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Zalesky, A.

Publications and source records attributed to Zalesky, A..

At least 19 recordsLinked to original sources

Frontolimbic Functional Connectivity Development from Birth to Emerging Adulthood

Frontolimbic circuits connecting the frontal cortex with the amygdala and the hippocampus are critical for emotion and learning. These connections undergo major changes throughout childhood and adolescence, yet the principles guiding their maturation remain unclear. Analyzing large developmental cohorts, we show that fronto-hippocampus connectivity develops rapidly in early childhood and stabilizes thereafter. In contrast, fronto-amygdala connectivity becomes progressively differentiated from fronto-hippocampus connectivity, with development most pronounced during adolescence. This entailed hippocampus and amygdala respectively becoming preferentially tethered to association-related regions and sensorimotor-related regions. Greater adversity exposure was associated with more differentiated fronto-amygdala connectivity for a given age. Higher cognitive ability was associated with less differentiated fronto-hippocampus connectivity. These findings suggest that frontolimbic connectivity development follows a principle of differentiation, with circuit-specific timing and sensitivity to stress and learning. This work provides a foundation for understanding typical and atypical frontolimbic circuitry development from birth to emerging adulthood. Significance StatementThe frontolimbic circuit, especially the fronto-hippocampus and fronto-amygdala circuitry, is integral for cognitive and affective processes. Yet its maturation has been challenging to characterize due to variable connectivity growth across the frontal cortex. Here, we reveal that this variability follows a principle of differentiation, where the hippocampus and the amygdala acquire respectively unique connectivity profiles with the frontal cortex at disparate developmental stages. Deviations from these normative trajectories were linked to cognitive ability and cumulative adversity, respectively. This approach provides a framework to unify inconsistent findings while serving as a foundation for identifying circuit-specific windows of plasticity and vulnerability.

neuroscience↗

Widespread use of invalid statistical tests in biomedical machine learning

Cross-validation is routinely used to compare performance in biomedical artificial intelligence. Standard tests ignore correlation across cross-validation folds, inflating false-positive rates. In a PRISMA-guided meta-analysis of 184 studies (impact factor [≥] 15) across 30 biomedical fields, 97% use invalid tests. Among studies with abstract-level claims supported by invalid tests, 59% rely on a spurious comparison: one that loses significance after correcting for this correlation. On average, regaining significance requires a 43% larger effect. Extending these findings to the broader literature, we estimate that spurious comparisons occur in nearly two in three studies and support abstract-level claims in nearly one in three studies. Simulations confirm false-positive rates paradoxically approach 100% when cross-validation is repeated to improve stability. We introduce SHARP, a redesign of cross-validation, which best balances false-positive control and power among 13 benchmarked tests. These results reveal widespread fragility in biomedical artificial intelligence and offer a practical route to valid comparisons.

bioinformatics↗

Polysynaptic signal propagation in networked neural masses

The routing of information across the brain's structural network is central to its wide range of functional capabilities. However, the mechanisms underlying information routing in complex brain networks, particularly between regions that do not share a direct anatomical connection, remain poorly understood. Neural mass models (NMMs), a computational modelling framework capable of capturing complex neural dynamics across scales, can potentially be used to study the dynamical and network bases of these vital polysynaptic routing processes. In this study, we investigate polysynaptic signalling in three widely used NMMs, obeying Ornstein-Uhlenbeck, Stuart-Landau, and Jansen-Rit dynamics, by tracking the propagation of a discrete, focal, high-amplitude perturbation across the underlying network. We find that polysynaptic propagation emerges in all tested NMMs when configured within dynamical regimes that effectively enhance the persistence of perturbations. We also find distinct parameter domains that maximise signal propagation to directly connected regions and to those separated from the source by at least two hops. Finally, we benchmark in silico stimulus propagation in the brain network against an empirical dataset of direct electrical stimulation trials, to explore the relative capabilities of the NMMs in capturing signal propagation to connected versus unconnected regions. This analysis highlights the significance of dynamical repertoire in capturing stimulus propagation outcomes. Overall, this study provides insights into how dynamical and network features shape signal propagation over complex brain networks.

neuroscience↗

SPICE: Fast parametric inference of significance for spatial associations between brain maps

