Biology subjects

Seraji, M.

Publications and source records attributed to Seraji, M..

17 recordsLinked to original sources

bioRxiv2026

NeuroMark dFNC: Transferable Dynamic-State Templates for Subject-Specific and Frequency-Resolved Chronnectomics

Dynamic functional network connectivity (dFNC) commonly identifies recurring connectivity states from resting-state fMRI, but states derived independently in each dataset lack guaranteed correspondence across studies and cannot be directly estimated in new participants. We introduce NeuroMark dFNC, which extends the NeuroMark principle of prior-guided network estimation to dynamic connectivity by using reproducible reference states as priors for estimating corresponding subject-specific states. Reference-state templates were derived from UK Biobank using windowed functional network connectivity and time-frequency moments (TFMs), with split-sample reproducibility evaluated for k-means, independent component analysis (ICA), and principal component analysis (PCA) template-generation approaches. Constrained ICA then used the templates to estimate subject-specific state patterns and continuous loadings in independent FBIRN schizophrenia and ADNI Alzheimer's disease cohorts. ICA loadings were calibrated by their contribution to reconstruction of the original feature matrix. Fractional occupancy and conditional mean dwell time were calculated from the state with the largest absolute calibrated loading at each observation. The predefined templates avoided the need for dataset-specific state discovery and post-hoc state matching. In both clinical cohorts, the analysis identified state-dependent, distributed edgewise differences and differences in selected temporal summaries. Nominal frequency-resolved findings varied across states and moment-frequency bins and were treated as exploratory. NeuroMark dFNC provides a common state space for cross-cohort comparison while retaining subject-specific connectivity patterns and continuous state expression.

neuroscience↗

bioRxiv2026

Comparing Nonlinear Trajectories Across Brain Networks: A Key to Understanding Complex Brain Dynamics

This study explores the nonlinear developmental trajectories of brain networks in neurotypically developing infants during their first six months. Using a longitudinal dataset of 137 resting-state functional MRI scans from 74 infants, we analyzed five spatial metrics across 13 intrinsic connectivity networks, including motor, visual, subcortical, and prefrontal networks. A cubic model was specifically employed to capture distinct linear and non-linear trends in the networks developmental patterns, allowing for the identification of significant differences in cubic, quadratic, and linear slope parameters across networks. This model choice was driven by the need to examine how specific non-linear components (e.g., inflection points and acceleration rates) uniquely characterize each networks trajectory, which a generalized approach might smooth out without pinpointing such network-specific features. Notably, the subcortical network exhibited a distinct cubic growth pattern, while secondary motor and visual networks showed pronounced quadratic variations, suggesting network-specific shifts in spatial organization and connectivity. These findings highlight the unique maturation timelines and interactions between functional systems, such as early sensory-motor coordination and later cognitive integration. The results underscore the importance of network-specific growth patterns, providing deeper insights into how infant brain networks evolve and interact to support emerging cognitive and behavioral functions.

neuroscience↗

bioRxiv2026

Individual differences in post-encoding sleep continuity predict context memory accuracy and supporting ERPs in younger and older adults

Post-encoding sleep plays an essential role in episodic memory consolidation. Much of the existing literature on sleep and memory relies on deprivation paradigms or laboratory-controlled sleep. Relatively few studies have examined how naturalistic post-encoding sleep relates to memory retrieval and its supporting neural activity, or whether age-related impairments in this sleep are linked to those in episodic memory. In the present study, we used actigraphy and electroencephalography to examine how post-encoding sleep quality relates to context memory performance and retrieval-related ERPs supporting performance in younger and older adults. Participants encoded object-scene pairs and were tested on matching and mismatching pairs after a 96-hour sleep-filled delay. We found that greater post-encoding sleep continuity predicted better delayed context memory performance for mismatching pairs across age groups. Post-encoding sleep continuity was also associated with larger ERP differences between context hits and misses for context-matching pairs, for ERP effects associated with post-retrieval monitoring operations across age groups. Together, these findings suggest that more continuous, naturalistic post-encoding sleep facilitates episodic memory performance and neural mechanisms supporting episodic memory retrieval across adult age.

neuroscience↗

bioRxiv2026

Age Alters the Relationship between Post-Encoding Sleep Quality and Context Memory Neural Reinstatement

