Abnormalities of intrinsic functional connectivity in autism spectrum disorders

Random forest and Shapley Additive exPlanations predict oxytocin targeted effects on brain functional networks involved in salience and sensorimotor processing, in a randomized clinical trial in autism

Intranasal oxytocin (IN-OXT) has shown some promises in rescuing social deficits in autism spectrum disorder (ASD) as well as some inconsistencies in long-term trials. We conducted a target engagement study to study the precise effects of different doses of IN-OXT on brain resting-state functional connectivity (rsFC) in ASD. We examined the effects of varying doses of IN-OXT (0 IU, 8 IU, 24 IU, 48 IU) on rsFC in a double-blind, placebo-controlled, within-subject design in 30 male adults with ASD and 17 neurotypical controls (NT) receiving placebo. Random forest analysis was used to classify individuals as ASD or NT. Shapely Additive explanations values were calculated to rank brain functional networks by level of contribution to ASD deficits and to evaluate IN-OXT dose effects. The model predicted ASD diagnosis with an AUC of 94%. Hypoconnectivity between salience/empathy and visual networks, and hyperconnectivity between reward and sensorimotor networks and theory of mind networks were among the strongest predictors of ASD deficits. IN-OXT had a dose-dependent effect on rescuing both deficits described above. Overall, 48 IU dose was more effective, and 24 IU dose was more effective in those who have lower DNA OXT receptor methylation and lower severity of clinical symptoms. Higher doses of OXT might be necessary to enhance empathic responses, and ASD individuals with less support needs and with a preserved OXT system might benefit most from OXT treatment. Applying machine learning approaches in OXT research can provide data-driven unbiased results that can inform future clinical trials.

Examining the relationship between functional connectivity and broader autistic traits in non-autistic children

In the current study, we used functional near-infrared spectroscopy (fNIRS) to examine functional connectivity (FC) in relation to measures of cognitive flexibility and autistic features in non-autistic children. Previous research suggests that disruptions in FC between brain regions may underlie the cognitive and behavioral traits of autism. Moreover, research has identified a broader autistic phenotype (BAP), which refers to a set of behavioral traits that fall along a continuum of behaviors typical for autism but which do not cross a clinically relevant threshold. Thus, by examining FC in relation to the BAP in non-autistic children, we can better understand the spectrum of behaviors related to this condition and their neural basis. Results indicated age-related differences in performance across three measures of cognitive flexibility, as expected given the rapid development of this skill within this time period. Additionally, results showed that across the flexibility tasks, measures of autistic traits were associated with weaker FC along the executive control network, though task performance was not associated with FC. These results suggest that behavioral scores may be less sensitive than neural measures to autistic traits. Further, these results corroborate the use of broader autistic traits and the BAP to better understand disruptions to neural function associated with autism.

The Impact of Atlas Parcellation on Functional Connectivity Analysis Across Six Psychiatric Disorders

Neuropsychiatric disorders are associated with altered functional connectivity (FC); however, the reported regional patterns of functional alterations suffered from low replicability and high variability. This is partly because of differences in the atlas and delineation techniques used to measure FC-related deficits within/across disorders. We systematically investigated the impact of the brain parcellation approach on the FC-based brain network analysis. We focused on identifying the replicable FCs using three structural brain atlases, including Automated Anatomical Labeling (AAL), Brainnetome atlas (BNA) and HCP_MMP_1.0, and four functional brain parcellation approaches: Yeo-Networks (Yeo), Gordon parcel (Gordon) and two Schaefer parcelletions, among correlation, group difference, and classification tasks in six neuropsychiatric disorders: attention deficit and hyperactivity disorder (ADHD, n = 340), autism spectrum disorder (ASD, n = 513), schizophrenia (SZ, n = 200), schizoaffective disorder (SAD, n = 142), bipolar disorder (BP, n = 172), and major depression disorder (MDD, n = 282). Our cross-atlas/disorder analyses demonstrated that frontal-related FC deficits were reproducible in all disorders, independent of the atlasing approach; however, replicable FC extraction in other areas and the classification accuracy were affected by the parcellation schema. Overall, functional atlases with finer granularity performed better in classification tasks. Specifically, the Schaefer atlases generated the most repeatable FC deficit patterns across six illnesses. These results indicate that frontal-related FCs may serve as potential common and robust neuro-abnormalities across 6 psychiatric disorders. Furthermore, in order to improve the replicability of rsfMRI-based FC analyses, this study suggests the use of functional templates at larger granularity.

Default Mode Network Functional Connectivity As a Transdiagnostic Biomarker of Cognitive Function

The default mode network (DMN) is intricately linked with processes such as self-referential thinking, episodic memory recall, goal-directed cognition, self-projection, and theory of mind. In recent years, there has been a surge in the number of studies examining its functional connectivity, particularly its relationship with frontoparietal networks involved in top-down attention, executive function, and cognitive control. The fluidity in switching between these internal and external modes of processing, which is highlighted by anticorrelated functional connectivity, has been proposed as an indicator of cognitive health. Due to the ease of estimation of functional connectivity-based measures through resting-state functional magnetic resonance imaging paradigms, there is now a wealth of large-scale datasets, paving the way for standardized connectivity benchmarks. In this review, we explore the promising role of DMN connectivity metrics as potential biomarkers of cognitive state across attention, internal mentation, mind wandering, and meditation states and investigate deviations in trait-level measures across aging and in clinical conditions such as Alzheimer's disease, Parkinson's disease, depression, attention-deficit/hyperactivity disorder, and others. We also tackle the issue of reliability of network estimation and functional connectivity and share recommendations for using functional connectivity measures as a biomarker of cognitive health.

Age-related changes in brain signal variability in autism spectrum disorder

BACKGROUND

Brain signal variability (BSV) is an important understudied aspect of brain function linked to cognitive flexibility and adaptive behavior. Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by social communication difficulties and restricted and repetitive behaviors (RRBs). While atypical brain function has been identified in individuals with ASD using fMRI task-activation and functional connectivity approaches, little is known about age-related relationships with resting-state BSV and repetitive behaviors in ASD.

METHODS

We conducted a cross-sectional examination of resting-state BSV and its relationship with age and RRBs in a cohort of individuals with Autism Brain Imaging Data Exchange (n = 351) and typically developing (TD) individuals (n = 402) aged 5-50 years obtained from the Autism Brain Imaging Data Exchange. RRBs were assessed using the Autism Diagnostic Interview-Revised (ADI-RRB) scale. BSV was quantified using the root-mean-square successive difference (rMSSD) of the resting-state fMRI time series. We examined categorical group differences in rMSSD between ASD and TD groups, controlling for both linear and quadratic age. To identify dimensional relationships between age, group, and rMSSD, we utilized interaction regressors for group x age and group x quadratic age. Within a subset of individuals with ASD (269 subjects), we explored the relationship between rMSSD and ADI-RRB scores, both with and without age considerations. The relationship between rMSSD and ADI-RRB scores was further analyzed while accounting for linear and quadratic age. Additionally, we investigated the relationship between BSV, age, and ADI-RRB scores using interaction regressors for age x RRB and quadratic age x RRB.

RESULTS

When controlling for linear age effects, we observed significant group differences between individuals with ASD and TD individuals in the default-mode network (DMN) and visual network, with decreased BSV in ASD. Similarly, controlling for quadratic age effects revealed significant group differences in the DMN and visual network. In both cases, individuals with ASD showed decreased BSV compared with TD individuals in these brain regions. The group × age interaction demonstrated significant group differences in the DMN, and visual network brain areas, indicating that rMSSD was greater in older individuals compared with younger individuals in the ASD group, while rMSSD was greater in younger individuals compared with older individuals in the TD group. The group × quadratic age interaction showed significant differences in the brain regions included in DMN, with an inverted U-shaped rMSSD-age relationship in ASD (higher rMSSD in younger individuals that slightly increased into middle age before decreasing) and a U-shaped rMSSD-age relationship in TD (higher rMSSD in younger and older individuals compared with middle-aged individuals). When controlling for linear and quadratic age effects, we found a significant positive association between rMSSD and ADI-RRB scores in brain regions within the DMN, salience, and visual network. While no significant results were observed for the linear age × RRB interaction, a significant association between quadratic age and ADI-RRB scores emerged in the DMN, dorsal attention network, and sensorimotor network. Individuals with high ADI-RRB scores exhibited an inverted U-shaped relationship between rMSSD and age, with lower rMSSD levels observed in both younger and older individuals, and higher rMSSD in middle-aged individuals. Those with mid-range ADI-RRB scores displayed a weak inverted U-shaped rMSSD-age association. In contrast, individuals with low ADI-RRB scores showed a U-shaped rMSSD-age association, with higher rMSSD levels in younger and older individuals, but a lower rMSSD in middle-aged individuals.

CONCLUSION

These findings highlight age-related atypical BSV patterns in ASD and their association with repetitive behaviors, contributing to the growing literature on understanding alterations in functional brain maturation in ASD.

