Tanguy Fardet, Emmanouil Giannakakis, Lukas Paulun
et al.
As more connectome data become available, the question of how to best analyse the structure of biological neural networks becomes increasingly pertinent. In brain networks, knowing that two areas are connected is often not sufficient, as the directionality and weight of the connection affect the dynamics in crucial ways. Still, the methods commonly used to estimate network properties, such as clustering and small-worldness, usually disregard features encoded in the directionality and strength of network connections. To address this issue, we propose using fully-weighted and directed clustering measures that provide higher sensitivity to non-random structural features. Using artificial networks, we demonstrate the problems with methods routinely used in the field and how fully-weighted and directed methods can alleviate them. Specifically, we highlight their robustness to noise and their ability to address thresholding issues, particularly in inferred networks. We further apply our method to the connectomes of different species and uncover regularities and correlations between neuronal structures and functions that cannot be detected with traditional clustering metrics. Finally, we extend the notion of small-worldness in brain networks to account for weights and directionality and show that some connectomes can no longer be considered ``small-world''. Overall, our study makes a case for a combined use of fully-weighted and directed measures to deal with the variability of brain networks and suggests the presence of complex patterns in neural connectivity that can only be revealed using such methods.
Joseph Bodenheimer, Paul Bogdan, Sérgio Pequito
et al.
Understanding the neural mechanisms underlying the transitions between different states of consciousness is a fundamental challenge in neuroscience. Thus, we investigate the underlying drivers of changes during the resting-state dynamics of the human brain, as captured by functional magnetic resonance imaging (fMRI) across varying levels of consciousness (awake, light sedation, deep sedation, and recovery). We deploy a model-based approach relying on linear time-invariant (LTI) dynamical systems under unknown inputs (UI). Our findings reveal distinct changes in the spectral profile of brain dynamics - particularly regarding the stability and frequency of the system's oscillatory modes during transitions between consciousness states. These models further enable us to identify external drivers influencing large-scale brain activity during naturalistic auditory stimulation. Our findings suggest that these identified inputs delineate how stimulus-induced co-activity propagation differs across consciousness states. Notably, our approach showcases the effectiveness of LTI models under UI in capturing large-scale brain dynamic changes and drivers in complex paradigms, such as naturalistic stimulation, which are not conducive to conventional general linear model analysis. Importantly, our findings shed light on how brain-wide dynamics and drivers evolve as the brain transitions towards conscious states, holding promise for developing more accurate biomarkers of consciousness recovery in disorders of consciousness.
Autism Spectrum Disorder (ASD) is a prevalent neurological disorder. However, the multi-faceted symptoms and large individual differences among ASD patients are hindering the diagnosis process, which largely relies on subject descriptions and lacks quantitative biomarkers. To remediate such problems, this paper explores the use of graph theory and topological data analysis (TDA) to study brain activity in ASD patients and normal controls. We employ the Mapper algorithm in TDA and the distance correlation graphical model (DCGM) in graph theory to create brain state networks, then innovatively adopt complex network metrics in Graph signal processing (GSP) and physical quantities to analyze brain activities over time. Our findings reveal statistical differences in network characteristics between ASD and control groups. Compared to normal subjects, brain state networks of ASD patients tend to have decreased modularity, higher von Neumann entropy, increased Betti-0 numbers, and decreased Betti-1 numbers. These findings attest to the biological traits of ASD, suggesting less organized and more variable brain dynamics. These findings offer potential biomarkers for ASD diagnosis and deepen our understanding of its neural correlations.