Testing for spatial correlations between pairs of brain maps has emerged as a central task in neuroimaging studies. Determining the statistical significance of such correlations is challenging due to the presence of spatial autocorrelation in brain maps. Here we establish a novel parametric method, Parametric Spatial Test for Associations (PaSTA), to infer the significance of spatial associations between brain maps via covariance-variance modelling and effective degrees of freedom estimation. Our method is fast, reliable, and sensitive, enabling flexible significance testing of brain map correlations over arbitrary cortical surface and brain volumetric domains. We examine the sensitivity and specificity of PaSTA using simulated datasets with known ground truth and demonstrate its utility when applied to empirical brain maps. We extend PaSTA to approximately model modest nonstationarity in spatial autocorrelation and show that, our method yields improved false positive control and statistical power relative to existing approaches when brain maps are spatially heterogeneous.

neuroscience↗

Evaluating oscillatory mechanisms underlying flexible neural communication in the human brain

How the brain orchestrates the flow of information between its multiple functional units flexibly, quickly, and accurately, remains a fundamental question in neuroscience. Multiple theories identify neural oscillations as a likely basis for this process. However, a lack of empirical validation of proposed theories, particularly at the whole-brain scale, has hampered consensus on oscillatory principles governing neural communication, limiting our understanding of a process central to perception and cognition and its integration into experiments and clinical applications. Here, we empirically validate previously proposed neural-oscillatory communication mechanisms in the human brain - specifically those involving power and interareal phase coherence - at the whole-brain scale. We do this by estimating the dependence of inferred communication on oscillatory measures that have been theorised to facilitate communication, in source-localised resting-state magnetoencephalography (MEG) recordings. We find that power and phase coherence in the alpha, beta, and high-gamma bands track communication better than others. Crucially, the relation between communication and oscillatory measures varied across regions, indicating spatial heterogeneity in routing mechanisms. Notably, power and coherence-based principles tracked communication patterns of unimodal regions better than those of transmodal regions. In sum, these findings suggest that the human brain implements regionally specific communication mechanisms with complex neural-oscillatory dependence. Significance statementFlexible and dynamic routing of information between neural elements is vital for human brain function. Despite its importance, the mechanisms underlying flexible communication in the brain are not fully understood. Several lines of evidence suggest that neural oscillations might mediate flexible communication, but whether such mechanisms operate at whole-brain scales remains uncertain. Here, we investigate the oscillatory underpinnings of communication by assessing how well observed communication patterns from magnetoencephalography data align with the predictions of established theories. Our findings suggest that the brain follows complex region-specific routing principles to realise flexible communication. Knowledge of these principles can develop our fundamental understanding of functions like perception and cognition, refine models of interareal interactions, and help develop more effective stimulation-based clinical interventions.

neuroscience↗

Identifying Neuroimaging Biomarkers of Resilience and Vulnerability to Chronic Stress in An Animal Model: An Exploratory Analysis

Stress is a main contributor to mood disorders, with individuals displaying great heterogeneity in response to stressful life events and adversity. Identifying biomarkers of vulnerability and resilience to stress would facilitate a prevention-based approach to mental illness that benefits individuals and reduces healthcare costs. The present study adopted a multivariate machine-learning approach to track neuroimaging biomarkers predictive of resilience and vulnerability following a chronic restraint stress (CRS) model. 96 male Sprague-Dawley rats underwent two sessions of MRI and behavioral tests, before and after CRS. Resilience and vulnerability to CRS were assessed with elevated plus maze and forced swimming tests. Hierarchical clustering was applied to construct brain networks. Partial correlation was used to compute network connectivity. Repeated nested cross validation with a support vector machine was employed to identify rs-fMRI biomarkers predictive of resilience and vulnerability following CRS. No strong group effect size of behavioral changes following CRS was observed within the same animals, suggesting the presence of resilient and vulnerable subgroups. Although the average model performance was modest (area under the receiver operating characteristic curve: 0.3 ~ 0.67), baseline functional connectivity across cerebellum, brainstem, striatum, prefrontal and salience-orbitofrontal regions, as well as functional alteration across hippocampus, striatum, prefrontal regions, auditory thalamus, cerebellum, inferior colliculi and brainstem were identified as stable features. The present study is the first to identify connectome-based neuroimaging biomarkers predictive of resilience and vulnerability using an animal model. The results may provide insights into neuroimaging biomarkers to aid diagnosis and prevention of mood disorders in humans.

