The neural basis of time-varying resting-state functional connectivity

Sparse Graph Representation Learning Based on Reinforcement Learning for Personalized Mild Cognitive Impairment (MCI) Diagnosis

Resting-state functional magnetic resonance imaging (rs-fMRI) has gained attention as a reliable technique for investigating the intrinsic function patterns of the brain. It facilitates the extraction of functional connectivity networks (FCNs) that capture synchronized activity patterns among regions of interest (ROIs). Analyzing FCNs enables the identification of distinctive connectivity patterns associated with mild cognitive impairment (MCI). For MCI diagnosis, various sparse representation techniques have been introduced, including statistical- and deep learning-based methods. However, these methods face limitations due to their reliance on supervised learning schemes, which restrict the exploration necessary for probing novel solutions. To overcome such limitation, prior work has incorporated reinforcement learning (RL) to dynamically select ROIs, but effective exploration remains challenging due to the vast search space during training. To tackle this issue, in this study, we propose an advanced RL-based framework that utilizes a divide-and-conquer approach to decompose the FCN construction task into smaller sub-problems in a subject-specific manner, enabling efficient exploration under each sub-problem condition. Additionally, we leverage the learned value function to determine the sparsity level of FCNs, considering individual characteristics of FCNs. We validate the effectiveness of our proposed framework by demonstrating its superior performance in MCI diagnosis on publicly available cohort datasets.

Brain states as wave-like motifs

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

Infraslow dynamic patterns in human cortical networks track a spectrum of external to internal attention

Early efforts to understand the human cerebral cortex focused on localization of function, assigning functional roles to specific brain regions. More recent evidence depicts the cortex as a dynamic system, organized into flexible networks with patterns of spatiotemporal activity corresponding to attentional demands. In functional MRI (fMRI), dynamic analysis of such spatiotemporal patterns is highly promising for providing non-invasive biomarkers of neurodegenerative diseases and neural disorders. However, there is no established neurotypical spectrum to interpret the burgeoning literature of dynamic functional connectivity from fMRI across attentional states. In the present study, we apply dynamic analysis of network-scale spatiotemporal patterns in a range of fMRI datasets across numerous tasks including a left-right moving dot task, visual working memory tasks, congruence tasks, multiple resting state datasets, mindfulness meditators, and subjects watching TV. We find that cortical networks show shifts in dynamic functional connectivity across a spectrum that tracks the level of external to internal attention demanded by these tasks. Dynamics of networks often grouped into a single task positive network show divergent responses along this axis of attention, consistent with evidence that definitions of a single task positive network are misleading. Additionally, somatosensory and visual networks exhibit strong phase shifting along this spectrum of attention. Results were robust on a group and individual level, further establishing network dynamics as a potential individual biomarker. To our knowledge, this represents the first study of its kind to generate a spectrum of dynamic network relationships across such an axis of attention.

Mapping and comparing fMRI connectivity networks across species

Technical advances in neuroimaging, notably in fMRI, have allowed distributed patterns of functional connectivity to be mapped in the human brain with increasing spatiotemporal resolution. Recent years have seen a growing interest in extending this approach to rodents and non-human primates to understand the mechanism of fMRI connectivity and complement human investigations of the functional connectome. Here, we discuss current challenges and opportunities of fMRI connectivity mapping across species. We underscore the critical importance of physiologically decoding neuroimaging measures of brain (dys)connectivity via multiscale mechanistic investigations in animals. We next highlight a set of general principles governing the organization of mammalian connectivity networks across species. These include the presence of evolutionarily conserved network systems, a dominant cortical axis of functional connectivity, and a common repertoire of topographically conserved fMRI spatiotemporal modes. We finally describe emerging approaches allowing comparisons and extrapolations of fMRI connectivity findings across species. As neuroscientists gain access to increasingly sophisticated perturbational, computational and recording tools, cross-species fMRI offers novel opportunities to investigate the large-scale organization of the mammalian brain in health and disease.

Aberrant brain entropy in posttraumatic stress disorder comorbid with major depressive disorder during the coronavirus disease 2019 pandemic

Aim

Previously, neuroimaging studies on comorbid Posttraumatic-Major depression disorder (PTSD-MDD) comorbidity found abnormalities in multiple brain regions among patients. Recent neuroimaging studies have revealed dynamic nature on human brain activity during resting state, and entropy as an indicator of dynamic regularity may provide a new perspective for studying abnormalities of brain function among PTSD-MDD patients. During the COVID-19 pandemic, there has been a significant increase in the number of patients with PTSD-MDD. We have decided to conduct research on resting-state brain functional activity of patients who developed PTSD-MDD during this period using entropy.

Methods

Thirty three patients with PTSD-MDD and 36 matched TCs were recruited. PTSD and depression symptoms were assessed using multiple clinical scales. All subjects underwent functional magnetic resonance imaging (fMRI) scans. And the brain entropy (BEN) maps were calculated using the BEN mapping toolbox. A two-sample t-test was used to compare the differences in the brain entropy between the PTSD-MDD comorbidity group and TC group. Furthermore, correlation analysis was conducted between the BEN changes in patients with PTSD-MDD and clinical scales.

Results

Compared to the TCs, PTSD-MDD patients had a reduced BEN in the right middle frontal orbital gyrus (R_MFOG), left putamen, and right inferior frontal gyrus, opercular part (R_IFOG). Furthermore, a higher BEN in the R_MFOG was related to higher CAPS and HAMD-24 scores in the patients with PTSD-MDD.

Conclusion

The results showed that the R_MFOG is a potential marker for showing the symptom severity of PTSD-MDD comorbidity. Consequently, PTSD-MDD may have reduced BEN in frontal and basal ganglia regions which are related to emotional dysregulation and cognitive deficits.

Development of top-down cortical propagations in youth

Hierarchical processing requires activity propagating between higher- and lower-order cortical areas. However, functional neuroimaging studies have chiefly quantified fluctuations within regions over time rather than propagations occurring over space. Here, we leverage advances in neuroimaging and computer vision to track cortical activity propagations in a large sample of youth (n = 388). We delineate cortical propagations that systematically ascend and descend a cortical hierarchy in all individuals in our developmental cohort, as well as in an independent dataset of densely sampled adults. Further, we demonstrate that top-down, descending hierarchical propagations become more prevalent with greater demands for cognitive control as well as with development in youth. These findings emphasize that hierarchical processing is reflected in the directionality of propagating cortical activity and suggest top-down propagations as a potential mechanism of neurocognitive maturation in youth.

Altered dynamic functional connectivity associates with post-traumatic stress disorder

Research has been looking into neural pathophysiology of post-traumatic stress disorder (PTSD) and dynamic functioning connectivity (dFC) applying resting state functional magnetic resonance imaging (rs-fMRI). Previous studies showed that PTSD related impairments are associated with alterations distributed across different brain regions and disorganized functional connectivity, especially in Default Mode Network and the cerebellar area. In this study, we specifically looked into dFC on a whole brain level, and we focused on critical regions such as DMN and cerebellum. To explore the characteristics of dFC among patients with PTSD, we collected rs-fMRI data from 27 PTSD patients and 30 healthy controls. The study also added a control group of 33 trauma-exposed individuals to further look into trauma impact. Utilizing group spatial independent component analysis (ICA), the dynamic properties on whole brain level were detected with sliding time window approach, and k-means clustering. Two reoccurring FC "States" were identified, with connections being more concentrated on a within-network level in one state and more strongly inter-connected in the other state. Abnormalities in dFC were found within DMN, between DMN and cerebellum, and between DMN and visual network for PTSD patients. The findings were in accordance with the study hypothesis that the dFC alterations might point to deficits in emotional modulation and dysfunctional self-referential thought. Abnormalities in dFC among PTSD patients might also be indicators of PTSD symptoms including depression and anxiety, hypervigilance, impaired cognitive functioning and self-referential information processing.