MHNet: Multi-view High-Order Network for Diagnosing Neurodevelopmental Disorders Using Resting-State fMRI

Deep learning models have shown promise in diagnosing neurodevelopmental disorders (NDD) like ASD and ADHD. However, many models either use graph neural networks (GNN) to construct single-level brain functional networks (BFNs) or employ spatial convolution filtering for local information extraction from rs-fMRI data, often neglecting high-order features crucial for NDD classification. We introduce a Multi-view High-order Network (MHNet) to capture hierarchical and high-order features from multi-view BFNs derived from rs-fMRI data for NDD prediction. MHNet has two branches: the Euclidean Space Features Extraction (ESFE) module and the Non-Euclidean Space Features Extraction (Non-ESFE) module, followed by a Feature Fusion-based Classification (FFC) module for NDD identification. ESFE includes a Functional Connectivity Generation (FCG) module and a High-order Convolutional Neural Network (HCNN) module to extract local and high-order features from BFNs in Euclidean space. Non-ESFE comprises a Generic Internet-like Brain Hierarchical Network Generation (G-IBHN-G) module and a High-order Graph Neural Network (HGNN) module to capture topological and high-order features in non-Euclidean space. Experiments on three public datasets show that MHNet outperforms state-of-the-art methods using both AAL1 and Brainnetome Atlas templates. Extensive ablation studies confirm the superiority of MHNet and the effectiveness of using multi-view fMRI information and high-order features. Our study also offers atlas options for constructing more sophisticated hierarchical networks and explains the association between key brain regions and NDD. MHNet leverages multi-view feature learning from both Euclidean and non-Euclidean spaces, incorporating high-order information from BFNs to enhance NDD classification performance.

Subregion-specific thalamocortical functional connectivity, executive function, and social behavior in children with autism spectrum disorders

The thalamus has extensive cortical connections and is an integrative hub for cognitive functions governing social behavior. This study examined (1) associations between thalamocortical resting-state functional connectivity (RSFC) and social behavior in children and (2) how various executive function (EF) subdomains mediate the association between thalamocortical RSFC and social behavior. Children from the autism brain imaging data exchange (ABIDE) initiative with neuroimaging, behavioral, and demographic data were included in our study (age < 14, ASD; n = 207, typically developing; n = 259). Thalamocortical RSFC was examined for associations with social communication and interaction (SCI) scores (SRS; social responsiveness scale) using Spearman's rank-order correlation, first in ASD children and then in typically developing children. This was followed by a more granular analysis at the thalamic subregion level. We then examined the mediating roles of eight EF subdomains in ASD children (n = 139). Right thalamus-default mode network (DMN) RSFC was significantly associated with SCI scores in ASD children (ρ = 0.23, pFDR = 0.012), primarily driven by the medial (ρ = 0.22, pFDR = 0.013), ventral (ρ = 0.17, pFDR = 0.036), and intralaminar (ρ = 0.17, pFDR = 0.036) thalamic subregions. Cognitive flexibility (ACME = 0.13, punc = 0.016) and emotional control (ACME = 0.08, punc = 0.020) significantly mediated the association between right thalamus-DMN RSFC and SCI scores. This study provided novel insights into the association between thalamocortical RSFC and social behavior in ASD children at the thalamic subregion level, providing higher levels of precision in brain-behavior mapping. Cognitive flexibility and emotion regulation were highlighted as potential targets to ameliorate the downstream effects of altered thalamocortical connectivity to improve social outcomes in ASD children.

Abnormalities in cerebellar subregions' volume and cerebellocerebral structural covariance in autism spectrum disorder

The cerebellum plays a crucial role in functions, including sensory-motor coordination, cognition, and emotional processing. Compared to the neocortex, the human cerebellum exhibits a protracted developmental trajectory. This delayed developmental timeline may lead to increased sensitivity of the cerebellum to external influences, potentially extending the vulnerability period for neurological disorders. Abnormal cerebellar development in individuals with autism has been confirmed, and these atypical cerebellar changes may affect the development of the neocortex. However, due to the heterogeneity of autism spectrum disorder (ASD), the regional changes in the cerebellum and cerebellocerebral structural relationship remain unknown. To address these issues, we utilized imaging methods optimized for the cerebellum and cerebrum on 817 individuals aged 5-18 years in the ABIDE II dataset. After FDR correction, significant differences between groups were found in the right crus II/VIIB and vermis VI-VII. Structural covariance analysis revealed enhanced structural covariance in individuals with autism between the cerebellum and parahippocampal gyrus, pars opercularis, and transverse temporal gyrus in the right hemisphere after FDR correction. Furthermore, the structural covariance between the cerebellum and some regions of the cerebrum varied across sexes. A significant increase in structural covariance between the cerebellum and specific subcortical structures was also observed in individuals with ASD. Our study found atypical patterns in the structural covariance between the cerebellum and cerebrum in individuals with autism, which suggested that the underlying pathological processes of ASD might concurrently affect these brain regions. This study provided insight into the potential of cerebellocerebral pathways as therapeutic targets for ASD.

Social behavior in ASD males: The interplay between cognitive flexibility, working memory, and functional connectivity deviations

Autism spectrum disorder (ASD) is highly heterogeneous in presentation. While abnormalities in brain functional connectivity are consistently observed in autistic males, the neurobiological basis underlying the different domains of autism symptoms is unclear. In this study, we evaluated whether individual variations in functional connectivity deviations map to social behavior in ASD males. Using neuroimaging data from the Autism Brain Imaging Data Exchange (ABIDE), we modeled normative trajectories of between-network resting-state functional connectivity (rsFC) in non-ASD males across childhood (n = 321). These normative charts were then applied to ASD males (n = 418) to calculate individual deviation scores (z-scores) that reflect the degree of rsFC atypicality. Deviations in rsFC patterns among the default mode network (DMN), ventral attention network (VAN), frontoparietal network (FPN), and somatomotor network (SMN) were associated with distinct dimensions of social behavior. Cognitive flexibility and working memory mediated the association between VANxDMN z-scores and social behavioral problems. Our findings underscore the potential of normative models to identify atypical brain connectivity at an individual level, revealing the neurobiological patterns associated with social behavioral problems in ASD that are critical for precision diagnosis and intervention. Social outcomes in ASD males may be improved by targeting cognitive flexibility and working memory.

Increased heterogeneity and task-related reconfiguration of functional connectivity during a lexicosemantic task in autism

Autism spectrum disorder (ASD) is highly heterogeneous in etiology and clinical presentation. Findings on intrinsic functional connectivity (FC) or task-induced FC in ASD have been inconsistent including both over- and underconnectivity and diverse regional patterns. As FC patterns change across different cognitive demands, a novel and more comprehensive approach to network architecture in ASD is to examine the change in FC patterns between rest and task states, referred to as reconfiguration. This approach is suitable for investigating inefficient network connectivity that may underlie impaired behavioral functioning in clinical disorders. We used functional magnetic resonance imaging (fMRI) to examine FC reconfiguration during lexical processing, which is often affected in ASD, with additional focus on interindividual variability. Thirty adolescents with ASD and a matched group of 23 typically developing (TD) participants completed a lexicosemantic decision task during fMRI, using multiecho-multiband pulse sequences with advanced BOLD signal sensitivity and artifact removal. Regions of interest (ROIs) were selected based on task-related activation across both groups, and FC and reconfiguration were compared between groups. The ASD group showed increased interindividual variability and overall greater reconfiguration than the TD group. An ASD subgroup with typical performance accuracy (at the level of TD participants) showed reduced similarity and typicality of FC during the task. In this ASD subgroup, greater FC reconfiguration was associated with increased language skills. Findings suggest that intrinsic functional networks in ASD may be inefficiently organized for lexicosemantic decisions and may require greater reconfiguration during task processing, with high performance levels in some individuals being achieved through idiosyncratic mechanisms.

Gray Matter Volume Correlates of Co-Occurring Depression in Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) involves neurodevelopmental syndromes with significant deficits in communication, motor behaviors, emotional and social comprehension. Often, individuals with ASD exhibit co-occurring depression characterized by a change in mood and diminished interest in previously enjoyable activities. Due to communicative challenges and a lack of appropriate assessments in this cohort, co-occurring depression can often go undiagnosed during routine clinical examinations and, thus, its management neglected. The literature on co-occurring depression in adults with ASD is limited. Therefore, understanding the neural basis of the co-occurring psychopathology of depression in ASD is crucial for identifying brain-based markers for its timely and effective management. Using structural MRI and phenotypic data from the Autism Brain Imaging Data Exchange (ABIDE II) repository, we examined the pattern of relationship regional grey matter volume (rGMV) has with co-occurring depression and autism severity within regions of a priori interest in adults with ASD (n = 44; age = 17-28 years). Further, we performed an exploratory analysis of the rGMV differences between ASD and matched typically developed (TD, n = 39; age = 18-31 years) samples. The severity of co-occurring depression correlated negatively with the rGMV of the right thalamus. Additionally, a significant interaction was evident between the severity of co-occurring depression and core ASD symptoms towards explaining the rGMV in the left cerebellum crus II. The results further the understanding of the neurobiological underpinnings of co-occurring depression in adults with ASD towards exploring neuroimaging-based biomarkers in the same cohort.