neuroscience↗

Optimizing the In Vitro Neuronal Microenvironment to Mitigate Phototoxicity in Live-cell Imaging

Long-term imaging formats are ideal for capturing dynamic neuronal network formation in vitro, yet fluorescent techniques are often constrained by the impact of phototoxicity on cell survival. Here we present a live-imaging protocol that was optimised via quantitative analysis of 3 target culturing conditions on neuromorphological health: extracellular matrix (human- versus murine-derived laminin), culture media (Neurobasal versus Brainphys Imaging media), and seeding density (1x105 versus 2x105 cells/cm2). A cortical neuron reporter line was differentiated from human embryonic stem cells by transduction of Neurogenin-2 and green fluorescent protein, then fluorescently imaged in 8 different microenvironments daily for 33 days. Alongside viability analysis by PrestoBlue assay and gene quantification by digital polymerase chain reaction, an automated image analysis pipeline was developed to characterise network morphology and organisation over time. Brainphys Imaging medium was observed to support neuron viability, outgrowth, and self-organisation to a greater extent than Neurobasal medium with either laminin type, while the combination of Neurobasal medium and human laminin reduced cell survival. Further, a higher seeding density fostered somata clustering, but did not significantly extend viability compared to low density. These findings suggest a synergistic relationship between species-specific laminin and culture media in phototoxic environments, which is positively mediated by light-protective compounds found in Brainphys Imaging medium.

cell biology↗

TRAMFIX: TRavelling Across Melbourne for FIXel-based analysis (a reproducibility study)

Fixel-based analysis (FBA) has gained substantial interest for its ability to probe fibre-specific changes in the brains white matter from diffusion-weighted imaging data. However, the reproducibility and reliability of fixel-based measures across different scanners remains largely unknown. In this work, we present TRAMFIX: a multisite dataset of travelling participants (n=10 healthy adults) scanned across four 3T MRI scanners using a harmonised multi-shell DWI protocol. DWI data were processed using two pipelines that can adopted when performing multi-site FBA studies (site-specific versus pooled processing). We extracted fixel-based measures of fibre density (FD), fibre cross-section (FC), and fibre density and cross-section (FDC), as well as diffusion tensor imaging (DTI)-based fractional anisotropy (FA) and mean diffusivity (MD) from the harmonised protocol. Within-subject coefficients of variation (CVws) and intraclass correlation coefficients (ICC) of FBA and DTI measures were computed at multiple resolutions of computation and analysis: (i) the whole-brain averaged level, (ii) tract-level, and (iii) fixel- or voxel-level. Fixel-based metrics demonstrated high reproducibility and reliability at the whole-brain level (CVws ranging between 0.51% to 1.57% and ICC between 0.93 and 0.996). While reproducibility and reliability remained high for tract-averaged FBA measures (particularly the FC and FDC metrics), some tracts exhibited lower ICC values < 0.8 for the FD measure. When examining fixel-level reliability and reproducibility clear spatial patterns emerged, with lower ICC across subcortical and cerebellar regions, and higher CVws at the cortical boundaries. Across all levels, tensor-based metrics demonstrated slightly lower reproducibility and reliability metrics than FBA measures, suggesting that FBA metrics are just as, if not more, reproducible than DTI metrics across scanners when using identical protocols. Our findings provide support for the reproducibility and reliability of fixel-based measures, highlighting their potential for use in multi-site FBA studies. Future work examining protocol-related differences, as well as appropriate harmonisation strategies when pooling data across sites and scanners, will be valuable.

neuroscience↗

MRI-Derived Markers of Acute and Chronic Inflammatory Processes in the VTA Associated with Depression