Vigilance associates with the low-dimensional structure of fMRI data

The human brain exhibits rich dynamics that reflect ongoing functional states. Patterns in fMRI data, detected in a data-driven manner, have uncovered recurring configurations that relate to individual and group differences in behavioral, cognitive, and clinical traits. However, resolving the neural and physiological processes that underlie such measurements is challenging, particularly without external measurements of brain state. A growing body of work points to underlying changes in vigilance as one driver of time-windowed fMRI connectivity states, calculated on the order of tens of seconds. Here we examine the degree to which the low-dimensional spatial structure of instantaneous fMRI activity is associated with vigilance levels, by testing whether vigilance-state detection can be carried out in an unsupervised manner based on individual BOLD time frames. To investigate this question, we first reduce the spatial dimensionality of fMRI data, and apply Gaussian Mixture Modeling to cluster the resulting low-dimensional data without any a priori vigilance information. Our analysis includes long-duration task and resting-state scans that are conducive to shifts in vigilance. We observe a close alignment between low-dimensional fMRI states (data-driven clusters) and measurements of vigilance derived from concurrent electroencephalography (EEG) and behavior. Whole-brain coactivation analysis revealed cortical anti-correlation patterns that resided primarily during higher behavioral- and EEG-defined levels of vigilance, while cortical activity was more often spatially uniform in states corresponding to lower vigilance. Overall, these findings indicate that vigilance states may be detected in the low-dimensional structure of fMRI data, even within individual time frames.

Brain dynamics in triple-network interactions and its relation to multiple cognitive impairments in mild traumatic brain injury

Traumatic brain injury (TBI) disrupt the coordinated activity of triple-network and produce impairments across several cognitive domains. The triple-network model posits a key role of the salience network (SN) that regulates interactions with the central executive network (CEN) and default mode network (DMN). However, the aberrant dynamic interactions among triple-network and associations with neurobehavioral symptoms in mild TBI was still unclear. In present study, we used brain network interaction index (NII) and dynamic functional connectivity to examine the time-varying cross-network interactions among the triple-network in 109 acute patients, 41 chronic patients, and 65 healthy controls. Dynamic cross-network interactions were significantly increased and more variable in mild TBI compared to controls. Crucially, mild TBI exhibited an increased NII as enhanced integrations between the SN and CEN while reduced coupling of the SN with DMN. The increased NII also implied much severer and multiple domains of cognitive impairments at both acute and chronic mild TBI. Abnormities in time-varying engagement of triple-network is a clinically relevant neurobiological signature of psychopathology in mild TBI. The findings provided align with and advance an emerging perspective on the importance of aberrant brain dynamics associated with highly disparate cognitive and behavioral outcomes in trauma.

Applying the Properties of Neurons in Machine Learning: A Brain-like Neural Model with Interactive Stimulation for Data Classification

Some neural models achieve outstanding results in image recognition, semantic segmentation and natural language processing. However, their classification performance on structured and small-scale datasets that do not involve feature extraction is worse than that of traditional algorithms, although they require more time to train. In this paper, we propose a brain-like neural model with interactive stimulation (NMIS) that focuses on data classification. It consists of a primary neural field and a senior neural field that play different cognitive roles. The former is used to correspond to real instances in the feature space, and the latter stores the category pattern. Neurons in the primary field exchange information through interactive stimulation and their activation is transmitted to the senior field via inter-field interaction, simulating the mechanisms of neuronal interaction and synaptic plasticity, respectively. The proposed NMIS is biologically plausible and does not involve complex optimization processes. Therefore, it exhibits better learning ability on small-scale and structured datasets than traditional BP neural networks. For large-scale data classification, a nearest neighbor NMIS (NN_NMIS), an optimized version of NMIS, is proposed to improve computational efficiency. Numerical experiments performed on some UCI datasets show that the proposed NMIS and NN_NMIS are significantly superior to some classification algorithms that are widely used in machine learning.

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

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

Building bridges: simultaneous multimodal neuroimaging approaches for exploring the organization of brain networks

Brain organization is evident across spatiotemporal scales as well as from structural and functional data. Yet, translating from micro- to macroscale (vice versa) as well as between different measures is difficult. Reconciling disparate observations from different modes is challenging because each specializes within a restricted spatiotemporal milieu, usually has bounded organ coverage, and has access to different contrasts. True intersubject biological heterogeneity, variation in experiment implementation (e.g., use of anesthesia), and true moment-to-moment variations in brain activity (maybe attributable to different brain states) also contribute to variability between studies. Ultimately, for a deeper and more actionable understanding of brain organization, an ability to translate across scales, measures, and species is needed. Simultaneous multimodal methods can contribute to bettering this understanding. We consider four modes, three optically based: multiphoton imaging, single-photon (wide-field) imaging, and fiber photometry, as well as magnetic resonance imaging. We discuss each mode as well as their pairwise combinations with regard to the definition and study of brain networks.

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

OBJECTIVE

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

MATERIALS AND METHODS

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

RESULTS

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

CONCLUSIONS

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

Aberrant Cross-Tissue Functional Connectivity in Alzheimer’s Disease: Static, Dynamic, and Directional Properties

Background: BOLD signals in the gray matter (GM) and white matter (WM) are tightly coupled. However, our understanding of the cross-tissue functional network in Alzheimer’s disease (AD) is limited. Objective: We investigated the changes of cross-tissue functional connectivity (FC) metrics for the GM regions susceptible to AD damage. Methods: For each GM region in the default mode (DMN) and limbic networks, we obtained its low-order static FC with any WM region, and the high-order static FC between any two WM regions based on their FC pattern similarity with multiple GM regions. The dynamic and directional properties of cross-tissue FC were then acquired, specifically for the regional pairs whose low- or high-order static FCs showed significant differences between AD and normal control (NC). Moreover, these cross-tissue FC metrics were correlated with voxel-based GM volumes and MMSE in all participants. Results: Compared to NC, AD patients showed decreased low-order static FCs between the intra-hemispheric GM-WM pairs (right ITG-right fornix; left MoFG-left posterior corona radiata), and increased low-order static, dynamic, and directional FCs between the inter-hemispheric GM-WM pairs (right MTG-left superior/posterior corona radiata). The high-order static and directional FCs between the left cingulate bundle-left tapetum were increased in AD, based on their FCs with the GMs of DMN. Those decreased and increased cross-tissue FC metrics in AD had opposite correlations with memory-related GM volumes and MMSE (positive for the decreased and negative for the increased). Conclusion: Cross-tissue FC metrics showed opposite changes in AD, possibly as useful neuroimaging biomarkers to reflect neurodegenerative and compensatory mechanisms.

Dynamic trajectories of connectome state transitions are heritable

The brain’s functional connectome is dynamic, constantly reconfiguring in an individual-specific manner. However, which characteristics of such reconfigurations are subject to genetic effects, and to what extent, is largely unknown. Here, we identified heritable dynamic features, quantified their heritability, and determined their association with cognitive phenotypes. In resting-state fMRI, we obtained multivariate features, each describing a temporal or spatial characteristic of connectome dynamics jointly over a set of connectome states. We found strong evidence for heritability of temporal features, particularly, Fractional Occupancy (FO) and Transition Probability (TP), representing the duration spent in each connectivity configuration and the frequency of shifting between configurations, respectively. These effects were robust against methodological choices of number of states and global signal regression. Genetic effects explained a substantial proportion of phenotypic variance of these features (h² = 0.39, 95% CI = [.24,.54] for FO; h² = 0. 43, 95% CI = [.29,.57] for TP). Moreover, these temporal phenotypes were associated with cognitive performance. Contrarily, we found no robust evidence for heritability of spatial features of the dynamic states (i.e., states’ Modularity and connectivity pattern). Genetic effects may therefore primarily contribute to how the connectome transitions across states, rather than the precise spatial instantiation of the states in individuals. In sum, genetic effects impact the dynamic trajectory of state transitions (captured by FO and TP), and such temporal features may act as endophenotypes for cognitive abilities.

