal pole that explained their poorer theory of mind behavioral performance. These findings broaden our understanding of aging and social cognition and reveal more specific mechanisms of how aging impacts theory of mind.

Reconstructing missing complex networks against adversarial interventions

Interactions within complex network components define their operational modes, collective behaviors and global functionality. Understanding the role of these interactions is limited by either sensing methodologies or intentional adversarial efforts that sabotage the network structure. To overcome the partial observability and infer with good fidelity the unobserved network structures (latent subnetworks that are not random samples of the full network), we propose a general causal inference framework for reconstructing network structures under unknown adversarial interventions. We explore its applicability in both biological and social systems to recover the latent structures of human protein complex interactions and brain connectomes, as well as to infer the camouflaged social network structure in a simulated removal process. The demonstrated effectiveness establishes its good potential for capturing hidden information in much broader research domains.

Atypical functional connectivity in adolescents and adults with persistent and remitted ADHD during a cognitive control task

We previously provided initial evidence for cognitive and event-related potential markers of persistence/remission of attention-deficit/hyperactivity disorder (ADHD) from childhood to adolescence and adulthood. Here, using a novel brain-network connectivity approach, we aimed to examine whether task-based functional connectivity reflects a marker of ADHD remission or an enduring deficit unrelated to ADHD outcome. High-density EEG was recorded in a follow-up of 110 adolescents and young adults with childhood ADHD (87 persisters, 23 remitters) and 169 typically developing individuals during an arrow-flanker task, eliciting cognitive control. Functional connectivity was quantified with network-based graph-theory metrics before incongruent (high-conflict) target onset (pre-stimulus), during target processing (post-stimulus) and in the degree of change between pre-stimulus/post-stimulus. ADHD outcome was examined with parent-reported symptoms and impairment using both a categorical (DSM-IV) and a dimensional approach. Graph-theory measures converged in indicating that, compared to controls, ADHD persisters showed increased connectivity in pre-stimulus theta, alpha, and beta and in post-stimulus beta (all p < .01) and reduced pre-stimulus/post-stimulus change in theta connectivity (p < .01). In the majority of indices showing ADHD persister-control differences, ADHD remitters differed from controls (all p < .05) but not from persisters. Similarly, connectivity measures were unrelated to continuous outcome measures of ADHD symptoms and impairment in participants with childhood ADHD. These findings indicate that adolescents and young adults with persistent and remitted ADHD share atypical over-connectivity profiles and reduced ability to modulate connectivity patterns with task demands, compared to controls. Task-based functional connectivity impairments may represent enduring deficits in individuals with childhood ADHD irrespective of diagnostic status in adolescence/young adulthood.

From micro- to macro-structures in multiple sclerosis: what is the added value of diffusion imaging

Diffusion imaging has been instrumental in understanding damage to the central nervous system as a result of its sensitivity to microstructural changes. Clinical applications of diffusion imaging have grown exponentially over the past couple of decades in many neurological and neurodegenerative diseases, such as multiple sclerosis (MS). For several reasons, MS has been extensively researched using advanced neuroimaging techniques, which makes it an 'example disease' to illustrate the potential of diffusion imaging for clinical applications. In addition, MS pathology is characterized by several key processes competing with each other, such as inflammation, demyelination, remyelination, gliosis and axonal loss, enabling the specificity of diffusion to be challenged. In this review, we describe how diffusion imaging can be exploited to investigate micro-, meso- and macro-scale properties of the brain structure and discuss how they are affected by different pathological substrates. Conclusions from the literature are that larger studies are needed to confirm the exciting results from initial investigations before current trends in diffusion imaging can be translated to the neurology clinic. Also, for a comprehensive understanding of pathological processes, it is essential to take a multiple-level approach, in which information at the micro-, meso- and macroscopic scales is fully integrated.

Quantification of structural brain connectivity via a conductance model

Connectomics has proved promising in quantifying and understanding the effects of development, aging and an array of diseases on the brain. In this work, we propose a new structural connectivity measure from diffusion MRI that allows us to incorporate direct brain connections, as well as indirect ones that would not be otherwise accounted for by standard techniques and that may be key for the better understanding of function from structure. From our experiments on the Human Connectome Project dataset, we find that our measure of structural connectivity better correlates with functional connectivity than streamline tractography does, meaning that it provides new structural information related to function. Through additional experiments on the ADNI-2 dataset, we demonstrate the ability of this new measure to better discriminate different stages of Alzheimer's disease. Our findings suggest that this measure is useful in the study of the normal brain structure, and for quantifying the effects of disease on the brain structure.