BackgroundDepression is a leading cause of disability worldwide, with inflammation increasingly recognized as a contributing factor. Inflammatory processes can disrupt the brains reward circuitry, particularly the ventral tegmental area (VTA), which is central to dopamine-mediated motivation and reward. This study investigates whether MRI-derived markers sensitive to neuroinflammation and microstructure in the VTA are associated with depression diagnosis and symptom severity. MethodsWe analyzed diffusion weighted imaging and quantitative susceptibility mapping data from 32,495 UK Biobank participants, including 3,807 individuals with ICD-10 diagnosed depression. Metrics sensitive to neuroinflammation (free water [FW], isotropic volume fraction [ISOVF], magnetic susceptibility) and microstructure (intracellular volume fraction [ICVF], orientation dispersion index [ODI] volume) were extracted from the VTA. Group differences between the major depression group and BMI, sex, and age-matched healthy controls were assessed using ANOVAs and linear regression was used to predict acute symptom severity based on Recent Depressive Symptoms scores. ResultsParticipants with depression diagnosis had significantly higher FW (p < 0.001) and ISOVF (p = 0.001) compared to HCs, indicating increased extracellular processes such as inflammation in the VTA. Lower ISOVF ({beta} = -0.46, p = 0.017) and higher ICVF ({beta} = 0.34, p = 0.007) and ODI ({beta} = 0.49, p = 0.004) were associated with higher depression severity, independent of depressive diagnosis history. ConclusionsOur findings reveal distinct patterns of VTA microstructural changes associated with depression history versus acute depressive symptom severity, suggesting different underlying pathophysiological mechanisms. Distinct patterns of neuroinflammation may differentiate acute from chronic depression, informing targeted interventions.

neuroscience↗

Mapping the coupling between tract reachability and cortical geometry of the human brain

The study of cortical geometry and connectivity is prevalent in research on the human brain. However, these two aspects of brain structure are usually examined separately, leaving the essential connections between the brains folding patterns and white matter connectivity unexplored. In this study, we aimed to elucidate fundamental links between cortical geometry and white matter tract connectivity. We developed the concept of tract-geometry coupling (TGC) by optimizing the alignment between tract connectivity to the cortex and multiscale cortical geometry. Specifically, spectral analyses of the cortical surface yielded a set of geometrical eigenmodes, which were then used to explain the locations on the cortical surface reached by specific white matter tracts, referred to as tract reachability. In two independent datasets, we confirmed that tract reachability was well characterized by cortical geometry. We further observed that TGC had high test-retest ability and was specific to each individual. Interestingly, low-frequency TGC was found to be heritable and more informative than the high-frequency components in behavior prediction. Finally, we found that TGC could reproduce task-evoked cortical activation patterns. Collectively, our study provides a new approach to mapping coupling between cortical geometry and connectivity, highlighting how these two aspects jointly shape the connected brain.

neuroscience↗

Deep generation of personalized connectomes based on individual attributes

An individuals connectome is unique. Interindividual variation in connectome architecture associates with disease status, cognition, lifestyle factors, and other personal attributes. While models to predict personal attributes from a persons connectome are abundant, the inverse task-- inferring connectome architecture from an individuals personal profile--has not been widely studied. Here, we introduce a deep model to generate a persons entire connectome exclusively based on their age, sex, body phenotypes, cognition, and lifestyle factors. Using the richly phenotyped UK Biobank connectome cohort (N=8,086), we demonstrate that our model can generate network architectures that closely recapitulate connectomes mapped empirically using diffusion MRI and tractography. We find that age, sex, and body phenotypes exert the strongest influence on the connectome generation process, with an impact approximately four times greater than that of cognition and lifestyle factors. Regional differences in the importance of measures were observed, including an increased importance of cognition in the association cortex relative to the visual system. We further show that generated connectomes can improve the training of machine learning models and reduce their predictive errors. Our work demonstrates the feasibility of inferring brain connectivity from an individuals personal data and enables future applications of connectome generation such as data augmentation and anonymous data sharing.

neuroscience↗

On reconstruction of cortical functional maps using subject-specific geometric and connectome eigenmodes

Understanding the interplay between human brain structure and function is crucial to discern neural dynamics. This study explores the relation between brain structure and macroscale functional activity using subject-specific structural connectome eigenmodes, complementing prior work that focused on group-level models and geometry. Leveraging data from the Human Connectome Project, we assess accuracy in reconstructing various functional MRI-based cortical maps using individualised eigenmodes, specifically, across a range of connectome construction parameters. Our results show only minor differences in performance between surface geometric eigenmodes, a local neighborhood graph, a highly smoothed null model, and individual and group-level connectomes at modest smoothing and density levels. Furthermore, our results suggest that spatially smooth eigenmodes best explain functional data. The absence of improvement of individual connectomes and surface geometry over smoothed null models calls for further methodological innovation to better quantify and understand the degree to which brain structure constrains brain function.