Comparison of Resting-State Functional MRI Methods for Characterizing Brain Dynamics

Resting-state functional MRI (fMRI) exhibits time-varying patterns of functional connectivity. Several different analysis approaches have been developed for examining these resting-state dynamics including sliding window connectivity (SWC), phase synchrony (PS), co-activation pattern (CAP), and quasi-periodic patterns (QPP). Each of these approaches can be used to generate patterns of activity or inter-areal coordination which vary across time. The individual frames can then be clustered to produce temporal groupings commonly referred to as “brain states.” Several recent publications have investigated brain state alterations in clinical populations, typically using a single method for quantifying frame-wise functional connectivity. This study directly compares the results of k-means clustering in conjunction with three of these resting-state dynamics methods (SWC, CAP, and PS) and quantifies the brain state dynamics across several metrics using high resolution data from the human connectome project. Additionally, these three dynamics methods are compared by examining how the brain state characterizations vary during the repeated sequences of brain states identified by a fourth dynamic analysis method, QPP. The results indicate that the SWC, PS, and CAP methods differ in the clusters and trajectories they produce. A clear illustration of these differences is given by how each one results in a very different clustering profile for the 24s sequences explicitly identified by the QPP algorithm. PS clustering is sensitive to QPPs with the mid-point of most QPP sequences grouped into the same single cluster. CAPs are also highly sensitive to QPPs, separating each phase of the QPP sequences into different sets of clusters. SWC (60s window) is less sensitive to QPPs. While the QPPs are slightly more likely to occur during specific SWC clusters, the SWC clustering does not vary during the 24s QPP sequences, the goal of this work is to improve both the practical and theoretical understanding of different resting-state dynamics methods, thereby enabling investigators to better conceptualize and implement these tools for characterizing functional brain networks.

Functional Connectivity of the Brain Across Rodents and Humans

Resting-state functional magnetic resonance imaging (rs-fMRI), which measures the spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal, is increasingly utilized for the investigation of the brain's physiological and pathological functional activity. Rodents, as a typical animal model in neuroscience, play an important role in the studies that examine the neuronal processes that underpin the spontaneous fluctuations in the BOLD signal and the functional connectivity that results. Translating this knowledge from rodents to humans requires a basic knowledge of the similarities and differences across species in terms of both the BOLD signal fluctuations and the resulting functional connectivity. This review begins by examining similarities and differences in anatomical features, acquisition parameters, and preprocessing techniques, as factors that contribute to functional connectivity. Homologous functional networks are compared across species, and aspects of the BOLD fluctuations such as the topography of the global signal and the relationship between structural and functional connectivity are examined. Time-varying features of functional connectivity, obtained by sliding windowed approaches, quasi-periodic patterns, and coactivation patterns, are compared across species. Applications demonstrating the use of rs-fMRI as a translational tool for cross-species analysis are discussed, with an emphasis on neurological and psychiatric disorders. Finally, open questions are presented to encapsulate the future direction of the field.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Altered Dynamic Functional Connectivity in de novo Parkinson’s Disease Patients With Depression

Background

Depression is one of the most prevalent and disturbing non-motor symptoms in Parkinson’s disease (PD), with few dynamic functional connectivity (dFC) features measured in previous studies. Our aim was to investigate the alterations of the dynamics in de novo patients with PD with depression (dPD).

Methods

We performed dFC analysis on the data of resting-state functional MRI from 21 de novo dPD, 34 de novo patients with PD without depression (ndPD), and 43 healthy controls (HCs). Group independent component analysis, a sliding window approach, followed by k-means clustering were conducted to assess functional connectivity states (which represented highly structured connectivity patterns reoccurring over time) and temporal properties for comparison between groups. We further performed dynamic graph-theoretical analysis to examine the variability of topological metrics.

Results

Four distinct functional connectivity states were clustered via dFC analysis. Compared to patients with ndPD and HCs, patients with dPD showed increased fractional time and mean dwell time in state 2, characterized by default mode network (DMN)-dominated and cognitive executive network (CEN)-disconnected patterns. Besides, compared to HCs, patients with dPD and patients with ndPD both showed weaker dynamic connectivity within the sensorimotor network (SMN) in state 4, a regionally densely connected state. We additionally observed that patients with dPD presented less variability in the local efficiency of the network.

Conclusions

Our study demonstrated that altered network connection over time, mainly involving the DMN and CEN, with abnormal dynamic graph properties, may contribute to the presence of depression in patients with PD.

Multi-timepoint pattern analysis: Influence of personality and behavior on decoding context-dependent brain connectivity dynamics

Behavioral traits are rarely considered in task‐evoked functional magnetic resonance imaging (MRI) studies, yet these traits can affect how an individual engages with the task, and thus lead to heterogeneity in task‐evoked brain responses. We aimed to investigate whether interindividual variation in behavior associates with the accuracy of predicting task‐evoked changes in the dynamics of functional brain connectivity measured with functional MRI. We developed a novel method called multi‐timepoint pattern analysis (MTPA), in which binary logistic regression classifiers were trained to distinguish rest from each of 7 tasks (i.e., social cognition, working memory, language, relational, motor, gambling, emotion) based on functional connectivity dynamics measured in 1,000 healthy adults. We found that connectivity dynamics for multiple pairs of large‐scale networks enabled individual classification between task and rest with accuracies exceeding 70%, with the most discriminatory connections relatively unique to each task. Crucially, interindividual variation in classification accuracy significantly associated with several behavioral, cognition and task performance measures. Classification between task and rest was generally more accurate for individuals with higher intelligence and task performance. Additionally, for some of the tasks, classification accuracy improved with lower perceived stress, lower aggression, higher alertness, and greater endurance. We conclude that heterogeneous dynamic adaptations of functional brain networks to changing cognitive demands can be reliably captured as linearly separable patterns by MTPA. Future studies should account for interindividual variation in behavior when investigating context‐dependent dynamic functional connectivity.

Development of functional connectivity within and among the resting-state networks in anesthetized rhesus monkeys

OBJECTIVE

The age-related changes in the resting-state networks (RSNs) exhibited temporally specific patterns in humans, and humans and rhesus monkeys have similar RSNs. We hypothesized that the RSNs in rhesus monkeys experienced similar developmental patterns as humans.

METHODS

We acquired resting-state fMRI data from 62 rhesus monkeys, which were divided into childhood, adolescence, and early adulthood groups. Group independent component analysis (ICA) was used to identify monkey RSNs. We detected the between-group differences in the RSNs and static, dynamic, and effective functional network connections (FNCs) using one-way variance analysis (ANOVA) and post-hoc analysis.

RESULTS

Eight rhesus RSNs were identified, including cerebellum (CN), left and right lateral visual (LVN and RVN), posterior default mode (pDMN), visuospatial (VSN), frontal (FN), salience (SN), and sensorimotor networks (SMN). In internal connections, the CN, SN, FN, and SMN mainly matured in early adulthood. The static FNCs associated with FN, SN, pDMN primarily experienced fast descending slow ascending type (U-shaped) developmental patterns for maturation, and the dynamic FNCs related to pDMN (RVN, CN, and SMN) and SMN (CN) were mature in early adulthood. The effective FNC results showed that the pDMN and VSN (stimulated), SN (inhibited), and FN (first inhibited then stimulated) chiefly matured in early adulthood.