MAFT-SO: A novel multi-atlas fusion template based on spatial overlap for ASD diagnosis

Autism spectrum disorder (ASD) is a common neurological condition. Early diagnosis and treatment are essential for enhancing the life quality of individuals with ASD. However, most existing studies either focus solely on the brain networks of subjects within a single atlas or merely employ simple matrix concatenation to represent the fusion of multi-atlas. These approaches neglected the natural spatial overlap that exists between brain regions across multi-atlas and did not fully capture the comprehensive information of brain regions under different atlases. To tackle this weakness, in this paper, we propose a novel multi-atlas fusion template based on spatial overlap degree of brain regions, which aims to obtain a comprehensive representation of brain networks. Specifically, we formally define a measurement of the spatial overlap among brain regions across different atlases, named spatial overlap degree. Then, we fuse the multi-atlas to obtain brain networks of each subject based on spatial overlap. Finally, the GCN is used to perform the final classification. The experimental results on Autism Brain Imaging Data Exchange (ABIDE) demonstrate that our proposed method achieved an accuracy of 0.757. Overall, our method outperforms SOTA methods in ASD/TC classification.

BrainNPT: Pre-Training Transformer Networks for Brain Network Classification

Deep learning methods have advanced quickly in brain imaging analysis over the past few years, but they are usually restricted by the limited labeled data. Pre-trained model on unlabeled data has presented promising improvement in feature learning in many domains, such as natural language processing. However, this technique is under-explored in brain network analysis. In this paper, we focused on pre-training methods with Transformer networks to leverage existing unlabeled data for brain functional network classification. First, we proposed a Transformer-based neural network, named as BrainNPT, for brain functional network classification. The proposed method leveraged token as a classification embedding vector for the Transformer model to effectively capture the representation of brain networks. Second, we proposed a pre-training framework for BrainNPT model to leverage unlabeled brain network data to learn the structure information of brain functional networks. The results of classification experiments demonstrated the BrainNPT model without pre-training achieved the best performance with the state-of-the-art models, and the BrainNPT model with pre-training strongly outperformed the state-of-the-art models. The pre-training BrainNPT model improved 8.75% of accuracy compared with the model without pre-training. We further compared the pre-training strategies and the data augmentation methods, analyzed the influence of the parameters of the model, and explained the trained model.

Leveraging Brain Modularity Prior for Interpretable Representation Learning of fMRI

Resting-state functional magnetic resonance imaging (rs-fMRI) can reflect spontaneous neural activities in the brain and is widely used for brain disorder analysis. Previous studies focus on extracting fMRI representations using machine/deep learning methods, but these features typically lack biological interpretability. The human brain exhibits a remarkable modular structure in spontaneous brain functional networks, with each module comprised of functionally interconnected brain regions-of-interest (ROIs). However, existing learning-based methods cannot adequately utilize such brain modularity prior. In this paper, we propose a brain modularity-constrained dynamic representation learning framework for interpretable fMRI analysis, consisting of dynamic graph construction, dynamic graph learning via a novel modularity-constrained graph neural network (MGNN), and prediction and biomarker detection. The designed MGNN is constrained by three core neurocognitive modules (i.e., salience network, central executive network, and default mode network), encouraging ROIs within the same module to share similar representations. To further enhance discriminative ability of learned features, we encourage the MGNN to preserve network topology of input graphs via a graph topology reconstruction constraint. Experimental results on 534 subjects with rs-fMRI scans from two datasets validate the effectiveness of the proposed method. The identified discriminative brain ROIs and functional connectivities can be regarded as potential fMRI biomarkers to aid in clinical diagnosis.

Functional connectivity of the posterior cingulate cortex in autism spectrum disorder

The purpose of this study was to assess the functional connectivity of the posterior cingulate cortex in autism spectrum disorder (ASD). We used resting-state functional magnetic resonance imaging (rsfMRI) brain scans of adolescents diagnosed with ASD and a neurotypical control group. The Autism Brain Imaging Data Exchange (ABIDE) consortium was utilized to acquire data from the University of Michigan (145 subjects) and data from the New York University (183 subjects). The posterior cingulate cortex showed reduced connectivity with the anterior cingulate cortex for the ASD group compared to the control group. These two brain regions have previously both been linked to ASD symptomology. Specifically, the posterior cingulate cortex has been associated with behavioral control and executive functions, which appear to be responsible for the repetitive and restricted behaviors (RRB) in ASD. Our findings support previous data indicating a neurobiological basis of the disorder, and the specific functional connectivity changes involving the posterior cingulate cortex and anterior cingulate cortex may be a potential neurobiological biomarker for the observed RRBs in ASD.

Childhood exposure to organophosphate pesticides: Functional connectivity and working memory in adolescents

BACKGROUND

Early life exposure to organophosphate (OP) pesticides is linked with adverse neurodevelopment and brain function in children. However, we have limited knowledge of how these exposures affect functional connectivity, a measure of interaction between brain regions. To address this gap, we examined the association between early life OP pesticide exposure and functional connectivity in adolescents.

METHODS

We administered functional near-infrared spectroscopy (fNIRS) to 291 young adults with measured prenatal or childhood dialkylphosphates (DAPs) in the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) study, a longitudinal study of women recruited during pregnancy and their offspring. We measured DAPs in urinary samples collected from mothers during pregnancy (13 and 26 weeks) and children in early life (ages 6 months, 1, 2, 3, and 5 years). Youth underwent fNIRS while they performed executive function and semantic language tasks during their 18-year-old visit. We used covariate-adjusted regression models to estimate the associations of prenatal and childhood DAPs with functional connectivity between the frontal, temporal, and parietal regions, and a mediation model to examine the role of functional connectivity in the relationship between DAPs and task performance.

RESULTS

We observed null associations of prenatal and childhood DAP concentrations and functional connectivity for the entire sample. However, when we looked for sex differences, we observed an association between childhood DAPs and functional connectivity for the right interior frontal and premotor cortex after correcting for the false discovery rate, among males, but not females. In addition, functional connectivity appeared to mediate an inverse association between DAPs and working memory accuracy among males.

CONCLUSION

In CHAMACOS, a secondary analysis showed that adolescent males with elevated childhood OP pesticide exposure may have altered brain regional connectivity. This altered neurofunctional pattern in males may partially mediate working memory impairment associated with childhood DAP exposure.

Assessing the impact of repetitive transcranial magnetic stimulation on effective connectivity in autism spectrum disorder: An initial exploration using TMS-EEG analysis

Initial indications propose that repetitive transcranial magnetic stimulation (rTMS) could mitigate clinical manifestations in patients with autism spectrum disorder (ASD). Nevertheless, the precise mechanisms responsible for these therapeutic and behavioral outcomes remain elusive. We examined alterations in effective connectivity induced by rTMS using concurrent transcranial magnetic stimulation and electroencephalography (TMS-EEG) in children with ASD. TMS-EEG data were acquired from 12 children diagnosed with ASD both before and following rTMS treatment. The rTMS intervention regimen included delivering 5-s trains at a frequency of 15 Hz, with 10-min intervals between trains, targeting the left parietal lobe. This was conducted on each consecutive weekday over 3 weeks, totaling 15 sessions. The dynamic EEG network analysis revealed that following the rTMS intervention, long-range feedback connections within the brains of ASD patients were strengthened (e.g., frontal to parietal regions, frontal to occipital regions, and frontal to posterior temporal regions), and short-range connections were weakened (e.g., between the bilateral occipital regions, and between the occipital and posterior temporal regions). In alignment with alterations in network connectivity, there was a corresponding amelioration in fundamental ASD symptoms, as assessed through clinical scales post-treatment. According to our findings, people with ASD may have increased long-range frontal-posterior feedback connection on application of rTMS to the parietal lobe.

Explaining deep learning-based representations of resting state functional connectivity data: focusing on interpreting nonlinear patterns in autism spectrum disorder

Background

Resting state Functional Magnetic Resonance Imaging fMRI (rs-fMRI) has been used extensively to study brain function in psychiatric disorders, yielding insights into brain organization. However, the high dimensionality of the rs-fMRI data presents significant challenges for data analysis. Variational autoencoders (VAEs), a type of neural network, have been instrumental in extracting low-dimensional latent representations of resting state functional connectivity (rsFC) patterns, thereby addressing the complex nonlinear structure of rs-fMRI data. Despite these advances, interpreting these latent representations remains a challenge. This paper aims to address this gap by developing explainable VAE models and testing their utility using rs-fMRI data in autism spectrum disorder (ASD).

Methods

One-thousand one hundred and fifty participants (601 healthy controls [HC] and 549 patients with ASD) were included in the analysis. RsFC correlation matrices were extracted from the preprocessed rs-fMRI data using the Power atlas, which includes 264 regions of interest (ROIs). Then VAEs were trained in an unsupervised manner. Lastly, we introduce our latent contribution scores to explain the relationship between estimated representations and the original rs-fMRI brain measures.

