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Gosti G, Milanetti E, Folli V, de Pasquale F, Leonetti M, Corbetta M, Ruocco G, Della Penna S. A recurrent Hopfield network for estimating meso-scale effective connectivity in MEG. Neural Netw 2024; 170:72-93. [PMID: 37977091 DOI: 10.1016/j.neunet.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The architecture of communication within the brain, represented by the human connectome, has gained a paramount role in the neuroscience community. Several features of this communication, e.g., the frequency content, spatial topology, and temporal dynamics are currently well established. However, identifying generative models providing the underlying patterns of inhibition/excitation is very challenging. To address this issue, we present a novel generative model to estimate large-scale effective connectivity from MEG. The dynamic evolution of this model is determined by a recurrent Hopfield neural network with asymmetric connections, and thus denoted Recurrent Hopfield Mass Model (RHoMM). Since RHoMM must be applied to binary neurons, it is suitable for analyzing Band Limited Power (BLP) dynamics following a binarization process. We trained RHoMM to predict the MEG dynamics through a gradient descent minimization and we validated it in two steps. First, we showed a significant agreement between the similarity of the effective connectivity patterns and that of the interregional BLP correlation, demonstrating RHoMM's ability to capture individual variability of BLP dynamics. Second, we showed that the simulated BLP correlation connectomes, obtained from RHoMM evolutions of BLP, preserved some important topological features, e.g, the centrality of the real data, assuring the reliability of RHoMM. Compared to other biophysical models, RHoMM is based on recurrent Hopfield neural networks, thus, it has the advantage of being data-driven, less demanding in terms of hyperparameters and scalable to encompass large-scale system interactions. These features are promising for investigating the dynamics of inhibition/excitation at different spatial scales.
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Affiliation(s)
- Giorgio Gosti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, Piazzale Aldo Moro, 5, 00185, Rome, Italy; Istituto di Scienze del Patrimonio Culturale, Sede di Roma, Consiglio Nazionale delle Ricerche, CNR-ISPC, Via Salaria km, 34900 Rome, Italy.
| | - Edoardo Milanetti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185, Rome, Italy.
| | - Viola Folli
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; D-TAILS srl, Via di Torre Rossa, 66, 00165, Rome, Italy.
| | - Francesco de Pasquale
- Faculty of Veterinary Medicine, University of Teramo, 64100 Piano D'Accio, Teramo, Italy.
| | - Marco Leonetti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, Piazzale Aldo Moro, 5, 00185, Rome, Italy; D-TAILS srl, Via di Torre Rossa, 66, 00165, Rome, Italy.
| | - Maurizio Corbetta
- Department of Neuroscience, University of Padova, Via Belzoni, 160, 35121, Padova, Italy; Padova Neuroscience Center (PNC), University of Padova, Via Orus, 2/B, 35129, Padova, Italy; Veneto Institute of Molecular Medicine (VIMM), Via Orus, 2, 35129, Padova, Italy.
| | - Giancarlo Ruocco
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185, Rome, Italy.
| | - Stefania Della Penna
- Department of Neuroscience, Imaging and Clinical Sciences, and Institute for Advanced Biomedical Technologies, "G. d'Annunzio" University of Chieti-Pescara, Via Luigi Polacchi, 11, 66100 Chieti, Italy.
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2
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Srivastava P, Fotiadis P, Parkes L, Bassett DS. The expanding horizons of network neuroscience: From description to prediction and control. Neuroimage 2022; 258:119250. [PMID: 35659996 PMCID: PMC11164099 DOI: 10.1016/j.neuroimage.2022.119250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 01/11/2023] Open
Abstract
The field of network neuroscience has emerged as a natural framework for the study of the brain and has been increasingly applied across divergent problems in neuroscience. From a disciplinary perspective, network neuroscience originally emerged as a formal integration of graph theory (from mathematics) and neuroscience (from biology). This early integration afforded marked utility in describing the interconnected nature of neural units, both structurally and functionally, and underscored the relevance of that interconnection for cognition and behavior. But since its inception, the field has not remained static in its methodological composition. Instead, it has grown to use increasingly advanced graph-theoretic tools and to bring in several other disciplinary perspectives-including machine learning and systems engineering-that have proven complementary. In doing so, the problem space amenable to the discipline has expanded markedly. In this review, we discuss three distinct flavors of investigation in state-of-the-art network neuroscience: (i) descriptive network neuroscience, (ii) predictive network neuroscience, and (iii) a perturbative network neuroscience that draws on recent advances in network control theory. In considering each area, we provide a brief summary of the approaches, discuss the nature of the insights obtained, and highlight future directions.