CONCLUSION

We identified eight monkey RSNs, which exhibited similar development patterns as humans. All the RSNs and FNCs in monkeys were not widely changed but fine-tuned. Our study clarified that the progressive synchronization, exploration, and regulation of cognitive RSNs within the pDMN, FN, SN, and VSN denoted potential maturation of the RSNs throughout development. We confirmed the development patterns of RSNs and FNCs would support the use of monkeys as a best animal model for human brain function.

Midazolam and Ketamine Produce Distinct Neural Changes in Memory, Pain, and Fear Networks during Pain

BACKGROUND

Despite the well-known clinical effects of midazolam and ketamine, including sedation and memory impairment, the neural mechanisms of these distinct drugs in humans are incompletely understood. The authors hypothesized that both drugs would decrease recollection memory, task-related brain activity, and long-range connectivity between components of the brain systems for memory encoding, pain processing, and fear learning.

METHODS

In this randomized within-subject crossover study of 26 healthy adults, the authors used behavioral measures and functional magnetic resonance imaging to study these two anesthetics, at sedative doses, in an experimental memory paradigm using periodic pain. The primary outcome, recollection memory performance, was quantified with d' (a difference of z scores between successful recognition versus false identifications). Secondary outcomes were familiarity memory performance, serial task response times, task-related brain responses, and underlying brain connectivity from 17 preselected anatomical seed regions. All measures were determined under saline and steady-state concentrations of the drugs.

RESULTS

Recollection memory was reduced under midazolam (median [95% CI], d' = 0.73 [0.43 to 1.02]) compared with saline (d' = 1.78 [1.61 to 1.96]) and ketamine (d' = 1.55 [1.12 to 1.97]; P < 0.0001). Task-related brain activity was detected under saline in areas involved in memory, pain, and fear, particularly the hippocampus, insula, and amygdala. Compared with saline, midazolam increased functional connectivity to 20 brain areas and decreased to 8, from seed regions in the precuneus, posterior cingulate, and left insula. Compared with saline, ketamine decreased connectivity to 17 brain areas and increased to 2, from 8 seed regions including the hippocampus, parahippocampus, amygdala, and anterior and primary somatosensory cortex.

CONCLUSIONS

Painful stimulation during light sedation with midazolam, but not ketamine, can be accompanied by increased coherence in brain connectivity, even though details are less likely to be recollected as explicit memories.

EDITOR’S PERSPECTIVE

Multimodal EEG-fMRI: advancing insight into large-scale human brain dynamics

Advances in the acquisition and analysis of functional magnetic resonance imaging (fMRI) data are revealing increasingly rich spatiotemporal structure across the human brain. Nonetheless, uncertainty surrounding the origins of fMRI hemodynamic signals, and in the link between large-scale fMRI patterns and ongoing functional states, presently limits the neurobiological conclusions one can draw from fMRI alone. Electroencephalography (EEG) provides complementary information about neural electrical activity and state change, and simultaneously acquiring EEG together with fMRI presents unique opportunities for studying large-scale brain activity and gaining more information from fMRI itself. Here, we discuss recent progress in the use of concurrent EEG-fMRI to enrich the investigation of neural and physiological states and clarify the origins of fMRI hemodynamic signals. Throughout, we outline perspectives on future directions and open challenges.

Modeling and analyzing neural signals with phase variability using Fisher-Rao registration

BACKGROUND

The dynamic time warping (DTW) has recently been introduced to analyze neural signals such as EEG and fMRI where phase variability plays an important role in the data.

NEW METHOD

In this study, we propose to adopt a more powerful method, referred to as the Fisher-Rao Registration (FRR), to study the phase variability.

COMPARISON WITH EXISTING METHODS

We systematically compare FRR with DTW in three aspects: (1) basic framework, (2) mathematical properties, and (3) computational efficiency.

RESULTS

We show that FRR has superior performance in all these aspects and the advantages are well illustrated with simulation examples.

CONCLUSIONS

We then apply the FRR method to two real experimental recordings - one fMRI and one EEG data set. It is found the FRR method properly removes the phase variability in each set. Finally, we use the FRR framework to examine brain networks in these two data sets and the result demonstrates the effectiveness of the new method.

Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI

Achieving a comprehensive understanding of brain function requires multiple imaging modalities with complementary strengths. We present an approach for concurrent widefield optical and functional magnetic resonance imaging. By merging these modalities, we can simultaneously acquire whole-brain blood-oxygen-level-dependent (BOLD) and whole-cortex calcium-sensitive fluorescent measures of brain activity. In a transgenic murine model, we show that calcium predicts the BOLD signal, using a model that optimizes a gamma-variant transfer function. We find consistent predictions across the cortex, which are best at low frequency (0.009-0.08 Hz). Furthermore, we show that the relationship between modality connectivity strengths varies by region. Our approach links cell-type-specific optical measurements of activity to the most widely used method for assessing human brain function.

Resting Brain Fluctuations Are Intrinsically Coupled to Visual Response Dynamics

How do intrinsic brain dynamics interact with processing of external sensory stimuli? We sought new insights using functional magnetic resonance imaging to track spatiotemporal activity patterns at the whole brain level in lightly anesthetized mice, during both resting conditions and visual stimulation trials. Our results provide evidence that quasiperiodic patterns (QPPs) are the most prominent component of mouse resting brain dynamics. These QPPs captured the temporal alignment of anticorrelation between the default mode (DMN)- and task-positive (TPN)-like networks, with global brain fluctuations, and activity in neuromodulatory nuclei of the reticular formation. Specifically, the phase of QPPs prior to stimulation could significantly stratify subsequent visual response magnitude, suggesting QPPs relate to brain state fluctuations. This is the first observation in mice that dynamics of the DMN- and TPN-like networks, and particularly their anticorrelation, capture a brain state dynamic that affects sensory processing. Interestingly, QPPs also displayed transient onset response properties during visual stimulation, which covaried with deactivations in the reticular formation. We conclude that QPPs appear to capture a brain state fluctuation that may be orchestrated through neuromodulation. Our findings provide new frontiers to understand the neural processes that shape functional brain states and modulate sensory input processing.

Reconfiguration of Dynamic Functional Connectivity in Sensory and Perceptual System in Schizophrenia

Schizophrenia is thought as a self-disorder with dysfunctional brain connectivity. This self-disorder is often attributed to high-order cognitive impairment. Yet due to the frequent report of sensorial and perceptual deficits, it has been hypothesized that self-disorder in schizophrenia is dysfunctional communication between sensory and cognitive processes. To further verify this assumption, the present study comprehensively examined dynamic reconfigurations of resting-state functional connectivity (rsFC) in schizophrenia at voxel level, region level, and network levels (102 patients vs. 124 controls). We found patients who show consistently increased rsFC variability in sensory and perceptual system, including visual network, sensorimotor network, attention network, and thalamus at all the three levels. However, decreased variability in high-order networks, such as default mode network and frontal-parietal network were only consistently observed at region and network levels. Taken together, these findings highlighted the rudimentary role of elevated instability of information communication in sensory and perceptual system and attenuated whole-brain integration of high-order network in schizophrenia, which provided novel neural evidence to support the hypothesis of disrupted perceptual and cognitive function in schizophrenia. The foci of effects also highlighted that targeting perceptual deficits can be regarded as the key to enhance our understanding of pathophysiology in schizophrenia and promote new treatment intervention.