Results

We quantified the latent contribution scores for both the ASD and HC groups at the network level. We found that both ASD and HC groups share the top network connectivitives contributing to all estimated latent components. For example, latent 0 was driven by rsFC within ventral attention network (VAN) in both the ASD and HC. However, we found significant differences in the latent contribution scores between the ASD and HC groups within the VAN for latent 0 and the sensory/somatomotor network for latent 2.

Conclusion

This study introduced latent contribution scores to interpret nonlinear patterns identified by VAEs. These scores effectively capture changes in each observed rsFC feature as the estimated latent representation changes, enabling an explainable deep learning model that better understands the underlying neural mechanisms of ASD.

Functional connectivity in autism spectrum disorder evaluated using rs-fMRI and DKI

We evaluated functional connectivity (FC) in patients with adult autism spectrum disorder (ASD) using resting-state functional MRI (rs-fMRI) and diffusion kurtosis imaging (DKI). We acquired rs-fMRI data from 33 individuals with ASD and 33 healthy controls (HC) and DKI data from 18 individuals with ASD and 17 HC. ASD showed attenuated FC between the right frontal pole (FP) and the bilateral temporal fusiform cortex (TFusC) and enhanced FC between the right thalamus and the bilateral inferior division of lateral occipital cortex, and between the cerebellar vermis and the right occipital fusiform gyrus (OFusG) and the right lingual gyrus, compared with HC. ASD demonstrated increased axial kurtosis (AK) and mean kurtosis (MK) in white matter (WM) tracts, including the right anterior corona radiata (ACR), forceps minor (FM), and right superior longitudinal fasciculus (SLF). In ASD, there was also a significant negative correlation between MK and FC between the cerebellar vermis and the right OFusG in the corpus callosum, FM, right SLF and right ACR. Increased DKI metrics might represent neuroinflammation, increased complexity, or disrupted WM tissue integrity that alters long-distance connectivity. Nonetheless, protective or compensating adaptations of inflammation might lead to more abundant glial cells and cytokine activation effectively alleviating the degeneration of neurons, resulting in increased complexity. FC abnormality in ASD observed in rs-fMRI may be attributed to microstructural alterations of the commissural and long-range association tracts in WM as indicated by DKI.

Altered intra- and inter-network brain functional connectivity associated with prolonged screen time in pre-school children with autism spectrum disorder

Prolonged screen time (ST) has adverse effects on autistic characteristics and language development. However, the mechanisms underlying the effects of prolonged ST on the neurodevelopment of children with autism spectrum disorder (ASD) remain unclear. Neuroimaging technology may help to further explain the role of prolonged ST in individuals with ASD. This study included 164 cases, all cases were divided into low-dose ST exposure (LDE group 108 cases) and high-dose ST exposure (HDE group 56 cases) based on the average ST of all subjects. Spatial independent component analysis (ICA) was used to identify resting state networks (RSNs) and investigate intra- and inter-network alterations in ASD children with prolonged ST. We found that the total Childhood Autism Rating Scale (CARS) scores in the HDE group were significantly higher than those in the LDE group (36.2 ± 3.1 vs. 34.6 ± 3.9, p = 0.008). In addition, the developmental quotient (DQ) of hearing and language in the HDE group were significantly lower than those in the LDE group (31.5 ± 13.1 vs. 42.5 ± 18.5, p < 0.001). A total of 13 independent components (ICs) were identified. Between-group comparison revealed that the HDE group exhibited decreased functional connectivity (FC) in the left precuneus (PCUN) of the default mode network (DMN), the right middle temporal gyrus (MTG) of the executive control network (ECN), and the right median cingulate and paracingulate gyri (MCG) of the attention network (ATN), compared with the LDE group. Additionally, there was an increase in FC in the right orbital part of the middle frontal gyrus (ORBmid) of the salience network (SAN), compared with the LDE group. The inter-network analysis revealed increased FC between the visual network (VN) and basal ganglia (BG) and decreased FC between the sensorimotor network (SMN) and DMN, SMN and ATN, SMN and auditory network (AUN), and DMN and SAN in the HDE group, compared with the LDE group. There was a significant negative correlation between altered FC values in MTG and total CARS scores in subjects (r =  - 0.18, p = 0.018).  Conclusion: ASD children with prolonged ST often exhibit lower DQ of language development and more severe autistic characteristics. The alteration of intra- and inter-network FC may be a key neuroimaging feature of the effect of prolonged ST on neurodevelopment in ASD children.  Clinical trial registration: ChiCTR2100051141. What is Known: • Prolonged ST has adverse effects on autistic characteristics and language development. • Neuroimaging technology may help to further explain the role of prolonged ST in ASD. What is New: • This is the first study to explore the impact of ST on intra- and inter-network FC in children with ASD. • ASD children with prolonged ST have atypical changes in intra- and inter-brain network FC.

Disentangling the Individual-Shared and Individual-Specific Subspace of Altered Brain Functional Connectivity in Autism Spectrum Disorder

BACKGROUND

Despite considerable effort toward understanding the neural basis of autism spectrum disorder (ASD) using case-control analyses of resting-state functional magnetic resonance imaging data, findings are often not reproducible, largely due to biological and clinical heterogeneity among individuals with ASD. Thus, exploring the individual-shared and individual-specific altered functional connectivity (AFC) in ASD is important to understand this complex, heterogeneous disorder.

METHODS

We considered 254 individuals with ASD and 295 typically developing individuals from the Autism Brain Imaging Data Exchange to explore the individual-shared and individual-specific subspaces of AFC. First, we computed AFC matrices of individuals with ASD compared with typically developing individuals. Then, common orthogonal basis extraction was used to project AFC of ASD onto 2 subspaces: an individual-shared subspace, which represents altered connectivity patterns shared across ASD, and an individual-specific subspace, which represents the remaining individual characteristics after eliminating the individual-shared altered connectivity patterns.

RESULTS

Analysis yielded 3 common components spanning the individual-shared subspace. Common components were associated with differences of functional connectivity at the group level. AFC in the individual-specific subspace improved the prediction of clinical symptoms. The default mode network-related and cingulo-opercular network-related magnitudes of AFC in the individual-specific subspace were significantly correlated with symptom severity in social communication deficits and restricted, repetitive behaviors in ASD.

CONCLUSIONS

Our study decomposed AFC of ASD into individual-shared and individual-specific subspaces, highlighting the importance of capturing and capitalizing on individual-specific brain connectivity features for dissecting heterogeneity. Our analysis framework provides a blueprint for parsing heterogeneity in other prevalent neurodevelopmental conditions.

EAG-RS: A Novel Explainability-Guided ROI-Selection Framework for ASD Diagnosis via Inter-Regional Relation Learning

Deep learning models based on resting-state functional magnetic resonance imaging (rs-fMRI) have been widely used to diagnose brain diseases, particularly autism spectrum disorder (ASD). Existing studies have leveraged the functional connectivity (FC) of rs-fMRI, achieving notable classification performance. However, they have significant limitations, including the lack of adequate information while using linear low-order FC as inputs to the model, not considering individual characteristics (i.e., different symptoms or varying stages of severity) among patients with ASD, and the non-explainability of the decision process. To cover these limitations, we propose a novel explainability-guided region of interest (ROI) selection (EAG-RS) framework that identifies non-linear high-order functional associations among brain regions by leveraging an explainable artificial intelligence technique and selects class-discriminative regions for brain disease identification. The proposed framework includes three steps: (i) inter-regional relation learning to estimate non-linear relations through random seed-based network masking, (ii) explainable connection-wise relevance score estimation to explore high-order relations between functional connections, and (iii) non-linear high-order FC-based diagnosis-informative ROI selection and classifier learning to identify ASD. We validated the effectiveness of our proposed method by conducting experiments using the Autism Brain Imaging Database Exchange (ABIDE) dataset, demonstrating that the proposed method outperforms other comparative methods in terms of various evaluation metrics. Furthermore, we qualitatively analyzed the selected ROIs and identified ASD subtypes linked to previous neuroscientific studies.

Strength and resilience of developing brain circuits predict adolescent emotional and stress responses during the COVID-19 pandemic

The COVID-19 pandemic has had profound but incompletely understood adverse effects on youth. To elucidate the role of brain circuits in how adolescents responded to the pandemic's stressors, we investigated their prepandemic organization as a predictor of mental/emotional health in the first ~15 months of the pandemic. We analyzed resting-state networks from n = 2,641 adolescents [median age (interquartile range) = 144.0 (13.0) months, 47.7% females] in the Adolescent Brain Cognitive Development study, and longitudinal assessments of mental health, stress, sadness, and positive affect, collected every 2 to 3 months from May 2020 to May 2021. Topological resilience and/or network strength predicted overall mental health, stress and sadness (but not positive affect), at multiple time points, but primarily in December 2020 and May 2021. Higher resilience of the salience network predicted better mental health in December 2020 (β = 0.19, 95% CI = [0.06, 0.31], P = 0.01). Lower connectivity of left salience, reward, limbic, and prefrontal cortex and its thalamic, striatal, amygdala connections, predicted higher stress (β = -0.46 to -0.20, CI = [-0.72, -0.07], P < 0.03). Lower bilateral robustness (higher fragility) and/or connectivity of these networks predicted higher sadness in December 2020 and May 2021 (β = -0.514 to -0.19, CI = [-0.81, -0.05], P < 0.04). These findings suggest that the organization of brain circuits may have played a critical role in adolescent stress and mental/emotional health during the pandemic.