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Affiliation(s)
- Pragya Srivastava
- Department of Bioengineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Panagiotis Fotiadis
- Department of Bioengineering, University of Pennsylvania, Philadelphia PA 19104, USA; Department of Neuroscience, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Linden Parkes
- Department of Bioengineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Dani S Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia PA 19104, USA; Department of Physics & Astronomy, University of Pennsylvania, Philadelphia PA 19104, USA; Department of Electrical & Systems Engineering, University of Pennsylvania, Philadelphia PA 19104, USA; Department of Neurology, University of Pennsylvania, Philadelphia PA 19104, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia PA 19104, USA; Santa Fe Institute, Santa Fe NM 87501, USA.
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3
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Li G, Yap PT. From descriptive connectome to mechanistic connectome: Generative modeling in functional magnetic resonance imaging analysis. Front Hum Neurosci 2022; 16:940842. [PMID: 36061504 PMCID: PMC9428697 DOI: 10.3389/fnhum.2022.940842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/28/2022] [Indexed: 01/28/2023] Open
Abstract
As a newly emerging field, connectomics has greatly advanced our understanding of the wiring diagram and organizational features of the human brain. Generative modeling-based connectome analysis, in particular, plays a vital role in deciphering the neural mechanisms of cognitive functions in health and dysfunction in diseases. Here we review the foundation and development of major generative modeling approaches for functional magnetic resonance imaging (fMRI) and survey their applications to cognitive or clinical neuroscience problems. We argue that conventional structural and functional connectivity (FC) analysis alone is not sufficient to reveal the complex circuit interactions underlying observed neuroimaging data and should be supplemented with generative modeling-based effective connectivity and simulation, a fruitful practice that we term "mechanistic connectome." The transformation from descriptive connectome to mechanistic connectome will open up promising avenues to gain mechanistic insights into the delicate operating principles of the human brain and their potential impairments in diseases, which facilitates the development of effective personalized treatments to curb neurological and psychiatric disorders.
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Affiliation(s)
- Guoshi Li
- Department of Radiology, University of North Carolina, Chapel Hill, NC, United States,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, United States,*Correspondence: Guoshi Li,
| | - Pew-Thian Yap
- Department of Radiology, University of North Carolina, Chapel Hill, NC, United States,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, United States
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4
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Reliability and subject specificity of personalized whole-brain dynamical models. Neuroimage 2022; 257:119321. [PMID: 35580807 DOI: 10.1016/j.neuroimage.2022.119321] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/06/2022] [Accepted: 05/12/2022] [Indexed: 11/23/2022] Open
Abstract
Dynamical whole-brain models were developed to link structural (SC) and functional connectivity (FC) together into one framework. Nowadays, they are used to investigate the dynamical regimes of the brain and how these relate to behavioral, clinical and demographic traits. However, there is no comprehensive investigation on how reliable and subject specific the modeling results are given the variability of the empirical FC. In this study, we show that the parameters of these models can be fitted with a "poor" to "good" reliability depending on the exact implementation of the modeling paradigm. We find, as a general rule of thumb, that enhanced model personalization leads to increasingly reliable model parameters. In addition, we observe no clear effect of the model complexity evaluated by separately sampling results for linear, phase oscillator and neural mass network models. In fact, the most complex neural mass model often yields modeling results with "poor" reliability comparable to the simple linear model, but demonstrates an enhanced subject specificity of the model similarity maps. Subsequently, we show that the FC simulated by these models can outperform the empirical FC in terms of both reliability and subject specificity. For the structure-function relationship, simulated FC of individual subjects may be identified from the correlations with the empirical SC with an accuracy up to 70%, but not vice versa for non-linear models. We sample all our findings for 8 distinct brain parcellations and 6 modeling conditions and show that the parcellation-induced effect is much more pronounced for the modeling results than for the empirical data. In sum, this study provides an exploratory account on the reliability and subject specificity of dynamical whole-brain models and may be relevant for their further development and application. In particular, our findings suggest that the application of the dynamical whole-brain modeling should be tightly connected with an estimate of the reliability of the results.