Trait and state anxiety are mapped differently in the human brain

Anxiety is a mental state characterized by an intense sense of tension, worry or apprehension, relative to something adverse that might happen in the future. Researchers differentiate aspects of anxiety into state and trait, respectively defined as a more transient reaction to an adverse situation, and as a more stable personality attribute in experiencing events. It is yet unclear whether brain structural and functional features may distinguish these aspects of anxiety. To study this, we assessed 42 healthy participants with the State-Trait Anxiety Inventory and then investigated with MRI to characterize structural grey matter covariance and resting-state functional connectivity (rs-FC). We found several differences in the structural-functional patterns across anxiety types: (1) trait anxiety was associated to both structural covariance of Default Mode Network (DMN), with an increase in dorsal nodes and a decrease in its ventral part, and to rs-FC of DMN within frontal regions; (2) state anxiety, instead, was widely related to rs-FC of Salience Network and of DMN, specifically in its ventral nodes, but not associated with any structural pattern. In conclusion, our study provides evidence of a neuroanatomical and functional distinction between state and trait anxiety. These neural features may be additional markers in future studies evaluating early diagnosis or treatment effects.

Functional MRI Signal Complexity Analysis Using Sample Entropy

Resting-state functional magnetic resonance imaging (rs-fMRI) is an immensely powerful method in neuroscience that uses the blood oxygenation level-dependent (BOLD) signal to record and analyze neural activity in the brain. We examined the complexity of brain activity acquired by rs-fMRI to determine whether it exhibits variation across brain regions. In this study the complexity of regional brain activity was analyzed by calculating the sample entropy of 200 whole-brain BOLD volumes as well as of distinct brain networks, cortical regions, and subcortical regions of these brain volumes. It can be seen that different brain regions and networks exhibit distinctly different levels of entropy/complexity, and that entropy in the brain significantly differs between brains at rest and during task performance.

Concurrent EEG- and fMRI-derived functional connectomes exhibit linked dynamics

Long-range connectivity has become the most studied feature of human functional Magnetic Resonance Imaging (fMRI), yet the spatial and temporal relationship between its whole-brain dynamics and electrophysiological connectivity remains largely unknown. FMRI-derived functional connectivity exhibits spatial reconfigurations or time-varying dynamics at infraslow (<0.1Hz) speeds. Conversely, electrophysiological connectivity is based on cross-region coupling of fast oscillations (~1-100Hz). It is unclear whether such fast oscillation-based coupling varies at infraslow speeds, temporally coinciding with infraslow dynamics across the fMRI-based connectome. If so, does the association of fMRI-derived and electrophysiological dynamics spatially vary over the connectome across the functionally distinct electrophysiological oscillation bands? In two concurrent electroencephalography (EEG)-fMRI resting-state datasets, oscillation-based coherence in all canonical bands (delta through gamma) indeed reconfigured at infraslow speeds in tandem with fMRI-derived connectivity changes in corresponding region-pairs. Interestingly, irrespective of EEG frequency-band the cross-modal tie of connectivity dynamics comprised a large proportion of connections distributed across the entire connectome. However, there were frequency-specific differences in the relative strength of the cross-modal association. This association was strongest in visual to somatomotor connections for slower EEG-bands, and in connections involving the Default Mode Network for faster EEG-bands. Methodologically, the findings imply that neural connectivity dynamics can be reliably measured by fMRI despite heavy susceptibility to noise, and by EEG despite shortcomings of source reconstruction. Biologically, the findings provide evidence that contrast with known territories of oscillation power, oscillation coupling in all bands slowly reconfigures in a highly distributed manner across the whole-brain connectome.

The (Un)Conscious Mouse as a Model for Human Brain Functions: Key Principles of Anesthesia and Their Impact on Translational Neuroimaging

In recent years, technical and procedural advances have brought functional magnetic resonance imaging (fMRI) to the field of murine neuroscience. Due to its unique capacity to measure functional activity non-invasively, across the entire brain, fMRI allows for the direct comparison of large-scale murine and human brain functions. This opens an avenue for bidirectional translational strategies to address fundamental questions ranging from neurological disorders to the nature of consciousness. The key challenges of murine fMRI are: (1) to generate and maintain functional brain states that approximate those of calm and relaxed human volunteers, while (2) preserving neurovascular coupling and physiological baseline conditions. Low-dose anesthetic protocols are commonly applied in murine functional brain studies to prevent stress and facilitate a calm and relaxed condition among animals. Yet, current mono-anesthesia has been shown to impair neural transmission and hemodynamic integrity. By linking the current state of murine electrophysiology, Ca2+ imaging and fMRI of anesthetic effects to findings from human studies, this systematic review proposes general principles to design, apply and monitor anesthetic protocols in a more sophisticated way. The further development of balanced multimodal anesthesia, combining two or more drugs with complementary modes of action helps to shape and maintain specific brain states and relevant aspects of murine physiology. Functional connectivity and its dynamic repertoire as assessed by fMRI can be used to make inferences about cortical states and provide additional information about whole-brain functional dynamics. Based on this, a simple and comprehensive functional neurosignature pattern can be determined for use in defining brain states and anesthetic depth in rest and in response to stimuli. Such a signature can be evaluated and shared between labs to indicate the brain state of a mouse during experiments, an important step toward translating findings across species.

Deep Temporal Organization of fMRI Phase Synchrony Modes Promotes Large-Scale Disconnection in Schizophrenia

Itinerant dynamics of the brain generates transient and recurrent spatiotemporal patterns in neuroimaging data. Characterizing metastable functional connectivity (FC) - particularly at rest and using functional magnetic resonance imaging (fMRI) - has shaped the field of dynamic functional connectivity (DFC). Mainstream DFC research relies on (sliding window) correlations to identify recurrent FC patterns. Recently, functional relevance of the instantaneous phase synchrony (IPS) of fMRI signals has been revealed using imaging studies and computational models. In the present paper, we identify the repertoire of whole-brain inter-network IPS states at rest. Moreover, we uncover a hierarchy in the temporal organization of IPS modes. We hypothesize that connectivity disorder in schizophrenia (SZ) is related to the (deep) temporal arrangement of large-scale IPS modes. Hence, we analyze resting-state fMRI data from 68 healthy controls (HC) and 51 SZ patients. Seven resting-state networks (and their sub-components) are identified using spatial independent component analysis. IPS is computed between subject-specific network time courses, using analytic signals. The resultant phase coupling patterns, across time and subjects, are clustered into eight IPS states. Statistical tests show that the relative expression and mean lifetime of certain IPS states have been altered in SZ. Namely, patients spend (45%) less time in a globally coherent state and a subcortical-centered state, and (40%) more time in states reflecting anticoupling within the cognitive control network, compared to the HC. Moreover, the transition profile (between states) reveals a deep temporal structure, shaping two metastates with distinct phase synchrony profiles. A metastate is a collection of states such that within-metastate transitions are more probable than across. Remarkably, metastate occupation balance is altered in SZ, in favor of the less synchronous metastate that promotes disconnection across networks. Furthermore, the trajectory of IPS patterns is less efficient, less smooth, and more restricted in SZ subjects, compared to the HC. Finally, a regression analysis confirms the diagnostic value of the defined IPS measures for SZ identification, highlighting the distinctive role of metastate proportion. Our results suggest that the proposed IPS features may be used for classification studies and for characterizing phase synchrony modes in other (clinical) populations.