Atypical local brain connectivity in pediatric autism spectrum disorder? A coordinate-based meta-analysis of regional homogeneity studies

Despite decades of massive neuroimaging research, the comprehensive characterization of short-range functional connectivity in autism spectrum disorder (ASD) remains a major challenge for scientific advances and clinical translation. From the theoretical point of view, it has been suggested a generalized local over-connectivity that would characterize ASD. This stance is known as the general local over-connectivity theory. However, there is little empirical evidence supporting such hypothesis, especially with regard to pediatric individuals with ASD (age [Formula: see text] 18 years old). To explore this issue, we performed a coordinate-based meta-analysis of regional homogeneity studies to identify significant changes of local connectivity. Our analyses revealed local functional under-connectivity patterns in the bilateral posterior cingulate cortex and superior frontal gyrus (key components of the default mode network) and in the bilateral paracentral lobule (a part of the sensorimotor network). We also performed a functional association analysis of the identified areas, whose dysfunction is clinically consistent with the well-known deficits affecting individuals with ASD. Importantly, we did not find relevant clusters of local hyper-connectivity, which is contrary to the hypothesis that ASD may be characterized by generalized local over-connectivity. If confirmed, our result will provide a valuable insight into the understanding of the complex ASD pathophysiology.

Modulatory effects of fMRI acquisition time of day, week and year on adolescent functional connectomes across spatial scales: Implications for inference

Metabolic, hormonal, autonomic and physiological rhythms may have a significant impact on cerebral hemodynamics and intrinsic brain synchronization measured with fMRI (the resting-state connectome). The impact of their characteristic time scales (hourly, circadian, seasonal), and consequently scan timing effects, on brain topology in inherently heterogeneous developing connectomes remains elusive. In a cohort of 4102 early adolescents with resting-state fMRI (median age = 120.0 months; 53.1 % females) from the Adolescent Brain Cognitive Development Study, this study investigated associations between scan time-of-day, time-of-week (school day vs weekend) and time-of-year (school year vs summer vacation) and topological properties of resting-state connectomes at multiple spatial scales. On average, participants were scanned around 2 pm, primarily during school days (60.9 %), and during the school year (74.6 %). Scan time-of-day was negatively correlated with multiple whole-brain, network-specific and regional topological properties (with the exception of a positive correlation with modularity), primarily of visual, dorsal attention, salience, frontoparietal control networks, and the basal ganglia. Being scanned during the weekend (vs a school day) was correlated with topological differences in the hippocampus and temporoparietal networks. Being scanned during the summer vacation (vs the school year) was consistently positively associated with multiple topological properties of bilateral visual, and to a lesser extent somatomotor, dorsal attention and temporoparietal networks. Time parameter interactions suggested that being scanned during the weekend and summer vacation enhanced the positive effects of being scanned in the morning. Time-of-day effects were overall small but spatially extensive, and time-of-week and time-of-year effects varied from small to large (Cohen's f ≤ 0.1, Cohen's d<0.82, p < 0.05). Together, these parameters were also positively correlated with temporal fMRI signal variability but only in the left hemisphere. Finally, confounding effects of scan time parameters on relationships between connectome properties and cognitive task performance were assessed using the ABCD neurocognitive battery. Although most relationships were unaffected by scan time parameters, their combined inclusion eliminated associations between properties of visual and somatomotor networks and performance in the Matrix Reasoning and Pattern Comparison Processing Speed tasks. Thus, scan time of day, week and year may impact measurements of adolescent brain's functional circuits, and should be accounted for in studies on their associations with cognitive performance, in order to reduce the probability of incorrect inference.

Early-in-life isoflurane exposure alters resting-state functional connectivity in juvenile non-human primates

BACKGROUND

Clinical studies suggest that anaesthesia exposure early in life affects neurobehavioural development. We designed a non-human primate (NHP) study to evaluate cognitive, behavioural, and brain functional and structural alterations after isoflurane exposure during infancy. These NHPs displayed decreased close social behaviour and increased astrogliosis in specific brain regions, most notably in the amygdala. Here we hypothesise that resting-state functional connectivity MRI can detect alterations in connectivity of brain areas that relate to these social behaviours and astrogliosis.

METHODS

Imaging was performed in 2-yr-old NHPs under light anaesthesia, after early-in-life (postnatal days 6-12) exposure to 5 h of isoflurane either one or three times, or to room air. Brain images were segmented into 82 regions of interest; the amygdala and the posterior cingulate cortex were chosen for a seed-based resting-state functional connectivity MRI analysis.

RESULTS

We found differences between groups in resting-state functional connectivity of the amygdala and the auditory cortices, medial premotor cortex, and posterior cingulate cortex. There were also alterations in resting-state functional connectivity between the posterior cingulate cortex and secondary auditory, polar prefrontal, and temporal cortices, and the anterior insula. Relationships were identified between resting-state functional connectivity alterations and the decrease in close social behaviour and increased astrogliosis.

CONCLUSIONS

Early-in-life anaesthesia exposure in NHPs is associated with resting-state functional connectivity alterations of the amygdala and the posterior cingulate cortex with other brain regions, evident at the juvenile age of 2 yr. These changes in resting-state functional connectivity correlate with the decrease in close social behaviour and increased astrogliosis. Using resting-state functional connectivity MRI to study the neuronal underpinnings of early-in-life anaesthesia-induced behavioural alterations could facilitate development of a biomarker for anaesthesia-induced developmental neurotoxicity.

A heterogeneous graph convolutional attention network method for classification of autism spectrum disorder

BACKGROUND

Autism spectrum disorder (ASD) is a serious developmental disorder of the brain. Recently, various deep learning methods based on functional magnetic resonance imaging (fMRI) data have been developed for the classification of ASD. Among them, graph neural networks, which generalize deep neural network models to graph structured data, have shown great advantages. However, in graph neural methods, because the graphs constructed are homogeneous, the phenotype information of the subjects cannot be fully utilized. This affects the improvement of the classification performance.

METHODS

To fully utilize the phenotype information, this paper proposes a heterogeneous graph convolutional attention network (HCAN) model to classify ASD. By combining an attention mechanism and a heterogeneous graph convolutional network, important aggregated features can be extracted in the HCAN. The model consists of a multilayer HCAN feature extractor and a multilayer perceptron (MLP) classifier. First, a heterogeneous population graph was constructed based on the fMRI and phenotypic data. Then, a multilayer HCAN is used to mine graph-based features from the heterogeneous graph. Finally, the extracted features are fed into an MLP for the final classification.

RESULTS

The proposed method is assessed on the autism brain imaging data exchange (ABIDE) repository. In total, 871 subjects in the ABIDE I dataset are used for the classification task. The best classification accuracy of 82.9% is achieved. Compared to the other methods using exactly the same subjects in the literature, the proposed method achieves superior performance to the best reported result.

CONCLUSIONS

The proposed method can effectively integrate heterogeneous graph convolutional networks with a semantic attention mechanism so that the phenotype features of the subjects can be fully utilized. Moreover, it shows great potential in the diagnosis of brain functional disorders with fMRI data.

Application of Multimodal MRI in the Early Diagnosis of Autism Spectrum Disorders: A Review

Autism spectrum disorder (ASD) is a neurodevelopmental disorder in children. Early diagnosis and intervention can remodel the neural structure of the brain and improve quality of life but may be inaccurate if based solely on clinical symptoms and assessment scales. Therefore, we aimed to analyze multimodal magnetic resonance imaging (MRI) data from the existing literature and review the abnormal changes in brain structural-functional networks, perfusion, neuronal metabolism, and the glymphatic system in children with ASD, which could help in early diagnosis and precise intervention. Structural MRI revealed morphological differences, abnormal developmental trajectories, and network connectivity changes in the brain at different ages. Functional MRI revealed disruption of functional networks, abnormal perfusion, and neurovascular decoupling associated with core ASD symptoms. Proton magnetic resonance spectroscopy revealed abnormal changes in the neuronal metabolites during different periods. Decreased diffusion tensor imaging signals along the perivascular space index reflected impaired glymphatic system function in children with ASD. Differences in age, subtype, degree of brain damage, and remodeling in children with ASD led to heterogeneity in research results. Multimodal MRI is expected to further assist in early and accurate clinical diagnosis of ASD through deep learning combined with genomics and artificial intelligence.

Explaining Deep Learning-Based Representations of Resting State Functional Connectivity Data: Focusing on Interpreting Nonlinear Patterns in Autism Spectrum Disorder

Background

Resting state Functional Magnetic Resonance Imaging fMRI (rs-fMRI) has been used to study brain function in psychiatric disorders, yielding insight into brain organization. However, the high dimensionality of the rs-fMRI data presents challenges, and requires dimensionality reduction before applying machine learning techniques. Neural networks, specifically variational autoencoders (VAEs), have been instrumental in extracting low-dimensional latent representations of resting state functional connectivity patterns, addressing the complex nonlinear structure of rs-fMRI. However, interpreting those latent representations remains a challenge. This paper aims to address this gap by creating explainable VAE models and testing their utility using rs-fMRI data in autism spectrum disorder (ASD).