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Computational synthesis of cortical dendritic morphologies. Cell Rep 2022; 39:110586. [PMID: 35385736 DOI: 10.1016/j.celrep.2022.110586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/22/2021] [Accepted: 03/08/2022] [Indexed: 12/30/2022] Open
Abstract
Neuronal morphologies provide the foundation for the electrical behavior of neurons, the connectomes they form, and the dynamical properties of the brain. Comprehensive neuron models are essential for defining cell types, discerning their functional roles, and investigating brain-disease-related dendritic alterations. However, a lack of understanding of the principles underlying neuron morphologies has hindered attempts to computationally synthesize morphologies for decades. We introduce a synthesis algorithm based on a topological descriptor of neurons, which enables the rapid digital reconstruction of entire brain regions from few reference cells. This topology-guided synthesis generates dendrites that are statistically similar to biological reconstructions in terms of morpho-electrical and connectivity properties and offers a significant opportunity to investigate the links between neuronal morphology and brain function across different spatiotemporal scales. Synthesized cortical networks based on structurally altered dendrites associated with diverse brain pathologies revealed principles linking branching properties to the structure of large-scale networks.
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Okuno T, Woodward A. Vector Auto-Regressive Deep Neural Network: A Data-Driven Deep Learning-Based Directed Functional Connectivity Estimation Toolbox. Front Neurosci 2021; 15:764796. [PMID: 34899167 PMCID: PMC8651499 DOI: 10.3389/fnins.2021.764796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
An important goal in neuroscience is to elucidate the causal relationships between the brain's different regions. This can help reveal the brain's functional circuitry and diagnose lesions. Currently there are a lack of approaches to functional connectome estimation that leverage the state-of-the-art in deep learning architectures and training methodologies. Therefore, we propose a new framework based on a vector auto-regressive deep neural network (VARDNN) architecture. Our approach consists of a set of nodes, each with a deep neural network structure. These nodes can be mapped to any spatial sub-division based on the data to be analyzed, such as anatomical brain regions from which representative neural signals can be obtained. VARDNN learns to reproduce experimental time series data using modern deep learning training techniques. Based on this, we developed two novel directed functional connectivity (dFC) measures, namely VARDNN-DI and VARDNN-GC. We evaluated our measures against a number of existing functional connectome estimation measures, such as partial correlation and multivariate Granger causality combined with large dimensionality counter-measure techniques. Our measures outperformed them across various types of ground truth data, especially as the number of nodes increased. We applied VARDNN to fMRI data to compare the dFC between 41 healthy control vs. 32 Alzheimer's disease subjects. Our VARDNN-DI measure detected lesioned regions consistent with previous studies and separated the two groups well in a subject-wise evaluation framework. Summarily, the VARDNN framework has powerful capabilities for whole brain dFC estimation. We have implemented VARDNN as an open-source toolbox that can be freely downloaded for researchers who wish to carry out functional connectome analysis on their own data.
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Affiliation(s)
- Takuto Okuno
- Connectome Analysis Unit, RIKEN Center for Brain Science, Wako, Japan
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7
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Yakushev I, Ripp I, Wang M, Savio A, Schutte M, Lizarraga A, Bogdanovic B, Diehl-Schmid J, Hedderich DM, Grimmer T, Shi K. Mapping covariance in brain FDG uptake to structural connectivity. Eur J Nucl Med Mol Imaging 2021; 49:1288-1297. [PMID: 34677627 PMCID: PMC8921091 DOI: 10.1007/s00259-021-05590-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE Inter-subject covariance of regional 18F-fluorodeoxyglucose (FDG) PET measures (FDGcov) as proxy of brain connectivity has been gaining an increasing acceptance in the community. Yet, it is still unclear to what extent FDGcov is underlied by actual structural connectivity via white matter fiber tracts. In this study, we quantified the degree of spatial overlap between FDGcov and structural connectivity networks. METHODS We retrospectively analyzed neuroimaging data from 303 subjects, both patients with suspected neurodegenerative disorders and healthy individuals. For each subject, structural magnetic resonance, diffusion tensor imaging, and FDG-PET data were available. The images were spatially normalized to a standard space and segmented into 62 anatomical regions using a probabilistic atlas. Sparse inverse covariance estimation was employed to estimate FDGcov. Structural connectivity was measured by streamline tractography through fiber assignment by continuous tracking. RESULTS For the whole brain, 55% of detected connections were found to be convergent, i.e., present in both FDGcov and structural networks. This metric for random networks was significantly lower, i.e., 12%. Convergent were 80% of intralobe connections and only 30% of interhemispheric interlobe connections. CONCLUSION Structural connectivity via white matter fiber tracts is a relevant substrate of FDGcov, underlying around a half of connections at the whole brain level. Short-range white matter tracts appear to be a major substrate of intralobe FDGcov connections.