Intrinsic connectome organization across temporal scales: New insights from cross-modal approaches

The discovery of a stable, whole-brain functional connectivity organization that is largely independent of external events has drastically extended our view of human brain function. However, this discovery has been primarily based on functional magnetic resonance imaging (fMRI). The role of this whole-brain organization in fast oscillation-based connectivity as measured, for example, by electroencephalography (EEG) and magnetoencephalography (MEG) is only beginning to emerge. Here, we review studies of intrinsic connectivity and its whole-brain organization in EEG, MEG, and intracranial electrophysiology with a particular focus on direct comparisons to connectome studies in fMRI. Synthesizing this literature, we conclude that irrespective of temporal scale over four orders of magnitude, intrinsic neurophysiological connectivity shows spatial similarity to the connectivity organization commonly observed in fMRI. A shared structural connectivity basis and cross-frequency coupling are possible mechanisms contributing to this similarity. Acknowledging that a stable whole-brain organization governs long-range coupling across all timescales of neural processing motivates researchers to take "baseline" intrinsic connectivity into account when investigating brain-behavior associations, and further encourages more widespread exploration of functional connectomics approaches beyond fMRI by using EEG and MEG modalities.

Dynamic effective connectivity

Metastability is a key source of itinerant dynamics in the brain; namely, spontaneous spatiotemporal reorganization of neuronal activity. This itinerancy has been the focus of numerous dynamic functional connectivity (DFC) analyses - developed to characterize the formation and dissolution of distributed functional patterns over time, using resting state fMRI. However, aside from technical and practical controversies, these approaches cannot recover the neuronal mechanisms that underwrite itinerant (e.g., metastable) dynamics-due to their descriptive, model-free nature. We argue that effective connectivity (EC) analyses are more apt for investigating the neuronal basis of metastability. To this end, we appeal to biologically-grounded models (i.e., dynamic causal modelling, DCM) and dynamical systems theory (i.e., heteroclinic sequential dynamics) to create a probabilistic, generative model of haemodynamic fluctuations. This model generates trajectories in the parametric space of EC modes (i.e., states of connectivity) that characterize functional brain architectures. In brief, it extends an established spectral DCM, to generate functional connectivity data features that change over time. This foundational paper tries to establish the model's face validity by simulating non-stationary fMRI time series and recovering key model parameters (i.e., transition probabilities among connectivity states and the parametric nature of these states) using variational Bayes. These data are further characterized using Bayesian model comparison (within and between subjects). Finally, we consider practical issues that attend applications and extensions of this scheme. Importantly, the scheme operates within a generic Bayesian framework - that can be adapted to study metastability and itinerant dynamics in any non-stationary time series.

The relationship between BOLD and neural activity arises from temporally sparse events

Resting state functional magnetic resonance (rs-fMRI) imaging offers insights into how different brain regions are connected into functional networks. It was recently shown that networks that are almost identical to the ones created from conventional correlation analysis can be obtained from a subset of high-amplitude data, suggesting that the functional networks may be driven by instantaneous co-activations of multiple brain regions rather than ongoing oscillatory processes. The rs-fMRI studies, however, rely on the blood oxygen level dependent (BOLD) signal, which is only indirectly sensitive to neural activity through neurovascular coupling. To provide more direct evidence that the neuronal co-activation events produce the time-varying network patterns seen in rs-fMRI studies, we examined the simultaneous rs-fMRI and local field potential (LFP) recordings in rats performed in our lab over the past several years. We developed complementary analysis methods that focus on either the temporal or spatial domain, and found evidence that the interaction between LFP and BOLD may be driven by instantaneous co-activation events as well. BOLD maps triggered on high-amplitude LFP events resemble co-activation patterns created from rs-fMRI data alone, though the co-activation time points are defined differently in the two cases. Moreover, only LFP events that fall into the highest or lowest thirds of the amplitude distribution result in a BOLD signal that can be distinguished from noise. These findings provide evidence of an electrophysiological basis for the time-varying co-activation patterns observed in previous studies.

The Neural Correlates of Consciousness and Attention: Two Sister Processes of the Brain

During the last three decades our understanding of the brain processes underlying consciousness and attention has significantly improved, mainly because of the advances in functional neuroimaging techniques. Still, caution is needed for the correct interpretation of these empirical findings, as both research and theoretical proposals are hampered by a number of conceptual difficulties. We review some of the most significant theoretical issues concerning the concepts of consciousness and attention in the neuroscientific literature, and put forward the implications of these reflections for a coherent model of the neural correlates of these brain functions. Even though consciousness and attention have an overlapping pattern of neural activity, they should be considered as essentially separate brain processes. The contents of phenomenal consciousness are supposed to be associated with the activity of multiple synchronized networks in the temporo-parietal-occipital areas. Only subsequently, attention, supported by fronto-parietal networks, enters the process of consciousness to provide focal awareness of specific features of reality.

Sampling Rate Effects on Resting State fMRI Metrics

Low image sampling rates used in resting state functional magnetic resonance imaging (rs-fMRI) may cause aliasing of the cardiorespiratory pulsations over the very low frequency (VLF) BOLD signal fluctuations which reflects to functional connectivity (FC). In this study, we examine the effect of sampling rate on currently used rs-fMRI FC metrics. Ultra-fast fMRI magnetic resonance encephalography (MREG) data, sampled with TR 0.1 s, was downsampled to different subsampled repetition times (sTR, range 0.3–3 s) for comparisons. Echo planar k-space sampling (TR 2.15 s) and interleaved slice collection schemes were also compared against the 3D single shot trajectory at 2.2 s sTR. The quantified connectivity metrics included stationary spatial, time, and frequency domains, as well as dynamic analyses. Time domain methods included analyses of seed-based functional connectivity, regional homogeneity (ReHo), coefficient of variation, and spatial domain group level probabilistic independent component analysis (ICA). In frequency domain analyses, we examined fractional and amplitude of low frequency fluctuations. Aliasing effects were spatially and spectrally analyzed by comparing VLF (0.01–0.1 Hz), respiratory (0.12–0.35 Hz) and cardiac power (0.9–1.3 Hz) FFT maps at different sTRs. Quasi-periodic pattern (QPP) of VLF events were analyzed for effects on dynamic FC methods. The results in conventional time and spatial domain analyses remained virtually unchanged by the different sampling rates. In frequency domain, the aliasing occurred mainly in higher sTR (1–2 s) where cardiac power aliases over respiratory power. The VLF power maps suffered minimally from increasing sTRs. Interleaved data reconstruction induced lower ReHo compared to 3D sampling (p < 0.001). Gradient recalled echo-planar imaging (EPI BOLD) data produced both better and worse metrics. In QPP analyses, the repeatability of the VLF pulse detection becomes linearly reduced with increasing sTR. In conclusion, the conventional resting state metrics (e.g., FC, ICA) were not markedly affected by different TRs (0.1–3 s). However, cardiorespiratory signals showed strongest aliasing in central brain regions in sTR 1–2 s. Pulsatile QPP and other dynamic analyses benefit linearly from short TR scanning.

Functional networks are impaired by elevated tau-protein but reversible in a regulatable Alzheimer's disease mouse model

Background

Aggregation of tau proteins is a distinct hallmark of tauopathies and has been a focus of research and clinical trials for Alzheimer’s Disease. Recent reports have pointed towards a toxic effect of soluble or oligomeric tau in the spreading of tau pathology in Alzheimer’s disease. Here we investigated the effects of expressing human tau repeat domain (tauRD) with pro- or anti-aggregant mutations in regulatable transgenic mouse models of Alzheimer’s Disease on the functional neuronal networks and the structural connectivity strength.

Methods

Pro-aggregant and anti-aggregant mice were studied when their mutant tauRD was switched on for 12 months to reach the stage where pro-aggregant mice show cognitive impairment, whereas anti-aggregant mice remained cognitively normal. Then, mutant tauRD was switched off by doxycycline treatment for 8 weeks so that soluble transgenic tau disappeared and cognition recovered in the pro-aggregant mice, although some aggregates remained. At these two time points, at baseline after 12 months of mutant tau expression and after 8 weeks of doxycycline treatment, resting state fMRI and diffusion MRI were used to determine functional neuronal networks and fiber connectivities. Results of the transgenic mice were compared with wildtype littermates.