Sleep supports episodic memory consolidation, yet it remains unclear how naturalistic post-encoding sleep quality relates to the neural reinstatement of episodic representations across adulthood. The present study examined whether sleep discontinuity during the retention interval predicted delayed context memory and encoding-retrieval similarity (ERS) of EEG in younger and older adults. Participants completed an object-scene context memory task with immediate and delayed retrieval, while EEG was recorded during encoding and retrieval. Actigraphy was used to measure sleep across the post-encoding retention period, and principal component analysis identified sleep discontinuity and sleep time components. Behavioral results showed that greater post-encoding sleep discontinuity, but not sleep time, was associated with poorer delayed memory accuracy for mismatching object-context pairs across age. ERS analyses further showed that greater sleep discontinuity was associated with reduced ERS for correctly rejected mismatching pairs across frontal and posterior spatiotemporal clusters. Age moderated sleep-ERS associations: greater sleep discontinuity was generally related to lower ERS in younger adults, whereas some spatiotemporal clusters showed positive associations in older adults, potentially reflecting compensatory or effortful retrieval-related processing in poorer sleepers. Together, these findings suggest that sleep continuity during the post-encoding retention interval is important for preserving high-fidelity episodic representations needed for later context discrimination. More broadly, the results demonstrate that naturalistic sleep fragmentation is linked to both behavioral memory outcomes and neural reinstatement across adults.

neuroscience↗

bioRxiv2026

Explicitly nonlinear fMRI networks reveal hidden trajectories of infant brain development

Nonlinearity is a hallmark of brain complexity at multiple scales. However, existing functional magnetic resonance imaging (fMRI) functional connectivity studies typically utilize linear methods. Therefore, links between nonlinear fMRI connectivity patterns and the development of the human brain during critical periods such as infancy remain unclear. To address this gap in knowledge, we developed a data-driven approach to capture brain intrinsic connectivity networks from explicitly nonlinear resting-state fMRI connectivity and profiled their developmental associations in a cohort of typically developing human infants. We identified neurobiologically structured nonlinear fMRI connectivity patterns during early postnatal life, indicating that macroscopic brain ensembles systematically participate in nonlinear relationships at birth. Furthermore, we found that linear and explicitly nonlinear network counterparts are linked to partially overlapping but complementary developmental profiles during this period of rapid brain maturation, with the explicitly nonlinear approach unveiling insights into the development of networks that have been associated with sensorimotor capacities, default mode processes, executive functioning, language production, and stimulus saliency. Our study marks the first comprehensive developmental investigation of whole-brain nonlinear fMRI networks in human infants and deepens contemporary perspectives on neuroimaging data discovery by emphasizing the informational richness of nonlinear relationships at fMRI scales of observation.

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bioRxiv2025

The Role of Sleep Duration and Age in Neural Reactivation and Episodic Memory Performance Across the Adult Lifespan

Sleep is essential for episodic memory consolidation, involving the reactivation of neural patterns during encoding and retrieval. This study examined how sleep duration influences encoding-retrieval similarity (ERS) and memory performance across the adult lifespan. Fifty-five adults (18-79 years) participated in a seven-day protocol, combining actigraphy-based sleep monitoring with EEG and memory assessments during a paired associate learning task. Significant correlations between sleep duration and ERS were observed, with clusters showing positive and negative associations across brain regions. In match context trials, ERS in the left frontal region correlated with sleep duration, and age moderated these effects. In mismatch context trials, positive correlations were identified in the left posterior, left frontal, and right posterior regions. These results highlight the role of sleep in modulating neural reactivation patterns during memory retrieval and emphasize the influence of age. The study advances our understanding of how sleep variability impacts memory consolidation and provides a basis for exploring targeted sleep interventions. Clinical RelevanceThis study highlights the impact of habitual sleep variability on neural reactivation patterns and memory retrieval across the adult lifespan. The findings emphasize the moderating role of age and suggest that improving sleep duration may enhance episodic memory performance. These insights could guide clinicians in developing personalized sleep interventions to support cognitive health and mitigate age-related memory decline.

neuroscience↗

bioRxiv2025

DECODING BRAIN DYNAMICS VIA CROSS-NETWORK NON-LINEAR TRAJECTORIES

Infant brain networks mature rapidly and nonlinearly, yet cross-network comparisons of developmental trajectories remain rare. We introduce cross-network non-linear trajectory characterization (CNTC), which fits cubic polynomials to age-related change in three spatial measures--network-averaged spatial similarity (NASS), network strength, and network size--derived from resting-state fMRI. Using 137 scans from 74 neurotypical infants spanning 0-6 months of age, we estimated networks via group ICA, modeled age trajectories within each network, and then contrasted coefficients across networks. Across seven canonical systems, trajectories showed robust age effects. Cross-network differences were dominated by linear terms, with selective quadratic effects and few cubic effects. Visual and cerebellar systems exhibited the steepest NASS slopes and pronounced increases in strength and size, whereas motor/attention changes were more gradual. CNTC provides a compact, coefficient-level summary of inter-network maturation and a basis for benchmarking atypical development in future work.