Methods

One-thousand one hundred and fifty participants (601 HC and 549 patients with ASD) were included in the analysis. We extracted functional connectivity correlation matrices from the preprocessed rs-fMRI data using Power atlas with 264 ROIs. Then VAEs were trained in an unsupervised fashion. Lastly, we introduce our latent contribution scores to explain the relationship between estimated representations and the original rs-fMRI brain measures.

Results

We quantified the latent contribution scores for the ASD and control groups at the network level. We found that both ASD and control groups share the top network connectivity that contribute to all estimated latent components. For example, latent 0 was driven by resting state functional connectivity patterns (rsFC) within ventral attention network in both the ASD and control. However, significant differences in the latent contribution scores between the ASD and control groups were discovered within the ventral attention network in latent 0 and the sensory/somatomotor network in latent 2.

Conclusion

This study introduced latent contribution scores to interpret nonlinear patterns identified by VAEs. These scores effectively capture changes in each observed rsFC features as estimated latent representation changes, enabling an explainable deep learning model to better understand the underlying neural mechanism of ASD.

A scoping review of physiological biomarkers in autism

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by pervasive deficits in social interaction, communication impairments, and the presence of restricted and repetitive behaviors. This complex disorder is a significant public health concern due to its escalating incidence and detrimental impact on quality of life. Currently, extensive investigations are underway to identify prospective susceptibility or predictive biomarkers, employing a physiological biomarker-based framework. However, knowledge regarding physiological biomarkers in relation to Autism is sparse. We performed a scoping review to explore putative changes in physiological activities associated with behaviors in individuals with Autism. We identified studies published between January 2000 and June 2023 from online databases, and searched keywords included electroencephalography (EEG), magnetoencephalography (MEG), electrodermal activity markers (EDA), eye-tracking markers. We specifically detected social-related symptoms such as impaired social communication in ASD patients. Our results indicated that the EEG/ERP N170 signal has undergone the most rigorous testing as a potential biomarker, showing promise in identifying subgroups within ASD and displaying potential as an indicator of treatment response. By gathering current data from various physiological biomarkers, we can obtain a comprehensive understanding of the physiological profiles of individuals with ASD, offering potential for subgrouping and targeted intervention strategies.

Identification and analysis of autism spectrum disorder via large-scale dynamic functional network connectivity

Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder with severe cognitive impairment. Several studies have reported that brain functional network connectivity (FNC) has great potential for identifying ASD from healthy control (HC) and revealing the relationships between the brain and behaviors of ASD. However, few studies have explored dynamic large-scale FNC as a feature to identify individuals with ASD. This study used a time-sliding window method to study the dynamic FNC (dFNC) on the resting-state fMRI. To avoid arbitrarily determining the window length, we set a window length range of 10-75 TRs (TR = 2 s). We constructed linear support vector machine classifiers for all window length conditions. Using a nested 10-fold cross-validation framework, we obtained a grand average accuracy of 94.88% across window length conditions, which is higher than those reported in previous studies. In addition, we determined the optimal window length using the highest classification accuracy of 97.77%. Based on the optimal window length, we found that the dFNCs were located mainly in dorsal and ventral attention networks (DAN and VAN) and exhibited the highest weight in classification. Specifically, we found that the dFNC between DAN and temporal orbitofrontal network (TOFN) was significantly negatively correlated with social scores of ASD. Finally, using the dFNCs with high classification weights as features, we construct a model to predict the clinical score of ASD. Overall, our findings demonstrated that the dFNC could be a potential biomarker to identify ASD and provide new perspectives to detect cognitive changes in ASD.

16p11.2 deletion mice exhibit compromised fronto-temporal connectivity, GABAergic dysfunction, and enhanced attentional ability

Autism spectrum disorders are more common in males, and have a substantial genetic component. Chromosomal 16p11.2 deletions in particular carry strong genetic risk for autism, yet their neurobiological impact is poorly characterised, particularly at the integrated systems level. Here we show that mice reproducing this deletion (16p11.2 DEL mice) have reduced GABAergic interneuron gene expression (decreased parvalbumin mRNA in orbitofrontal cortex, and male-specific decreases in Gad67 mRNA in parietal and insular cortex and medial septum). Metabolic activity was increased in medial septum, and in its efferent targets: mammillary body and (males only) subiculum. Functional connectivity was altered between orbitofrontal, insular and auditory cortex, and between septum and hippocampus/subiculum. Consistent with this circuit dysfunction, 16p11.2 DEL mice showed reduced prepulse inhibition, but enhanced performance in the continuous performance test of attentional ability. Level 1 autistic individuals show similarly heightened performance in the equivalent human test, also associated with parietal, insular-orbitofrontal and septo-subicular dysfunction. The data implicate cortical and septal GABAergic dysfunction, and resulting connectivity changes, as the cause of pre-attentional and attentional changes in autism.

The autism spectrum among transgender youth: default mode functional connectivity

The common intersection of autism and transgender identities has been described in clinical and community contexts. This study investigates autism-related neurophenotypes among transgender youth. Forty-five transgender youth, evenly balanced across non-autistic, slightly subclinically autistic, and full-criteria autistic subgroupings, completed resting-state functional magnetic resonance imaging to examine functional connectivity. Results confirmed hypothesized default mode network (DMN) hub hyperconnectivity with visual and motor networks in autism, partially replicating previous studies comparing cisgender autistic and non-autistic adolescents. The slightly subclinically autistic group differed from both non-autistic and full-criteria autistic groups in DMN hub connectivity to ventral attention and sensorimotor networks, falling between non-autistic and full-criteria autistic groups. Autism traits showed a similar pattern to autism-related group analytics, and also related to hyperconnectivity between DMN hub and dorsal attention network. Internalizing, gender dysphoria, and gender minority-related stigma did not show connectivity differences. Connectivity differences within DMN followed previously reported patterns by designated sex at birth (i.e. female birth designation showing greater within-DMN connectivity). Overall, findings suggest behavioral diagnostics and autism traits in transgender youth correspond to observable differences in DMN hub connectivity. Further, this study reveals novel neurophenotypic characteristics associated with slightly subthreshold autism, highlighting the importance of research attention to this group.

Altered default mode network causal connectivity patterns in autism spectrum disorder revealed by Liang information flow analysis

Autism spectrum disorder (ASD) is a pervasive developmental disorder with severe cognitive impairment in social communication and interaction. Previous studies have reported that abnormal functional connectivity patterns within the default mode network (DMN) were associated with social dysfunction in ASD. However, how the altered causal connectivity pattern within the DMN affects the social functioning in ASD remains largely unclear. Here, we introduced the Liang information flow method, widely applied to climate science and quantum mechanics, to uncover the brain causal network patterns in ASD. Compared with the healthy controls (HC), we observed that the interactions among the dorsal medial prefrontal cortex (dMPFC), ventral medial prefrontal cortex (vMPFC), hippocampal formation, and temporo-parietal junction showed more inter-regional causal connectivity differences in ASD. For the topological property analysis, we also found the clustering coefficient of DMN and the In-Out degree of anterior medial prefrontal cortex were significantly decreased in ASD. Furthermore, we found that the causal connectivity from dMPFC to vMPFC was correlated with the clinical symptoms of ASD. These altered causal connectivity patterns indicated that the DMN inter-regions information processing was perturbed in ASD. In particular, we found that the dMPFC acts as a causal source in the DMN in HC, whereas it plays a causal target in ASD. Overall, our findings indicated that the Liang information flow method could serve as an important way to explore the DMN causal connectivity patterns, and it also can provide novel insights into the nueromechanisms underlying DMN dysfunction in ASD.

Altered resting-state functional connectivity of the brain in children with autism spectrum disorder

Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders. Brain mapping has shown that functional brain connections are altered in autism. This study investigated the pattern of brain connection changes in autistic people compared to healthy people. This study aimed to analyze functional abnormalities within the brain due to ASD, using resting-state functional magnetic resonance imaging (fMRI). Resting-state functional magnetic resonance images of 26 individuals with ASD and 26 healthy controls were obtained from the Autism Brain Imaging Data Exchange (ABIDE) database. The DPARSF (data processing assistant for resting-state fMRI) toolbox was used for resting-state functional image processing, and features related to functional connections were extracted from these images. Then, the extracted features from both groups were compared using an Independent Two-Sample T Test, and the features with significant differences between the two groups were identified. Compared with healthy controls, individuals with ASD showed hyper-connectivity in the frontal lobe, anterior cingulum, parahippocampal, left precuneus, angular, caudate, superior temporal, and left pallidum, as well as hypo-connectivity in the precentral, left superior frontal, left middle orbitofrontal, right amygdala, and left posterior cingulum. Our findings show that abnormal functional connectivity exists in patients with ASD. This study makes an important advancement in our understanding of the abnormal neurocircuits causing autism.