Results

Functional connectivity was strongly reduced in transgenic animals during mutant tauRD expression, in relation to WT mice. Interestingly, transgenic mice with the non-aggregant tau mutant showed identical functional deficits as the pro-aggregant mice, even though in this case there was no cognitive decline by behavioral testing. Upon 8 weeks doxycycline treatment and transgene switch-off, functional connectivity in both transgenic groups presented complete normalization of functional connectivity strength, equivalent to the situation in WT littermates. Structural connectivity was found only marginally sensitive to mutant tau expression (both pro- and anti-aggregant tauRD) and by doxycycline treatment.

Conclusions

Our in vivo investigations unravel for the first time a strong reduction of functional neuronal networks by the presence of increased soluble rather than fibrillary tau, independent of its intrinsic propensity of aggregation, which is reversible by switching tau off. Our functional MRI study thus is an unexpected in vivo validation of a novel property of tau, while previous results pointed to a role of aggregation propensity for a pathological state by histopathology and cognitive decline. Our results present further evidence for early tauopathy biomarkers or a potential early stage drug target by functional networks analysis.

Electronic supplementary material

The online version of this article (10.1186/s13024-019-0316-6) contains supplementary material, which is available to authorized users.

Brain networks of happiness: dynamic functional connectivity among the default, cognitive and salience networks relates to subjective well-being

Subjective well-being (SWB) reflects the cognitive and emotional evaluations of an individual's life and plays an important role in individual's success in health, work and social relationships. Although previous studies have revealed the spontaneous brain activity underlying SWB, little is known about the relationship between brain network interactions and SWB. The present study investigated the static and dynamic functional connectivity among large-scale brain networks during resting state functional magnetic resonance imaging (fMRI) in relation to SWB in two large independent datasets. The results showed that SWB is negatively correlated with static functional connectivity between the salience network (SN) and the anterior default mode network (DMN). Dynamic functional network connectivity (dFNC) analysis found that SWB is negatively correlated with the fraction of time that participants spent in a brain state characterized by weak cross-network connectivity (between the DMN, SN and frontal-parietal network [FPN]) and strong within-network connectivity (within the DMN and within the FPN). This connectivity profile may account for the good mental adaptability and flexible information communication of people with high levels of SWB. The dFNC results were well replicated with different analysis parameters and further validated in an independent sample. Taken together, these findings reveal that the dynamic interaction between networks involved in self-reflection, emotional regulation and cognitive control underlies SWB.

Brain Map of Intrinsic Functional Flexibility in Anesthetized Monkeys and Awake Humans

Emerging neuroimaging studies emphasize the dynamic organization of spontaneous brain activity in both human and non-human primates, even under anesthesia. In a recent study, we were able to characterize the heterogeneous architecture of intrinsic functional flexibility in the awake, resting human brain using time-resolved analysis and a probabilistic model. However, it is unknown whether this organizational principle is preserved in the anesthetized monkey brain, and how anesthesia affects dynamic and static measurements of spontaneous brain activity. To investigate these issues, we collected resting-state functional magnetic resonance imaging (fMRI) datasets from 178 awake humans and 11 anesthetized monkeys (all healthy). Our recently established method, a complexity measurement (i.e., Shannon entropy) of dynamic functional connectivity patterns of each brain region, was used to map the intrinsic functional flexibility across the cerebral cortex. To further explore the potential effects of anesthesia, we performed time series analysis and correlation analysis between dynamic and static measurements within awake human and anesthetized monkey brains, respectively. We observed a heterogeneous profile of intrinsic functional flexibility in the anesthetized monkey brain, which showed some similarities to that of awake humans (r = 0.30, p = 0.007). However, we found that brain activity in anesthetized monkeys generally shifted toward random fluctuations. Moreover, there is a negative correlation between nodal entropy for the distribution of dynamic functional connectivity patterns and static functional connectivity strength in anesthetized monkeys, but not in awake humans. Our findings indicate that the heterogeneous architecture of intrinsic functional flexibility across cortex probably reflects an evolutionarily conserved aspect of functional brain organization, which persists across levels of cognitive processing (states of consciousness). The coupling between nodal entropy for the distribution of dynamic functional connectivity patterns and static functional connectivity strength may serve as a potential signature of anesthesia. This study not only offers fresh insight into the evolution of brain functional architecture, but also advances our understanding of the dynamics of spontaneous brain activity.

Functional Brain Connectivity Revealed by Sparse Coding of Large-Scale Local Field Potential Dynamics

Exploration of brain dynamics patterns has attracted increasing attention due to its fundamental significance in understanding the working mechanism of the brain. However, due to the lack of effective modeling methods, how the simultaneously recorded LFP can inform us about the brain dynamics remains a general challenge. In this paper, we propose a novel sparse coding based method to investigate brain dynamics of freely-behaving mice from the perspective of functional connectivity, using super-long local field potential (LFP) recordings from 13 distinct regions of the mouse brain. Compared with surrogate datasets, six and four reproducible common functional connectivities were discovered to represent the space of brain dynamics in the frequency bands of alpha and theta respectively. Modeled by a finite state machine, temporal transition framework of functional connectivities was inferred for each frequency band, and evident preference was discovered. Our results offer a novel perspective for analyzing neural recording data at such high temporal resolution and recording length, as common functional connectivities and their transition framework discovered in this work reveal the nature of the brain dynamics in freely behaving mice.

Dynamic resting state fMRI analysis in mice reveals a set of Quasi-Periodic Patterns and illustrates their relationship with the global signal

Time-resolved 'dynamic' over whole-period 'static' analysis of low frequency (LF) blood-oxygen level dependent (BOLD) fluctuations provides many additional insights into the macroscale organization and dynamics of neural activity. Although there has been considerable advancement in the development of mouse resting state fMRI (rsfMRI), very little remains known about its dynamic repertoire. Here, we report for the first time the detection of a set of recurring spatiotemporal Quasi-Periodic Patterns (QPPs) in mice, which show spatial similarity with known resting state networks. Furthermore, we establish a close relationship between several of these patterns and the global signal. We acquired high temporal rsfMRI scans under conditions of low (LA) and high (HA) medetomidine-isoflurane anesthesia. We then employed the algorithm developed by Majeed et al. (2011), previously applied in rats and humans, which detects and averages recurring spatiotemporal patterns in the LF BOLD signal. One type of observed patterns in mice was highly similar to those originally observed in rats, displaying propagation from lateral to medial cortical regions, which suggestively pertain to a mouse Task-Positive like network (TPN) and Default Mode like network (DMN). Other QPPs showed more widespread or striatal involvement and were no longer detected after global signal regression (GSR). This was further supported by diminished detection of subcortical dynamics after GSR, with cortical dynamics predominating. Observed QPPs were both qualitatively and quantitatively determined to be consistent across both anesthesia conditions, with GSR producing the same outcome. Under LA, QPPs were consistently detected at both group and single subject level. Under HA, consistency and pattern occurrence rate decreased, whilst cortical contribution to the patterns diminished. These findings confirm the robustness of QPPs across species and demonstrate a new approach to study mouse LF BOLD spatiotemporal dynamics and mechanisms underlying functional connectivity. The observed impact of GSR on QPPs might help better comprehend its controversial role in conventional resting state studies. Finally, consistent detection of QPPs at single subject level under LA promises a step forward towards more reliable mouse rsfMRI and further confirms the importance of selecting an optimal anesthesia regime.