neuroscience↗

bioRxiv2025

Mapping the Developmental Trajectory of Functional Brain Networks in Early Infancy: Insights into Typical Maturation

Early infancy is a crucial period for brain development, during which fundamental functional and structural frameworks are established. Understanding the maturation of large-scale brain networks during this stage is essential for characterizing normative neurodevelopment and identifying potential deviations linked to neurodevelopmental disorders. In this study, we investigated developmental changes in the spatial organization of functional brain networks in infants using a longitudinal resting-state fMRI dataset comprising 137 scans from 74 low-likelihood developing infants aged 0-6 months. We applied independent component analysis to extract large-scale brain networks and utilized advanced spatial metrics, including network-averaged spatial similarity (NASS) to assess alignment with group-level patterns, network strength to quantify neural engagement based on voxel intensities, and network size to examine spatial distribution. Our findings reveal significant age-related increases in NASS across multiple networks, indicating greater consistency in functional organization over time. Additionally, most networks demonstrated increased network strength, reflecting heightened neural involvement, while network size exhibited distinct developmental trajectories, with some networks expanding and others remaining stable. These results highlight the dynamic evolution of functional brain architecture during early infancy, providing critical insights into neurodevelopmental processes. Clinical RelevanceThis study provides critical insights into early brain network development, which is essential for identifying biomarkers of neurodevelopmental disorders such as autism and schizophrenia. By mapping typical maturation patterns using advanced spatial metrics, our findings offer a foundation for early detection of atypical development. Deviations in network organization and strength could serve as early indicators, supporting neuroimaging-based screening and intervention strategies to optimize neurodevelopmental outcomes.

neuroscience↗

bioRxiv2025

SPATIAL DISSIMILARITY TRAJECTORIES REVEAL RAPID FUNCTIONAL NETWORK REFINEMENT DURING EARLY INFANCY

The first six months of life mark a critical window for human brain development, characterized by rapid synaptic formation, axonal growth, and network reorganization. During this period, large-scale functional networks progressively mature. Although prior infant fMRI studies have characterized temporal functional connectivity, the spatial organization and refinement of brain networks during early infancy remain underexplored. In this study, we analyzed longitudinal resting-state fMRI from 74 typically developing infants (0-6 months; 137 scans) using group independent component analysis (ICA) with group-information-guided ICA (GIG-ICA) back-reconstruction. Spatial dissimilarity between each infants spatial map and the group-level map was quantified using cosine dissimilarity and Euclidean distance. Generalized additive models were applied to model age-related trends. Both cosine and Euclidean dissimilarity metrics showed significant decreases with age, indicating a progressive convergence of individual network topographies toward the group-level architecture. These findings reveal increasing spatial coherence and refinement of large-scale brain networks during early infancy, suggesting that spatial maturation complements the well-established functional integration observed in temporal connectivity studies.

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bioRxiv2025

Diagnosis-Optimized Dynamic Feature Learning Reveals Altered Default Mode Network Connectivity in Schizophrenia

Schizophrenia (SZ) is characterized by widespread neural dysconnectivity, with particularly pronounced alterations in the default mode network (DMN)--a set of brain regions involved in self-referential thought and mind-wandering. We investigated dynamic functional connectivity within the DMN in SZ by analyzing resting-state fMRI data from two independent cohorts (FBIRN and COBRE). Using a novel iterative feature-removal clustering approach focusing on DMN independent components, we identified distinct recurring connectivity states while iteratively removing dominant connectivity features to reveal subtler network patterns. This approach iteratively refines the set of features considered, ensuring a more balanced representation and facilitating the identification of significant interactions that would otherwise be overlooked. Cluster centroids for the four connectivity states were highly similar across both datasets, reflecting stable shared DMN patterns. State occupancy was compared between participants with SZ and healthy controls, and associations with clinical symptom severity were examined. The SZ group exhibited significant alterations in DMN connectivity dynamics, spending more time than controls in certain connectivity states characterized by atypical DMN coupling and less time in a state reflecting a normative DMN configuration. A comparison between the FBIRN and COBRE datasets reveals both similarities and differences in occupancy rate (OCR) states. Overall, the pattern of group effects converged while state-specific divergences likely reflected protocol/sample differences rather than conflicting biology. Crucially, the explainability pipeline yielded a highly similar feature-removal order across datasets, indicating that the same DMN edges drive the diagnostic signal in both cohorts. Several OCR effects also tracked symptom ratings, linking abnormal DMN dynamics to clinical expression. Our findings suggest that SZ is characterized by reproducible disturbances in the temporal organization of DMN connectivity. These dynamic DMN features may serve as potential biomarkers for SZ, offering diagnostic and clinical utility by capturing network dysfunction that static connectivity measures could overlook.