neuroscience↗

High-precision neurofeedback-guided meditation training optimises real-world self-guided meditation practice for well-being

Meditation can benefit well-being and mental health, but novices often struggle to effectively recognize and disengage from mental processes during meditation due to limited awareness, potentially diminishing meditations benefits. We investigated whether personalised high-precision neurofeedback (NF) can improve disengagement from mental activity during meditation and enhance meditations outcomes. In a single-blind, controlled, longitudinal paradigm, 40 novice meditators underwent two consecutive days of meditation training with intermittent visual feedback from either their own (N=20) or a matched participants (N=20; control group) posterior cingulate cortex (PCC) activity measured using 7 Tesla functional magnetic resonance imaging. During training, the experimental group showed stronger functional decoupling of PCC from dorsolateral prefrontal cortex, indicating better control over disengagement from mental processes during meditation. This led to greater improvements in emotional well-being and mindful awareness of mental processes during a week of real-world self-guided meditation. We provide compelling evidence supporting the utility of high-precision NF-guided meditation training to optimise real-world meditation practice for well-being.

neuroscience↗

Event-marked Windowed Communication: Inferring activity propagation from neural time series

Tracking signal propagation in nervous systems is crucial to our understanding of brain function and information processing. Current methods for inferring neural communication track patterns of sustained co-activation over time, making them unsuitable to detect discrete instances of signal transmission. Here, we propose Event-marked Windowed Communication (EWC), a new analytical framework to infer functional interactions arising from discrete signalling events between neural elements, in otherwise continuous time series data. In contrast to conventional measures of functional connectivity, our method utilises an event-based subsampling of neural time series, which allows it to capture the statistical analogue of activity propagation. We test EWC on simulations of neural dynamics and show that it is capable of retrieving ground truth motifs of directional signalling, over a range of model configurations. Critically, we demonstrate that EWCs subsampling approach affords profound reductions in computation times, compared to established network inference methods such as transfer entropy. Lastly, we showcase the utility of EWC to infer whole-brain functional networks from MEG recordings. Networks computed using EWC and transfer entropy were highly correlated (median r=0.821 across subjects), but EWC inference was approximately 6.5 times faster per epoch. In summary, our work presents a new method to infer signalling from time series of neural activity at low computational costs. Our framework is flexible and can be applied to activity time series captured by diverse functional neuroimaging modalities, opening up new avenues for the study of neural communication.

neuroscience↗

Spurious correlations in surface-based functional brain imaging

The study of functional MRI data is increasingly performed after mapping from volumetric voxels to surface vertices. Processing pipelines commonly used to achieve this mapping produce meshes with uneven vertex spacing, with closer neighbours in sulci compared to gyri. Consequently, correlations between the fMRI time series of neighbouring sulcal vertices are stronger than expected. However, the causes, extent, and impacts of this bias are not well understood or widely appreciated. We explain the origins of these biases, and using in-silico models of fMRI data, illustrate how they lead to spurious results. The bias leads to leakage of anatomical cortical folding information into fMRI time series. We show that many common analyses can be affected by this "gyral bias", including test-retest reliability, fingerprinting, functional parcellations, regional homogeneity, and brain-behaviour associations. Finally, we provide recommendations to avoid or remedy this spatial bias.