Electrophysiological Evidence for Interhemispheric Connectivity and Communication in Young Human Infants

Little is known empirically about connectivity and communication between the two hemispheres of the brain in the first year of life, and what theoretical opinion exists appears to be at variance with the meager extant anatomical evidence. To shed initial light on the question of interhemispheric connectivity and communication, this study investigated brain correlates of interhemispheric transmission of information in young human infants. We analyzed EEG data from 12 4-month-olds undergoing a face-related oddball ERP protocol. The activity in the contralateral hemisphere differed between odd-same and odd-difference trials, with the odd-different response being weaker than the response during odd-same trials. The infants' contralateral hemisphere "recognized" the odd familiar stimulus and "discriminated" the odd-different one. These findings demonstrate connectivity and communication between the two hemispheres of the brain in the first year of life and lead to a better understanding of the functional integrity of the developing human infant brain.

Cerebellar network changes in depressed patients with and without autism spectrum disorder: A case-control study

Pathophysiological difference of depression in patients with and without autistic spectrum disorder (ASD) has not been investigated previously. Therefore, we sought to determine whether there were differences between non-ASD and ASD groups on resting-state functional magnetic resonance imaging (rs-fMRI) in patients with depression. We performed 3T MRI under resting state in 8 patients with depression and ASD and 12 patients with depression but without ASD. The ASD group showed increased functional connectivity in the cerebellar network of the left posterior inferior temporal gyrus and anterior cerebellar lobes compared to the non-ASD group in an analysis of covariance. Adding antipsychotics, antidepressants, benzodiazepines, nonbenzodiazepines, anxiolytics, hypnotics, or age as covariates showed a similar increase in functional connectivity. Thus, this study found that depressive patients with ASD had increased functional connectivity in the cerebellar network. Our findings suggest that fMRI may be able to evaluate differences in depressed patients with and without ASD.

Meta-analytic connectivity modelling of functional magnetic resonance imaging studies in autism spectrum disorders

Social and non-social deficits in autism spectrum disorders (ASD) persist into adulthood and may share common regions of aberrant neural activations. The current meta-analysis investigated activation differences between ASD and neurotypical controls irrespective of task type. Activation likelihood estimation meta-analyses were performed to examine consistent hypo-activated and/or hyper-activated regions for all tasks combined, and for social and non-social tasks separately; meta-analytic connectivity modelling and behavioral/paradigm analyses were performed to examine co-activated regions and associated behaviors. One hundred studies (mean age range = 18-41 years) were included. For all tasks combined, the ASD group showed significant (p < .05) hypo-activation in one cluster around the left amygdala (peak - 26, -2, -20, volume = 1336 mm³, maximum ALE = 0.0327), and this cluster co-activated with two other clusters around the right cerebellum (peak 42, -56, -22, volume = 2560mm³, maximum ALE = 0.049) Lobule VI/Crus I and the left fusiform gyrus (BA47) (peak - 42, -46, -18, volume = 1616 mm³, maximum ALE = 0.046) and left cerebellum (peak - 42, -58, -20, volume = 1616mm³, maximum ALE = 0.033) Lobule VI/Crus I. While the left amygdala was associated with negative emotion (fear) (z = 3.047), the left fusiform gyrus/cerebellum Lobule VI/Crus I cluster was associated with language semantics (z = 3.724) and action observation (z = 3.077). These findings highlight the left amygdala as a region consistently hypo-activated in ASD and suggest the potential involvement of fusiform gyrus and cerebellum in social cognition in ASD. Future research should further elucidate if and how amygdala-fusiform/cerebellar connectivity relates to social and non-social cognition in adults with ASD.

Catecholaminergic and cholinergic neuromodulation in autism spectrum disorder: A comparison to attention-deficit hyperactivity disorder

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder characterized by social impairments and restricted, repetitive behaviors. Treatment of ASD is notoriously difficult and might benefit from identification of underlying mechanisms that overlap with those disturbed in other developmental disorders, for which treatment options are more obvious. One example of the latter is attention-deficit hyperactivity disorder (ADHD), given the efficacy of especially stimulants in treatment of ADHD. Deficiencies in catecholaminergic systems [dopamine (DA), norepinephrine (NE)] in ADHD are obvious targets for stimulant treatment. Recent findings suggest that dysfunction in catecholaminergic systems may also be a factor in at least a subgroup of ASD. In this review we scrutinize the evidence for catecholaminergic mechanisms underlying ASD symptoms, and also include in this analysis a third classic ascending arousing system, the acetylcholinergic (ACh) network. We complement this with a comprehensive review of DA-, NE-, and ACh-targeted interventions in ASD, and an exploratory search for potential treatment-response predictors (biomarkers) in ASD, genetically or otherwise. Based on this review and analysis we propose that (1) stimulant treatment may be a viable option for an ASD subcategory, possibly defined by genetic subtyping; (2) cerebellar dysfunction is pronounced for a relatively small ADHD subgroup but much more common in ASD and in both cases may point toward NE- or ACh-directed intervention; (3) deficiency of the cortical salience network is sizable in subgroups of both disorders, and biomarkers such as eye blink rate and pupillometric data may predict the efficacy of targeting this underlying deficiency via DA, NE, or ACh in both ASD and ADHD.

Amplitude of low frequency fluctuations during resting state fMRI in autistic children

Resting state fMRI (rs-fMRI) provides an excellent platform for examining the amplitude of low frequency fluctuations (ALFF) and fractional amplitude of low frequency fluctuations (fALFF), which are key indices of brain functioning. However, ALFF and fALFF have been used only sporadically to study autism. rs-fMRI data from 69 children (40 autistic, mean age = 8.47 ± 2.20 years; age range: 5.2 to 13.2; and 29 non-autistic, mean age = 9.02 ± 1.97 years; age range 5.9 to 12.9) were obtained from the Autism Brain Imaging Data Exchange (ABIDE II). ALFF and fALFF were measured using CONN connectivity toolbox and SPM12, at whole-brain & network-levels. A two-sampled t-test and a 2 Group (autistic, non-autistic) × 7 Networks ANOVA were conducted to test group differences in ALFF and fALFF. The whole-brain analysis identified significantly reduced ALFF values for autistic participants in left parietal opercular cortex, precuneus, and right insula. At the network level, there was a significant effect of diagnostic group and brain network on ALFF values, and only significant effect of network, not group, on fALFF values. Regression analyses indicated a significant effect of age on ALFF values of certain networks in autistic participants. Such intrinsically different network-level responses in autistic participants may have implications for task-level recruitment and synchronization of brain areas, which may in turn impact optimal cognitive functioning. Moreover, differences in low frequency fluctuations of key networks, such as the DMN and SN, may underlie alterations in brain responses in autism that are frequently reported in the literature.

Brain functional activity-based classification of autism spectrum disorder using an attention-based graph neural network combined with gene expression

Autism spectrum disorder (ASD) is a complex brain neurodevelopmental disorder related to brain activity and genetics. Most of the ASD diagnostic models perform feature selection at the group level without considering individualized information. Evidence has shown the unique topology of the individual brain has a fundamental impact on brain diseases. Thus, a data-constructing method fusing individual topological information and a corresponding classification model is crucial in ASD diagnosis and biomarker discovery. In this work, we trained an attention-based graph neural network (GNN) to perform the ASD diagnosis with the fusion of graph data. The results achieved an accuracy of 79.78%. Moreover, we found the model paid high attention to brain regions mainly involved in the social-brain circuit, default-mode network, and sensory perception network. Furthermore, by analyzing the covariation between functional magnetic resonance imaging data and gene expression, current studies detected several ASD-related genes (i.e. MUTYH, AADAT, and MAP2), and further revealed their links to image biomarkers. Our work demonstrated that the ASD diagnostic framework based on graph data and attention-based GNN could be an effective tool for ASD diagnosis. The identified functional features with high attention values may serve as imaging biomarkers for ASD.

The role of the anterior insular cortex in self-monitoring: A novel study protocol with electrical stimulation mapping and functional magnetic resonance imaging

Becoming aware of one's own states is a fundamental aspect for self-monitoring, allowing us to adjust our beliefs of the world to the changing context. Previous evidence points out to the key role of the anterior insular cortex (aIC) in evaluating the consequences of our own actions, especially whenever an error has occurred. In the present study, we propose a new multimodal protocol combining electrical stimulation mapping (ESM) and functional magnetic resonance imaging (fMRI) to explore the functional role of the aIC for self-monitoring in patients undergoing awake brain surgery. Our results using a modified version of the Stroop task tackling metacognitive abilities revealed new direct evidence of the involvement of the aIC in monitoring our performance, showing increased difficulties in detecting action-outcome mismatches when stimulating a cortical site located at the most posterior part of the aIC as well as significant BOLD activations at this region during outcome incongruences for self-made actions. Based on these preliminary results, we highlight the importance of assessing the aIC's functioning during tumor resection involving this region to evaluate metacognitive awareness of the self in patients undergoing awake brain surgery. In a similar vein, a better understanding of the aIC's role during self-monitoring may help shed light on action/outcome processing abnormalities reported in several neuropsychiatric disorders such as schizophrenia, anosognosia for hemiplegia or major depression.