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bioRxiv2025

Altered Functional Network Energy Across Multiscale Brain Networks in Preterm vs. Full-Term Subjects: Insights from the Adolescent Brain Cognitive Development (ABCD) Study

Infants born prematurely, or preterm, can experience altered brain connectivity, due in part to incomplete brain development at the time of parturition. Research has also shown structural and functional differences in the brain that persist in these individuals as they enter adolescence when compared to peers who were fully mature at birth. In this study, we examined functional network energy across multiscale functional connectivity in approximately 4600 adolescents from the Adolescent Brain Cognitive Development (ABCD) study who were either preterm or full term at birth. We identified three key brain networks that show significant differences in network energy between preterm and full-term subjects. These networks include the visual network (comprising the occipitotemporal and occipital subnetworks), the sensorimotor network, and the high cognitive network (including the temporoparietal and frontal subnetworks). Additionally, it was demonstrated that full-term subjects exhibit greater instability, leading to more dynamic reconfiguration of functional brain information and increased flexibility across the three identified canonical brain networks compared to preterm subjects. In contrast, those born prematurely show more stable networks but less dynamic and flexible organization of functional brain information within these key canonical networks. In summary, measuring multiscale functional network energy offered insights into the stability of canonical brain networks associated with subjects born prematurely. These findings enhance our understanding of how early birth impacts brain development.

neuroscience↗

bioRxiv2025

Deciphering Multiway Multiscale Brain Network Connectivity:Insights from Birth to 6 Months

Converging evidence suggests that understanding the human brain requires more than just examining pairwise functional brain interactions. The human brain is a complex, nonlinear system, and focusing solely on linear pairwise functional connectivity often overlooks important nonlinear and higher-order relationships. Infancy is a critical period marked by significant brain development that could contribute to future learning, health, and life success. Exploring higher-order functional relationships in the brain can provide insight into brain function and development. To the best of our knowledge, there is no existing research on multiway, multiscale brain network interactions in infants. In this study, we comprehensively investigate the interactions among brain intrinsic connectivity networks (ICNs), including both pairwise (pair-FNC) and triple relationships (tri-FNC). We focused on an infant dataset collected between birth and six months, a critical period for brain maturation. Our results revealed significant hierarchical, multiway, multiscale brain functional network interactions in the infant brain. These findings suggest that tri-FNC provide additional insights beyond what pairwise interactions reveal during early brain development. The tri-FNC predominantly involve the default mode, sensorimotor, visual, limbic, language, salience, and central executive domains. Notably, these triplet networks align with the classical triple network model of the human brain, which includes the default mode network, the salience network, and the central executive network. This suggests that the brain network system might already be initially established during the first six months of infancy. Interestingly, tri-FNC in the default mode and salience domains showed significantly stronger nonlinear interactions with age compared to pair-FNC. We also found that pair-FNC were less effective at detecting these networks. The present study suggests that exploring tri-FNC can offer additional insights beyond pair-FNC by capturing higher-order nonlinear interactions, potentially yielding more reliable biomarkers to characterize developmental trajectories.

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bioRxiv2024

Spontaneous Brain Dynamics Associated With Acceleration Of Longterm Functional Connectome In Postnatal Development

The first six postnatal months are a critical period for brain development, marked by rapid changes in functional neural circuits. However, long-term changes in neonatal functional connectome lacks an interpretive imaging indicator for the future development due to the non-linearity characteristics. In this study, we introduce an approach to extract intrinsic brain states from short-term brain dynamics to study the long-term (longitudinal) development. We found a high association (r=0.460) between the co-activated pattern of specific brain state and the acceleration pattern of non-linear development of static functional connectome. The fractional occupancy, self-sustaining probability of this short-term state share the similar age tendency with the long-term change rate within the majority of the function connectome. These findings suggest that short-term brain dynamics could serve as potential biomarkers for predicting the long-term development of functional connectome.

neuroscience↗

bioRxiv2024

Investigating the Impact of Habitual Sleep Quality on Episodic Memory Performance: An EEG-Based Representational Similarity Analysis