Based on the background of the change in the urban–rural relationship in Guangdong Province, this paper constructs an analysis framework of urban and rural coordination development. Using the data of 19 administrative units above prefecture level in Guangdong Province, this paper studies the space–time evolution of urban and rural coordination development during 2000–2015 through Principal Component Analysis (PCA) and Exploratory Spatial Data Analysis (ESDA) and explores the influencing factors and driving forces behind it. It is found that there is club convergence in the urban and rural coordination development in Guangdong Province. This kind of convergence is reflected in the findings that the east bank of the Pearl River estuary is the best area for the urban and rural coordination development where Guangzhou, Dongguan, Shenzhen is the core and the level of urban and rural coordination development in the east, west and north of Guangdong Province is relatively low, which also reflects a geographical polarization feature. Based on the analysis of the factors that promote the urban and rural coordination development in the main years of 2000–2015, it can be concluded that location, economic development and urbanization level are the most important driving forces, followed by industrial structure. This research can be used as a decision-making reference for urban and rural coordination development and new countryside construction in China in the New Era.
In the past three decades, neuroimaging has provided important insights into structure-function relationships in the human brain. Recently, however, the methods for analyzing functional magnetic resonance imaging (fMRI) data have come under scrutiny, with studies questioning cross-software comparability, the validity of statistical inference and interpretation, and the influence of the spatial filter size on neuroimaging analyses. As most fMRI studies only use a single filter for analysis, much information on the size and shape of the BOLD signal in Gaussian scale space remains hidden and constrains the interpretation of fMRI studies. To investigate the influence of the spatial observation scale on fMRI analysis, we use a spatial multiscale analysis with a range of Gaussian filters from 1-20 mm (full width at half maximum) to analyze fMRI data from a speech repetition paradigm in 25 healthy subjects. We show that analyzing the fMRI data over a range of Gaussian filter kernels reveals substantial variability in the neuroanatomical localization and the average signal strength and size of suprathreshold clusters depending on the filter size. We also demonstrate how small spatial filters bias the results towards subcortical and cerebellar clusters. Furthermore, we describe substantially different scale-dependent cluster size dynamics between cortical and cerebellar clusters. We discuss how spatial multiscale analysis may substantially improve the interpretation of fMRI data. We propose to further develop a spatial multiscale analysis to fully explore the deep structure of the BOLD signal in Gaussian scale space.
The brain is a highly complex system. Most of such complexity stems from the intermingled connections between its parts, which give rise to rich dynamics and to the emergence of high-level cognitive functions. Disentangling the underlying network structure is crucial to understand the brain functioning under both healthy and pathological conditions. Yet, analyzing brain networks is challenging, in part because their structure represents only one possible realization of a generative stochastic process which is in general unknown. Having a formal way to cope with such intrinsic variability is therefore central for the characterization of brain network properties. Addressing this issue entails the development of appropriate tools mostly adapted from network science and statistics. Here, we focus on a particular class of maximum entropy models for networks, i.e. exponential random graph models (ERGMs), as a parsimonious approach to identify the local connection mechanisms behind observed global network structure. Efforts are reviewed on the quest for basic organizational properties of human brain networks, as well as on the identification of predictive biomarkers of neurological diseases such as stroke. We conclude with a discussion on how emerging results and tools from statistical graph modeling, associated with forthcoming improvements in experimental data acquisition, could lead to a finer probabilistic description of complex systems in network neuroscience.
Transfer Entropy, a generalisation of Granger Causality, promises to measure "information transfer" from a source to a target signal by ignoring self-predictability of a target signal when quantifying the source-target relationship. A simple example for signals with such self-predictability are narrowband signals. These are both thought to be intrinsically generated by the brain as well as commonly dealt with in analyses of brain signals, where band-pass filters are used to separate responses from noise. However, the use of Transfer Entropy is usually discouraged in such cases. We simulate simplistic examples where we confirm the failure of classic implementations of Transfer Entropy when applied to narrow-band signals, as made evident by a flawed recovery of effect sizes and interaction delays. We propose an alternative approach based on a whitening of the input signals before computing a bivariate measure of directional time-lagged dependency. This approach solves the problems found in the simple simulated systems. Finally, we explore the behaviour of our measure when applied to delta and theta response components in Magnetoencephalography (MEG) responses to continuous speech. The small effects that our measure attributes to a directed interaction from the stimulus to the neuronal responses are stronger in the theta than in the delta band. This suggests that the delta band reflects a more predictive coupling, while the theta band is stronger involved in bottom-up, reactive processing. Taken together, we hope to increase the interest in directed perspectives on frequency-specific dependencies.