Bayesian Spatial Blind Source Separation via the Thresholded Gaussian Process

Blind source separation (BSS) aims to separate latent source signals from their mixtures. For spatially dependent signals in high dimensional and large-scale data, such as neuroimaging, most existing BSS methods do not take into account the spatial dependence and the sparsity of the latent source signals. To address these major limitations, we propose a Bayesian spatial blind source separation (BSP-BSS) approach for neuroimaging data analysis. We assume the expectation of the observed images as a linear mixture of multiple sparse and piece-wise smooth latent source signals, for which we construct a new class of Bayesian nonparametric prior models by thresholding Gaussian processes. We assign the vMF priors to mixing coefficients in the model. Under some regularity conditions, we show that the proposed method has several desirable theoretical properties including the large support for the priors, the consistency of joint posterior distribution of the latent source intensity functions and the mixing coefficients, and the selection consistency on the number of latent sources. We use extensive simulation studies and an analysis of the resting-state fMRI data in the Autism Brain Imaging Data Exchange (ABIDE) study to demonstrate that BSP-BSS outperforms the existing method for separating latent brain networks and detecting activated brain activation in the latent sources.

Group-level comparison of brain connectivity networks

BACKGROUND

Functional connectivity (FC) studies are often performed to discern different patterns of brain connectivity networks between healthy and patient groups. Since many neuropsychiatric disorders are related to the change in these patterns, accurate modelling of FC data can provide useful information about disease pathologies. However, analysing functional connectivity data faces several challenges, including the correlations of the connectivity edges associated with network topological characteristics, the large number of parameters in the covariance matrix, and taking into account the heterogeneity across subjects.

METHODS

This study provides a new statistical approach to compare the FC networks between subgroups that consider the network topological structure of brain regions and subject heterogeneity.

RESULTS

The power based on the heterogeneity structure of identity scaled in a sample size of 25 exhibited values greater than 0.90 without influencing the degree of correlation, heterogeneity, and the number of regions. This index had values above 0.80 in the small sample size and high correlation. In most scenarios, the type I error was close to 0.05. Moreover, the application of this model on real data related to autism was also investigated, which indicated no significant difference in FC networks between healthy and patient individuals.

CONCLUSIONS

The results from simulation data indicated that the proposed model has high power and near-nominal type I error rates in most scenarios.

Cognitive theories of autism based on the interactions between brain functional networks

Cognitive functions are directly related to interactions between the brain's functional networks. This functional organization changes in the autism spectrum disorder (ASD). However, the heterogeneous nature of autism brings inconsistency in the findings, and specific pattern of changes based on the cognitive theories of ASD still requires to be well-understood. In this study, we hypothesized that the theory of mind (ToM), and the weak central coherence theory must follow an alteration pattern in the network level of functional interactions. The main aim is to understand this pattern by evaluating interactions between all the brain functional networks. Moreover, the association between the significantly altered interactions and cognitive dysfunctions in autism is also investigated. We used resting-state fMRI data of 106 subjects (5-14 years, 46 ASD: five female, 60 HC: 18 female) to define the brain functional networks. Functional networks were calculated by applying four parcellation masks and their interactions were estimated using Pearson's correlation between pairs of them. Subsequently, for each mask, a graph was formed based on the connectome of interactions. Then, the local and global parameters of the graph were calculated. Finally, statistical analysis was performed using a two-sample t-test to highlight the significant differences between autistic and healthy control groups. Our corrected results show significant changes in the interaction of default mode, sensorimotor, visuospatial, visual, and language networks with other functional networks that can support the main cognitive theories of autism. We hope this finding sheds light on a better understanding of the neural underpinning of autism.

Excessive Functional Coupling With Less Variability Between Salience and Default Mode Networks in Autism Spectrum Disorder

BACKGROUND

Atypical activity in the salience network (SN) and default mode network (DMN) has been previously reported in individuals with autism spectrum disorder (ASD). However, no study to date has investigated the nature and dynamics of the interaction between these two networks in ASD.

METHODS

Here, we aimed to characterize the functional connectivity between the SN and the DMN by using resting-state functional magnetic resonance imaging data from the Autism Brain Imaging Data Exchange and comparing individuals with ASD (n = 325) to a typically developing group (n = 356). We examined static and dynamic levels of functional connectivity using the medial prefrontal cortex (mPFC) seed as a core region of the DMN.

RESULTS

We found that individuals with ASD have higher mPFC connectivity with the insula, a core region of the SN, when compared with the typical development group. Moreover, the mPFC-insula coupling showed less variability in ASD compared with the typical development group. A novel semblance-based network dynamic analysis further confirmed that the strong mPFC-insula coupling in the ASD group reduced spontaneous attentional shift for possible external elements of the environment. Indeed, we found that excessive mPFC-insula coupling was significantly associated with a tendency for reduced social responsiveness.

CONCLUSIONS

These findings suggest that the internally oriented cognition in individuals with ASD may be due to excessive coupling between the DMN and the SN.

EEG resting-state functional connectivity: evidence for an imbalance of external/internal information integration in autism

Background

Autism spectrum disorder (ASD) is associated with atypical neural activity in resting state. Most of the studies have focused on abnormalities in alpha frequency as a marker of ASD dysfunctions. However, few have explored alpha synchronization within a specific interest in resting-state networks, namely the default mode network (DMN), the sensorimotor network (SMN), and the dorsal attention network (DAN). These functional connectivity analyses provide relevant insight into the neurophysiological correlates of multimodal integration in ASD.

Methods

Using high temporal resolution EEG, the present study investigates the functional connectivity in the alpha band within and between the DMN, SMN, and the DAN. We examined eyes-closed EEG alpha lagged phase synchronization, using standardized low-resolution brain electromagnetic tomography (sLORETA) in 29 participants with ASD and 38 developing (TD) controls (age, sex, and IQ matched).

Results

We observed reduced functional connectivity in the ASD group relative to TD controls, within and between the DMN, the SMN, and the DAN. We identified three hubs of dysconnectivity in ASD: the posterior cingulate cortex, the precuneus, and the medial frontal gyrus. These three regions also presented decreased current source density in the alpha band.

Conclusion

These results shed light on possible multimodal integration impairments affecting the communication between bottom-up and top-down information. The observed hypoconnectivity between the DMN, SMN, and DAN could also be related to difficulties in switching between externally oriented attention and internally oriented thoughts.

Supplementary Information

The online version contains supplementary material available at 10.1186/s11689-022-09456-8.

The sense of agency for brain disorders: A comprehensive review and proposed framework

Sense of Agency (SoA) refers to the feeling of control over voluntary actions and the outcomes of those actions. Several brain disorders are characterized by an abnormal SoA. To date, there is no robust treatment for aberrant agency across disorders; this is, in large part, due to gaps in our understanding of the cognitive mechanisms and neural correlates of the SoA. This apparent gap stems from a lack of synthesis in established findings. As such, the current review reconciles previously established findings into a novel neurocognitive framework for future investigations of the SoA in brain disorders, which we term the Agency in Brain Disorders Framework (ABDF). In doing so, we highlight key top-down and bottom-up cues that contribute to agency prospectively (i.e., prior to action execution) and retrospectively (i.e., after action execution). We then examine brain disorders, including schizophrenia, autism spectrum disorders (ASD), obsessive-compulsive disorders (OCD), and cortico-basal syndrome (CBS), within the ABDF, to demonstrate its potential utility in investigating neurocognitive mechanisms underlying phenotypically variable presentations of the SoA in brain disorders.

Model-based stationarity filtering of long-term memory data applied to resting-state blood-oxygen-level-dependent signal

Resting-state blood-oxygen-level-dependent (BOLD) signal acquired through functional magnetic resonance imaging is a proxy of neural activity and a key mechanism for assessing neurological conditions. Therefore, practical tools to filter out artefacts that can compromise the assessment are required. On the one hand, a variety of tailored methods to preprocess the data to deal with identified sources of noise (e.g., head motion, heart beating, and breathing, just to mention a few) are in place. But, on the other hand, there might be unknown sources of unstructured noise present in the data. Therefore, to mitigate the effects of such unstructured noises, we propose a model-based filter that explores the statistical properties of the underlying signal (i.e., long-term memory). Specifically, we consider autoregressive fractional integrative process filters. Remarkably, we provide evidence that such processes can model the signals at different regions of interest to attain stationarity. Furthermore, we use a principled analysis where a ground-truth signal with statistical properties similar to the BOLD signal under the injection of noise is retrieved using the proposed filters. Next, we considered preprocessed (i.e., the identified sources of noise removed) resting-state BOLD data of 98 subjects from the Human Connectome Project. Our results demonstrate that the proposed filters decrease the power in the higher frequencies. However, unlike the low-pass filters, the proposed filters do not remove all high-frequency information, instead they preserve process-related higher frequency information. Additionally, we considered four different metrics (power spectrum, functional connectivity using the Pearson's correlation, coherence, and eigenbrains) to infer the impact of such filter. We provided evidence that whereas the first three keep most of the features of interest from a neuroscience perspective unchanged, the latter exhibits some variations that could be due to the sporadic activity filtered out.