Building connectomes using diffusion MRI: why, how and but

Why has diffusion MRI become a principal modality for mapping connectomes in vivo? How do different image acquisition parameters, fiber tracking algorithms and other methodological choices affect connectome estimation? What are the main factors that dictate the success and failure of connectome reconstruction? These are some of the key questions that we aim to address in this review. We provide an overview of the key methods that can be used to estimate the nodes and edges of macroscale connectomes, and we discuss open problems and inherent limitations. We argue that diffusion MRI-based connectome mapping methods are still in their infancy and caution against blind application of deep white matter tractography due to the challenges inherent to connectome reconstruction. We review a number of studies that provide evidence of useful microstructural and network properties that can be extracted in various independent and biologically relevant contexts. Finally, we highlight some of the key deficiencies of current macroscale connectome mapping methodologies and motivate future developments.

Fast consensus clustering in complex networks

Algorithms for community detection are usually stochastic, leading to different partitions for different choices of random seeds. Consensus clustering has proven to be an effective technique to derive more stable and accurate partitions than the ones obtained by the direct application of the algorithm. However, the procedure requires the calculation of the consensus matrix, which can be quite dense if (some of) the clusters of the input partitions are large. Consequently, the complexity can get dangerously close to quadratic, which makes the technique inapplicable on large graphs. Here, we present a fast variant of consensus clustering, which calculates the consensus matrix only on the links of the original graph and on a comparable number of additional node pairs, suitably chosen. This brings the complexity down to linear, while the performance remains comparable as the full technique. Therefore, our fast consensus clustering procedure can be applied on networks with millions of nodes and links.

The Challenges of Diagnostic Imaging in the Era of Big Data

The diagnostic imaging field has undergone considerable growth both in terms of technological development and market expansion; with the following increasing production of a considerable amount of data that potentially fully poses diagnostic imaging in the Big data in the context of healthcare. Nevertheless, the mere production of a large amount of data does not automatically permit the real exploitation of their intrinsic value. Therefore, it is necessary to develop digital platforms and applications that favor the correct and advantageous management of diagnostic images such as Big data. This work aims to frame the role of diagnostic imaging in this new scenario, emphasizing the open challenges in exploiting such intense data generation for decision making with Big data analytics.

On the Usage of Brain Atlases in Neuroimaging Research

Brain atlases play a key role in modern neuroimaging analysis of brain structure and function. We review available atlas databases for humans and animals and illustrate common state-of-the-art workflows in neuroimaging research based on image registration. Advances in noninvasive imaging methods, 3D ex vivo microscopy, and image processing are summarized which will eventually close the current resolution gap between brain atlases based on conventional 2D histology and those based on 3D in vivo imaging.

Hemisphere and Gender Differences in the Rich-Club Organization of Structural Networks

Structural and functional differences in brain hemispheric asymmetry have been well documented between female and male adults. However, potential differences in the connectivity patterns of the rich-club organization of hemispheric structural networks in females and males remain to be determined. In this study, diffusion tensor imaging was used to construct hemispheric structural networks in healthy subjects, and graph theoretical analysis approaches were applied to quantify hemisphere and gender differences in rich-club organization. The results showed that rich-club organization was consistently observed in both hemispheres of female and male adults. Moreover, a reduced level of connectivity was found in the left hemisphere. Notably, rightward asymmetries were mainly observed in feeder and local connections among one hub region and peripheral regions, many of which are implicated in visual processing and spatial attention functions. Additionally, significant gender differences were revealed in the rich-club, feeder, and local connections in rich-club organization. These gender-related hub and peripheral regions are involved in emotional, sensory, and cognitive control functions. The topological changes in rich-club organization provide novel insight into the hemisphere and gender effects on white matter connections and underlie a potential network mechanism of hemisphere- and gender-based differences in visual processing, spatial attention and cognitive control.

Discordant attributes of structural and functional brain connectivity in a two-layer multiplex network

Several studies have suggested that functional connectivity (FC) is constrained by the underlying structural connectivity (SC) and mutually correlated. However, not many studies have focused on differences in the network organization of SC and FC, and on how these differences may inform us about their mutual interaction. To explore this issue, we adopt a multi-layer framework, with SC and FC, constructed using Magnetic Resonance Imaging (MRI) data from the Human Connectome Project, forming a two-layer multiplex network. In particular, we examine node strength assortativity within and between the SC and FC layer. We find that, in general, SC is organized assortatively, indicating brain regions are on average connected to other brain regions with similar node strengths. On the other hand, FC shows disassortative mixing. This discrepancy is apparent also among individual resting-state networks within SC and FC. In addition, these patterns show lateralization, with disassortative mixing within FC subnetworks mainly driven from the left hemisphere. We discuss our findings in the context of robustness to structural failure, and we suggest that discordant and lateralized patterns of associativity in SC and FC may provide clues to understand laterality of some neurological dysfunctions and recovery.