Abida Sanjana Shemonti, Joshua D. Eisenberg, Robert O. Heuckeroth
et al.
We describe a generative network model of the architecture of the enteric nervous system (ENS) in the colon employing data from images of human and mouse tissue samples obtained through confocal microscopy. Our models combine spatial point pattern analysis with graph generation to characterize the spatial and topological properties of the ganglia (clusters of neurons and glial cells), the inter-ganglionic connections, and the neuronal organization within the ganglia. We employ a hybrid hardcore-Strauss process for spatial patterns and a planar random graph generation for constructing the spatially embedded network. We show that our generative model may be helpful in both basic and translational studies, and it is sufficiently expressive to model the ENS architecture of individuals who vary in age and health status. Increased understanding of the ENS connectome will enable the use of neuromodulation strategies in treatment and clarify anatomic diagnostic criteria for people with bowel motility disorders.
Neural interfaces using biocompatible scaffolds provide crucial properties for the functional repair of nerve injuries and neurodegenerative diseases, including cell adhesion, structural support, and mass transport. Neural stimulation has also been found to be effective in promoting neural regeneration. This work provides a new strategy to integrate photoacoustic (PA) neural stimulation into hydrogel scaffolds using a nanocomposite hydrogel approach. Specifically, polyethylene glycol (PEG)-functionalized carbon nanotubes (CNT), highly efficient photoacoustic agents, are embedded into silk fibroin to form biocompatible and soft photoacoustic materials. We show that these photoacoustic functional scaffolds enable non-genetic activation of neurons with a spatial precision defined by the area of light illumination, promoting neuron regeneration. These CNT/silk scaffolds offered reliable and repeatable photoacoustic neural stimulation. 94% of photoacoustic stimulated neurons exhibit a fluorescence change larger than 10% in calcium imaging in the light illuminated area. The on-demand photoacoustic stimulation increased neurite outgrowth by 1.74-fold in a dorsal root ganglion model, when compared to the unstimulated group. We also confirmed that photoacoustic neural stimulation promoted neurite outgrowth by impacting the brain-derived neurotrophic factor (BDNF) pathway. As a multifunctional neural scaffold, CNT/silk scaffolds demonstrated non-genetic PA neural stimulation functions and promoted neurite outgrowth, providing a new method for non-pharmacological neural regeneration.
Spikes can be easily detected inmostintracellular recordings as sharp peaks. However, insome experimental preparations,because of unipolar morphology or other characteristicsof the recorded neurons, the sizes of the spikes recorded from the soma can be much smaller. The experimental settings and the quality of the recording can also affect the observed amplitudes of the spikes. Whole-cell patch-clamp recordings from the somata of projection neurons of the antennal lobe in Drosophila or mosquitoes can show spikes with amplitudes as small as 2 mV. Moreover, the observed spikes often ride on relatively large depolarizations, which makes it difficult for the standard thresholding-based approaches to distinguish them from noise or sharp EPSPs present in the signal. For spike detection in such neuronal recordings, we propose a clustering-based algorithm that separates peaks corresponding to action potentials from those corresponding to noise. Candidate peaks, including many noise peaks, are first selected according to their sharpness, and then a feature vector is extracted for each peak. The 3-dimensional feature vector contains the absolute value of the peak voltage, height of the spike, and the magnitude of the second derivative minima attained during the spike. In most recordings, this 3D space reveals two natural clusters, separating the noise peaks from the true action potentials. Some parameters of the algorithm can be optionally altered by the user to improve detection, which comes handy in the few recordings where the default parameters do not work well. In summary, the algorithm facilitates accurate spike detection to enable the interpretation and analysis of patch-clamp data from neuronal recordings in invertebrates. The algorithm is implemented as an freely available open-source tool.