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Affiliation(s)
- Igor Yakushev
- Department of Nuclear Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, Munich, 81675, Germany.
- Klinikum rechts der Isar, School of Medicine, Neuroimaging Center (TUM-NIC), Technical University of Munich, Munich, Germany.
| | - Isabelle Ripp
- Department of Nuclear Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, Munich, 81675, Germany
- Klinikum rechts der Isar, School of Medicine, Neuroimaging Center (TUM-NIC), Technical University of Munich, Munich, Germany
| | - Min Wang
- Shanghai Institute for Advanced Communication and Data Science, Shanghai, China
| | - Alex Savio
- Department of Nuclear Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, Munich, 81675, Germany
| | - Michael Schutte
- Department of Nuclear Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, Munich, 81675, Germany
- Department Biology II, Ludwig Maximilian University of Munich, Munich, Germany
| | - Aldana Lizarraga
- Department of Nuclear Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, Munich, 81675, Germany
- Klinikum rechts der Isar, School of Medicine, Neuroimaging Center (TUM-NIC), Technical University of Munich, Munich, Germany
| | - Borjana Bogdanovic
- Department of Nuclear Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, Munich, 81675, Germany
| | - Janine Diehl-Schmid
- Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Dennis M Hedderich
- Department of Neuroradiology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Timo Grimmer
- Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Kuangyu Shi
- Department of Nuclear Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, Munich, 81675, Germany
- Department of Nuclear Medicine, University Hospital Bern, Bern, Switzerland
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8
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Li H, Wang Y, Yan G, Sun Y, Tanabe S, Liu CC, Quigg MS, Zhang T. A Bayesian State-Space Approach to Mapping Directional Brain Networks. J Am Stat Assoc 2021. [DOI: 10.1080/01621459.2020.1865985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Huazhang Li
- Department of Statistics, University of Virginia, Charlottesville, VA
| | - Yaotian Wang
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA
| | - Guofen Yan
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Yinge Sun
- Department of Statistics, University of Virginia, Charlottesville, VA
| | - Seiji Tanabe
- Department of Psychology, University of Virginia, Charlottesville, VA
| | - Chang-Chia Liu
- Department of Neurosurgery, University of Virginia, Charlottesville, VA
| | - Mark S. Quigg
- Department of Neurology, University of Virginia, Charlottesville, VA
| | - Tingting Zhang
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA
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9
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Structurally constrained effective brain connectivity. Neuroimage 2021; 239:118288. [PMID: 34147631 DOI: 10.1016/j.neuroimage.2021.118288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 05/01/2021] [Accepted: 06/17/2021] [Indexed: 11/23/2022] Open
Abstract
The relationship between structure and function is of interest in many research fields involving the study of complex biological processes. In neuroscience in particular, the fusion of structural and functional data can help to understand the underlying principles of the operational networks in the brain. To address this issue, this paper proposes a constrained autoregressive model leading to a representation of effective connectivity that can be used to better understand how the structure modulates the function. Or simply, it can be used to find novel biomarkers characterizing groups of subjects. In practice, an initial structural connectivity representation is re-weighted to explain the functional co-activations. This is obtained by minimizing the reconstruction error of an autoregressive model constrained by the structural connectivity prior. The model has been designed to also include indirect connections, allowing to split direct and indirect components in the functional connectivity, and it can be used with raw and deconvoluted BOLD signal. The derived representation of dependencies was compared to the well known dynamic causal model, giving results closer to known ground-truth. Further evaluation of the proposed effective network was performed on two typical tasks. In a first experiment the direct functional dependencies were tested on a community detection problem, where the brain was partitioned using the effective networks across multiple subjects. In a second experiment the model was validated in a case-control task, which aimed at differentiating healthy subjects from individuals with autism spectrum disorder. Results showed that using effective connectivity leads to clusters better describing the functional interactions in the community detection task, while maintaining the original structural organization, and obtaining a better discrimination in the case-control classification task.