neuroscience↗

Benchmarking methods for mapping functional connectivity in the brain

The networked architecture of the brain promotes synchrony among neuronal populations and the emergence of coherent dynamics. These communication patterns can be comprehensively mapped using noninvasive functional imaging, resulting in functional connectivity (FC) networks. Despite its popularity, FC is a statistical construct and its operational definition is arbitrary. While most studies use zero-lag Pearsons correlations by default, there exist hundreds of pairwise interaction statistics in the broader scientific literature that can be used to estimate FC. How the organization of the FC matrix varies with the choice of pairwise statistic is a fundamental methodological question that affects all studies in this rapidly growing field. Here we comprehensively benchmark the topological and geometric organization, neurobiological associations, and cognitive-behavioral relevance of FC matrices computed using a large library of 239 pairwise interaction statistics. We comprehensively investigate how canonical features of FC networks vary with the choice of pairwise statistic, including (1) hub mapping, (2) weight-distance trade-offs, (3) structure-function coupling, (4) correspondence with other neurophysiological networks, (5) individual fingerprinting, and (6) brain-behavior prediction. We find substantial quantitative and qualitative variation across FC methods. Throughout, we observe that measures such as covariance (full correlation), precision (partial correlation) and distance display multiple desirable properties, including close correspondence with structural connectivity, the capacity to differentiate individuals and to predict individual differences in behavior. Using information flow decomposition, we find that differences among FC methods may arise from differential sensitivity to the underlying mechanisms of inter-regional communication, with some more sensitive to redundant and some to synergistic information flow. In summary, our report highlights the importance of tailoring a pairwise statistic to a specific neurophysiological mechanism and research question, providing a blueprint for future studies to optimize their choice of FC method.

neuroscience↗

Eigenmodes of the brain: revisiting connectomics and geometry

Eigenmodes can be derived from various structural brain properties, including cortical surface geometry1 and interareal axonal connections comprising an organisms connectome2. Pang and colleagues map geometric and connectome eigenmodes to spatial patterns of human brain activity, assessing whether brain connectivity or geometry provide greater explanatory power of brain function3. The authors find that geometric eigenmodes are superior predictors of cortical activity compared to connectome eigenmodes. They conclude that this supports the predictions of neural field theory (NFT)4, in that "brain activity is best represented in terms of eigenmodes derived directly from the shape of the cortex, thus emphasizing a fundamental role of geometry in constraining dynamics". The experimental comparisons favoring geometric eigenmodes over connectome eigenmodes, in conjunction with specific statements regarding the relative efficacy of geometry in representing brain activity, have been widely interpreted to mean that geometry imposes stronger constraints on cortical dynamics than connectivity5-9. Here, we reconsider the comparative experimental evidence focusing on the impact of connectome mapping methodology. Utilizing established methods to mitigate connectome construction limitations, we map new connectomes for the same dataset, finding that eigenmodes derived from these connectomes reach comparable accuracy in explaining brain activity to that of geometric eigenmodes. We conclude that the evidence presented to support the comparative proposition that "eigenmodes derived from brain geometry represent a more fundamental anatomical constraint on dynamics than the connectome" may require reconsideration in light of our findings. Pang and colleagues present compelling evidence for the important role of geometric constraints on brain function, but their findings should not be interpreted to mean that geometry has superior explanatory power over the connectome.

neuroscience↗

A generative model of the connectome with dynamic axon growth

Connectome generative models, otherwise known as generative network models, provide insight into the wiring principles underpinning brain network organization. While these models can approximate numerous statistical properties of empirical networks, they typically fail to explicitly characterize an important contributor to brain organization - axonal growth. Emulating the chemoaffinity guided axonal growth, we provide a novel generative model in which axons dynamically steer the direction of propagation based on distance-dependent chemoattractive forces acting on their growth cones. This simple dynamic growth mechanism, despite being solely geometry-dependent, is shown to generate axonal fiber bundles with brain-like geometry and features of complex network architecture consistent with the human brain, including lognormally distributed connectivity weights, scale-free nodal degrees, small-worldness, and modularity. We demonstrate that our model parameters can be fitted to individual connectomes, enabling connectome dimensionality reduction and comparison of parameters between groups. Our work offers an opportunity to bridge studies of axon guidance and connectome development, providing new avenues for understanding neural development from a computational perspective. Author SummaryGenerative models of the human connectome provide insight into principles driving brain network development. However, current models do not capture axonal outgrowth, which is crucial to the formation of neural circuits. We develop a novel generative connectome model featuring dynamic axonal outgrowth, revealing the contribution of microscopic axonal guidance to the network topology and axonal geometry of macroscopic connectomes. Simple axonal outgrowth rules representing continuous chemoaffinity gradients are shown to generate complex, brain-like topologies and realistic axonal fascicle architectures. Our model is sufficiently sensitive to capture subtle interindividual differences in axonal outgrowth between healthy adults. Our results are significant because they reveal core principles that may give rise to both complex brain networks and brain-like axonal bundles, unifying neurogenesis across scales.

neuroscience↗