Gamma frequency oscillations (25-140 Hz), observed in the neural activities within many brain regions, have long been regarded as a physiological basis underlying many brain functions, such as memory and attention. Among numerous theoretical and computational modeling studies, gamma oscillations have been found in biologically realistic spiking network models of the primary visual cortex. However, due to its high dimensionality and strong nonlinearity, it is generally difficult to perform detailed theoretical analysis of the emergent gamma dynamics. Here we propose a suite of Markovian model reduction methods with varying levels of complexity and applied it to spiking network models exhibiting heterogeneous dynamical regimes, ranging from homogeneous firing to strong synchrony in the gamma band. The reduced models not only successfully reproduce gamma band oscillations in the full model, but also exhibit the same dynamical features as we vary parameters. Most remarkably, the invariant measure of the coarse-grained Markov process reveals a two-dimensional surface in state space upon which the gamma dynamics mainly resides. Our results suggest that the statistical features of gamma oscillations strongly depend on the subthreshold neuronal distributions. Because of the generality of the Markovian assumptions, our dimensional reduction methods offer a powerful toolbox for theoretical examinations of many other complex cortical spatio-temporal behaviors observed in both neurophysiological experiments and numerical simulations.
The oxytocin effects on large-scale brain networks such as Default Mode Network (DMN) and Frontoparietal Network (FPN) have been largely studied using fMRI data. However, these studies are mainly based on the statistical correlation or Bayesian causality inference, lacking interpretability at physical and neuroscience level. Here, we propose a physics-based framework of Kuramoto model to investigate oxytocin effects on the phase dynamic neural coupling in DMN and FPN. Testing on fMRI data of 59 participants administrated with either oxytocin or placebo, we demonstrate that oxytocin changes the topology of brain communities in DMN and FPN, leading to higher synchronization in the FPN and lower synchronization in the DMN, as well as a higher variance of the coupling strength within the DMN and more flexible coupling patterns across time. These results together indicate that oxytocin may increase the ability to overcome the corresponding internal oscillation dispersion and support the flexibility in neural synchrony in various social contexts, providing new evidence for explaining the oxytocin modulated social behaviors. Our proposed Kuramoto model-based framework can be a potential tool in network neuroscience and offers physical and neural insights into phase dynamics of the brain.
Abstract The main idea of this research is to define a new neutrosophic crisp points in neutrosophic crisp topological space namely (NncPN ), the concept of Nnc limit point was defined using (NncPN ), with some of its properties, the separation axioms (Nnceτi -space (i = 0,1, 2) were constructed in neutrosophic crisp topological space using (NncPN ) and examine the relationship between them in details.
Lancelot Da Costa, Thomas Parr, Biswa Sengupta
et al.
Active inference is a normative framework for explaining behaviour under the free energy principle -- a theory of self-organisation originating in neuroscience. It specifies neuronal dynamics for state-estimation in terms of a descent on (variational) free energy -- a measure of the fit between an internal (generative) model and sensory observations. The free energy gradient is a prediction error -- plausibly encoded in the average membrane potentials of neuronal populations. Conversely, the expected probability of a state can be expressed in terms of neuronal firing rates. We show that this is consistent with current models of neuronal dynamics and establish face validity by synthesising plausible electrophysiological responses. We then show that these neuronal dynamics approximate natural gradient descent, a well-known optimisation algorithm from information geometry that follows the steepest descent of the objective in information space. We compare the information length of belief updating in both schemes, a measure of the distance traveled in information space that has a direct interpretation in terms of metabolic cost. We show that neural dynamics under active inference are metabolically efficient and suggest that neural representations in biological agents may evolve by approximating steepest descent in information space towards the point of optimal inference.