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10
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Wein S, Deco G, Tomé AM, Goldhacker M, Malloni WM, Greenlee MW, Lang EW. Brain Connectivity Studies on Structure-Function Relationships: A Short Survey with an Emphasis on Machine Learning. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2021; 2021:5573740. [PMID: 34135951 PMCID: PMC8177997 DOI: 10.1155/2021/5573740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022]
Abstract
This short survey reviews the recent literature on the relationship between the brain structure and its functional dynamics. Imaging techniques such as diffusion tensor imaging (DTI) make it possible to reconstruct axonal fiber tracks and describe the structural connectivity (SC) between brain regions. By measuring fluctuations in neuronal activity, functional magnetic resonance imaging (fMRI) provides insights into the dynamics within this structural network. One key for a better understanding of brain mechanisms is to investigate how these fast dynamics emerge on a relatively stable structural backbone. So far, computational simulations and methods from graph theory have been mainly used for modeling this relationship. Machine learning techniques have already been established in neuroimaging for identifying functionally independent brain networks and classifying pathological brain states. This survey focuses on methods from machine learning, which contribute to our understanding of functional interactions between brain regions and their relation to the underlying anatomical substrate.
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Affiliation(s)
- Simon Wein
- CIML, Biophysics, University of Regensburg, Regensburg 93040, Germany
- Experimental Psychology, University of Regensburg, Regensburg 93040, Germany
| | - Gustavo Deco
- Center for Brain and Cognition, Department of Technology and Information, University Pompeu Fabra, Carrer Tanger, 122-140, Barcelona 08018, Spain
- Institució Catalana de la Recerca i Estudis Avançats, University Barcelona, Passeig Lluís Companys 23, Barcelona 08010, Spain
| | - Ana Maria Tomé
- IEETA/DETI, University de Aveiro, Aveiro 3810-193, Portugal
| | - Markus Goldhacker
- CIML, Biophysics, University of Regensburg, Regensburg 93040, Germany
- Experimental Psychology, University of Regensburg, Regensburg 93040, Germany
| | - Wilhelm M. Malloni
- Experimental Psychology, University of Regensburg, Regensburg 93040, Germany
| | - Mark W. Greenlee
- Experimental Psychology, University of Regensburg, Regensburg 93040, Germany
| | - Elmar W. Lang
- CIML, Biophysics, University of Regensburg, Regensburg 93040, Germany
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11
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Zhang Y, Yang Q, Zhang L, Ran Y, Wang G, Celler BG, Su SW, Xu P, Yao D. Noise-assisted Multivariate Empirical Mode Decomposition based Causal Decomposition for brain-physiological network in bivariate and multiscale time series. J Neural Eng 2021; 18. [PMID: 33690185 DOI: 10.1088/1741-2552/abecf2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/09/2021] [Indexed: 11/11/2022]
Abstract
Objective.Noise-assisted Multivariate Empirical Mode Decomposition (NA-MEMD) based Causal Decomposition depicts a cause and effect relationship that is not based on the term of prediction, but rather on the phase dependence of time series. Here, we present the NA-MEMD based Causal Decomposition approach according to the covariation and power views traced to Hume and Kant: a priori cause-effect interaction is first acquired, and the presence of a candidate cause and of the effect is then computed from the sensory input somehow.Approach.Based on the definition of NA-MEMD based Causal Decomposition, we show such causal relation is a phase relation where the candidate causes are not merely followed by effects, but rather produce effects.Main results.The predominant methods used in neuroscience (Granger causality, EMD-based Causal Decomposition) are validated, showing the applicability of NA-MEMD based Causal Decomposition, particular to brain physiological processes in bivariate and multiscale time series.Significance.We point to the potential use in the causality inference analysis in a complex dynamic process.
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Affiliation(s)
- Yi Zhang
- The School of Aeronautics and Astronautics, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu, 610054, CHINA
| | - Qin Yang
- The School of Aeronautics and Astronautics, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu, Sichuan, 611731, CHINA
| | - Lifu Zhang
- The School of Aeronautics and Astronautics, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu, 610054, CHINA
| | - Yu Ran
- The School of Aeronautics and Astronautics, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu, Sichuan, 611731, CHINA
| | - Guan Wang
- The School of Aeronautics and Astronautics, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu, Sichuan, 611731, CHINA
| | - Branko G Celler
- Biomedical Systems Laboratory, University of New South Wales, Sydney 2052, N.S.W., Sydney, New South Wales, 2052, AUSTRALIA
| | - Steven W Su
- Centre for Health Technologies, Faculty of Engineering and Information Technology, University of Technology Sydney, 15 Broadway, Ultimo, Sydney, New South Wales, 2007, AUSTRALIA
| | - Peng Xu
- Key Laboratory for Neuro Information of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu, Sichuan, 611731, CHINA
| | - Dezhong Yao
- Key Laboratory for Neuro Information of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu, 610054, CHINA
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12
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Signature of consciousness in brain-wide synchronization patterns of monkey and human fMRI signals. Neuroimage 2020; 226:117470. [PMID: 33137478 DOI: 10.1016/j.neuroimage.2020.117470] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/07/2020] [Accepted: 10/14/2020] [Indexed: 02/05/2023] Open
Abstract
During the sleep-wake cycle, the brain undergoes profound dynamical changes, which manifest subjectively as transitions between conscious experience and unconsciousness. Yet, neurophysiological signatures that can objectively distinguish different consciousness states based are scarce. Here, we show that differences in the level of brain-wide signals can reliably distinguish different stages of sleep and anesthesia from the awake state in human and monkey fMRI resting state data. Moreover, a whole-brain computational model can faithfully reproduce changes in global synchronization and other metrics such as functional connectivity, structure-function relationship, integration and segregation across vigilance states. We demonstrate that the awake brain is close to a Hopf bifurcation, which naturally coincides with the emergence of globally correlated fMRI signals. Furthermore, simulating lesions of individual brain areas highlights the importance of connectivity hubs in the posterior brain and subcortical nuclei for maintaining the model in the awake state, as predicted by graph-theoretical analyses of structural data.