Sleep is crucial for episodic memory consolidation, yet the impact of habitual sleep quality on memory performance remains underexplored. This study investigates the relationship between sleep quality and episodic memory retrieval using EEG-based representational similarity analysis (RSA). Thirty-six participants wore wrist accelerometers for one week to capture habitual sleep patterns, including total sleep time and restlessness. Memory performance was assessed through a paired associate learning task, with EEG data recorded during encoding and retrieval phases. RSA was applied to EEG oscillatory power across time-frequency windows to examine the neural similarity between encoding and retrieval. The results showed both positive and negative correlations between sleep metric and memory performance, with sleep restlessness being linked to both increases and decreases in neural similarity across specific clusters. These findings emphasize the important role of sleep quality in shaping the neural processes underlying episodic memory retrieval, indicating a strong connection between sleep patterns and memory function.

neuroscience↗

bioRxiv2024

Spatial Development of Brain Networks During The First Six Postnatal Months

The initial months of life constitute a crucial period for human development. A comprehensive understanding of this early phase is essential for unraveling the origins of neurodevelopmental disorders and promoting infant brain health. This study uniquely focuses on the spatial development of intrinsic brain connectivity networks during infancy, which has been less explored compared to functional connectivity. We utilized independent component analysis on resting-state fMRI data from 74 infants to assess how the spatial organization of infant brain networks evolves between birth and six months. Our findings reveal significant changes in spatial characteristics, including an a notable rise in the network-averaged spatial similarity across age, reflecting how closely each participant-specific spatial map aligns with the group-level map for each network. We also observed a marked reduction in the network engagement range by age, representing the extent of voxel intensity range fluctuation within each network. This suggests a continuing process of consolidation, where voxel contributions to the network become more uniform, as indicated by the narrowing of intensity values. The network strength, calculated as the average of all the voxel intensities in the network, indicating the degree of involvement to the specific functional network, increased across age in several networks, such as frontal-mPFC, primary, and secondary visual networks. The network size, along with the network center of mass, illustrating spatial distribution alterations of brain networks by age, varied across different networks. For instance, both metrics increased across age in the secondary visual network but decreased in the temporal network. Additionally, we examined the networks in relation to their linear versus non-linear developmental trajectories across all spatial characteristics, providing a deeper understanding of how these patterns evolve during early infancy. These findings contribute to early brain development understanding and offer insights into potential markers of consolidation and spatial reorganization in large-scale brain networks during infancy.

neuroscience↗

bioRxiv2024

Uncovering Effects of Schizophrenia upon a Maximally Significant, Minimally Complex Subset of Default Mode Network Connectivity Features

A common analysis approach for resting state functional magnetic resonance imaging (rs-fMRI) dynamic functional network connectivity (dFNC) data involves clustering windowed correlation time-series and assigning time windows to clusters (i.e., states) that can be quantified to summarize aspects of the dFNC dynamics. However, those methods can be dominated by a select few features and obscure key dynamics related to less dominant features. This study presents an iterative feature learning approach to identify a maximally significant and minimally complex subset of dFNC features within the default mode network (DMN) in schizophrenia (SZ). Utilizing dFNC data from individuals with SZ and healthy controls (HC), our approach uncovers a subset of features that has a greater number of dFNC states with disorder-related dynamics than is found when all features are present in the clustering. We find that anterior cingulate cortex/posterior cingulate cortex (ACC/PCC) interactions are consistently related to SZ across the most significant iterations of the feature learning analysis and that individuals with SZ tend to spend more time in states with greater intra-ACC anticorrelation and almost no time in a state of high intra-ACC correlation that HCs periodically enter. Our findings highlight the need for nuanced analyses to reveal disorder-related dynamics and advance our understanding of neuropsychiatric disorders.

neuroscience↗

bioRxiv2023

Complexity Measures Of Psychotic Brain Activity In The fMRI Signal

When viewing the brain as a sophisticated, nonlinear dynamic system, employing complexity measures offers a valuable way to measure the intricate and dynamic aspects of spontaneous psychotic brain activity. These measures can help us identify irregularities and patterns in complex systems. In our study, we utilized fuzzy recurrence plots and sample entropy to evaluate the dynamic characteristics of psychiatric disorders. This assessment focused on understanding the temporal and spatial neural activity patterns, and more specifically, we applied complexity measures to investigate the functional connectivity within the psychotic brain. This involves understanding how different brain regions synchronize their activity, and complexity measures can reveal the patterns of these connections. It provides a means to understand how different brain regions interact and communicate under resting-state abnormal conditions. This study offers evidence demonstrating that fuzzy recurrence plots can serve as descriptors for functional connectivity and discusses their relevance to sample entropy in the context of the psychotic brain. In summary, complexity measures offer valuable insights that enrich our comprehension of atypical brain activity and the complexities present in the psychotic brain1.

neuroscience↗