Spontaneous cognitive processes and the behavioral validation of time-varying brain connectivity

In cognitive neuroscience, focus is commonly placed on associating brain function with changes in objectively measured external stimuli or with actively generated cognitive processes. In everyday life, however, many forms of cognitive processes are initiated spontaneously, without an individual's active effort and without explicit manipulation of behavioral state. Recently, there has been increased emphasis, especially in functional neuroimaging research, on spontaneous correlated activity among spatially segregated brain regions (intrinsic functional connectivity) and, more specifically, on intraindividual fluctuations of such correlated activity on various time scales (time-varying functional connectivity). In this Perspective, we propose that certain subtypes of spontaneous cognitive processes are detectable in time-varying functional connectivity measurements. We define these subtypes of spontaneous cognitive processes and review evidence of their representations in time-varying functional connectivity from studies of attentional fluctuations, memory reactivation, and effects of baseline states on subsequent perception. Moreover, we describe how these studies are critical to validating the use of neuroimaging tools (e.g., fMRI) for assessing ongoing brain network dynamics. We conclude that continued investigation of the behavioral relevance of time-varying functional connectivity will be beneficial both in the development of comprehensive neural models of cognition, and in informing on best practices for studying brain network dynamics.

Dissociating tinnitus patients from healthy controls using resting-state cyclicity analysis and clustering

Chronic tinnitus is a common and sometimes debilitating condition that lacks scientific consensus on physiological models of how the condition arises as well as any known cure. In this study, we applied a novel cyclicity analysis, which studies patterns of leader-follower relationships between two signals, to resting-state functional magnetic resonance imaging (rs-fMRI) data of brain regions acquired from subjects with and without tinnitus. Using the output from the cyclicity analysis, we were able to differentiate between these two groups with 58–67% accuracy by using a partial least squares discriminant analysis. Stability testing yielded a 70% classification accuracy for identifying individual subjects’ data across sessions 1 week apart. Additional analysis revealed that the pairs of brain regions that contributed most to the dissociation between tinnitus and controls were those connected to the amygdala. In the controls, there were consistent temporal patterns across frontal, parietal, and limbic regions and amygdalar activity, whereas in tinnitus subjects, this pattern was much more variable. Our findings demonstrate a proof-of-principle for the use of cyclicity analysis of rs-fMRI data to better understand functional brain connectivity and to use it as a tool for the differentiation of patients and controls who may differ on specific traits.

Chronic tinnitus is a common, yet poorly understood, condition without a known cure. Understanding differences in the functioning of brains of tinnitus patients and controls may lead to better knowledge regarding the physiology of the condition and to subsequent treatments. There are many ways to characterize relationships between neural activity in different parts of the brain. Here, we apply a novel method, called cyclicity analysis, to functional MRI data obtained from tinnitus patients and controls over a period of wakeful rest. Cyclicity analysis lends itself to interpretation as analysis of temporal orderings between elements of time-series data; it is distinct from methods like periodicity analysis or time correlation analysis in that its theoretical underpinnings are invariant to changes in time scales of the generative process. In this proof-of-concept study, we use the feature generated from the cyclicity analysis of the fMRI data to investigate group level differences between tinnitus patients and controls. Our findings indicate that temporal ordering of regional brain activation is much more consistent in the control population than in tinnitus population. We also apply methods of classification from machine learning to differentiate between the two populations with moderate amount of success.

Principal States of Dynamic Functional Connectivity Reveal the Link Between Resting-State and Task-State Brain: An fMRI Study

Task-related reorganization of functional connectivity (FC) has been widely investigated. Under classic static FC analysis, brain networks under task and rest have been demonstrated a general similarity. However, brain activity and cognitive process are believed to be dynamic and adaptive. Since static FC inherently ignores the distinct temporal patterns between rest and task, dynamic FC may be more a suitable technique to characterize the brain’s dynamic and adaptive activities. In this study, we adopted [Formula: see text]-means clustering to investigate task-related spatiotemporal reorganization of dynamic brain networks and hypothesized that dynamic FC would be able to reveal the link between resting-state and task-state brain organization, including broadly similar spatial patterns but distinct temporal patterns. In order to test this hypothesis, this study examined the dynamic FC in default-mode network (DMN) and motor-related network (MN) using Blood-Oxygenation-Level-Dependent (BOLD)-fMRI data from 26 healthy subjects during rest (REST) and a hand closing-and-opening (HCO) task. Two principal FC states in REST and one principal FC state in HCO were identified. The first principal FC state in REST was found similar to that in HCO, which appeared to represent intrinsic network architecture and validated the broadly similar spatial patterns between REST and HCO. However, the second FC principal state in REST with much shorter “dwell time” implied the transient functional relationship between DMN and MN during REST. In addition, a more frequent shifting between two principal FC states indicated that brain network dynamically maintained a “default mode” in the motor system during REST, whereas the presence of a single principal FC state and reduced FC variability implied a more temporally stable connectivity during HCO, validating the distinct temporal patterns between REST and HCO. Our results further demonstrated that dynamic FC analysis could offer unique insights in understanding how the brain reorganizes itself during rest and task states, and the ways in which the brain adaptively responds to the cognitive requirements of tasks.

Quasi-Periodic Patterns of Neural Activity improve Classification of Alzheimer's Disease in Mice

Resting state (rs)fMRI allows measurement of brain functional connectivity and has identified default mode (DMN) and task positive (TPN) network disruptions as promising biomarkers for Alzheimer's disease (AD). Quasi-periodic patterns (QPPs) of neural activity describe recurring spatiotemporal patterns that display DMN with TPN anti-correlation. We reasoned that QPPs could provide new insights into AD network dysfunction and improve disease diagnosis. We therefore used rsfMRI to investigate QPPs in old TG2576 mice, a model of amyloidosis, and age-matched controls. Multiple QPPs were determined and compared across groups. Using linear regression, we removed their contribution from the functional scans and assessed how they reflected functional connectivity. Lastly, we used elastic net regression to determine if QPPs improved disease classification. We present three prominent findings: (1) Compared to controls, TG2576 mice were marked by opposing neural dynamics in which DMN areas were anti-correlated and displayed diminished anti-correlation with the TPN. (2) QPPs reflected lowered DMN functional connectivity in TG2576 mice and revealed significantly decreased DMN-TPN anti-correlations. (3) QPP-derived measures significantly improved classification compared to conventional functional connectivity measures. Altogether, our findings provide insight into the neural dynamics of aberrant network connectivity in AD and indicate that QPPs might serve as a translational diagnostic tool.

Stimulus Dependent Dynamic Reorganization of the Human Face Processing Network

Using the "face inversion effect", a hallmark of face perception, we examined network mechanisms supporting face representation by tracking functional magnetic resonance imaging (fMRI) stimulus-dependent dynamic functional connectivity within and between brain networks associated with the processing of upright and inverted faces. We developed a novel approach adapting the general linear model (GLM) framework classically used for univariate fMRI analysis to capture stimulus-dependent fMRI dynamic connectivity of the face network. We show that under the face inversion manipulation, the face and non-face networks have complementary roles that are evident in their stimulus-dependent dynamic connectivity patterns as assessed by network decomposition into components or communities. Moreover, we show that connectivity patterns are associated with the behavioral face inversion effect. Thus, we establish "a network-level signature" of the face inversion effect and demonstrate how a simple physical transformation of the face stimulus induces a dramatic functional reorganization across related brain networks. Finally, we suggest that the dynamic GLM network analysis approach, developed here for the face network, provides a general framework for modeling the dynamics of blocked stimulus-dependent connectivity experimental designs and hence can be applied to a host of neuroimaging studies.