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13
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Guo M, Wang T, Zhang Z, Chen N, Li Y, Wang Y, Yao Z, Hu B. Diagnosis of major depressive disorder using whole-brain effective connectivity networks derived from resting-state functional MRI. J Neural Eng 2020; 17:056038. [PMID: 32987369 DOI: 10.1088/1741-2552/abbc28] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE It is important to improve identification accuracy for possible early intervention of major depressive disorder (MDD). Recently, effective connectivity (EC), defined as the directed influence of spatially distant brain regions on each other, has been used to find the dysfunctional organization of brain networks in MDD. However, little is known about the ability of whole-brain resting-state EC features in identification of MDD. Here, we employed EC by whole-brain analysis to perform MDD diagnosis. APPROACH In this study, we proposed a high-order EC network capturing high-level relationship among multiple brain regions to discriminate 57 patients with MDD from 60 normal controls (NC). In high-order EC networks and traditional low-order EC networks, we utilized the network properties and connection strength for classification. Meanwhile, the support vector machine (SVM) was employed for model training. Generalization of the results was supported by 10-fold cross-validation. MAIN RESULTS The classification results showed that the high-order EC network performed better than the low-order EC network in diagnosing MDD, and the integration of these two networks yielded the best classification precision with 95% accuracy, 98.83% sensitivity, and 91% specificity. Furthermore, we found that the abnormal connections of high-order EC in MDD patients involved multiple widely concerned functional subnets, particularly the default mode network and the cerebellar network. SIGNIFICANCE The current study indicates whole-brain EC networks, measured by our high-order method, may be promising biomarkers for clinical diagnosis of MDD, and the complementary between high-order and low-order EC will better guide patients to get early interventions as well as treatments.
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Affiliation(s)
- Man Guo
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, People's Republic of China
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Martinez-Banaclocha M. Astroglial Isopotentiality and Calcium-Associated Biomagnetic Field Effects on Cortical Neuronal Coupling. Cells 2020; 9:cells9020439. [PMID: 32069981 PMCID: PMC7073214 DOI: 10.3390/cells9020439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 01/01/2023] Open
Abstract
Synaptic neurotransmission is necessary but does not sufficiently explain superior cognitive faculties. Growing evidence has shown that neuron-astroglial chemical crosstalk plays a critical role in the processing of information, computation, and memory. In addition to chemical and electrical communication among neurons and between neurons and astrocytes, other nonsynaptic mechanisms called ephaptic interactions can contribute to the neuronal synchronization from different brain regions involved in the processing of information. New research on brain astrocytes has clearly shown that the membrane potential of these cells remains very stable among neighboring and distant astrocytes due to the marked bioelectric coupling between them through gap junctions. This finding raises the possibility that the neocortical astroglial network exerts a guiding template modulating the excitability and synchronization of trillions of neurons by astroglial Ca2+-associated bioelectromagnetic interactions. We propose that bioelectric and biomagnetic fields of the astroglial network equalize extracellular local field potentials (LFPs) and associated local magnetic field potentials (LMFPs) in the cortical layers of the brain areas involved in the processing of information, contributing to the adequate and coherent integration of external and internal signals. This article reviews the current knowledge of ephaptic interactions in the cerebral cortex and proposes that the isopotentiality of cortical astrocytes is a prerequisite for the maintenance of the bioelectromagnetic crosstalk between neurons and astrocytes in the neocortex.
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