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Fang H, Berman SA, Wang Y, Yang Y. Robust adaptive deep brain stimulation control of in-silico non-stationary Parkinsonian neural oscillatory dynamics. J Neural Eng 2024; 21:036043. [PMID: 38834058 DOI: 10.1088/1741-2552/ad5406] [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: 01/23/2024] [Accepted: 06/04/2024] [Indexed: 06/06/2024]
Abstract
Objective. Closed-loop deep brain stimulation (DBS) is a promising therapy for Parkinson's disease (PD) that works by adjusting DBS patterns in real time from the guidance of feedback neural activity. Current closed-loop DBS mainly uses threshold-crossing on-off controllers or linear time-invariant (LTI) controllers to regulate the basal ganglia (BG) Parkinsonian beta band oscillation power. However, the critical cortex-BG-thalamus network dynamics underlying PD are nonlinear, non-stationary, and noisy, hindering accurate and robust control of Parkinsonian neural oscillatory dynamics.Approach. Here, we develop a new robust adaptive closed-loop DBS method for regulating the Parkinsonian beta oscillatory dynamics of the cortex-BG-thalamus network. We first build an adaptive state-space model to quantify the dynamic, nonlinear, and non-stationary neural activity. We then construct an adaptive estimator to track the nonlinearity and non-stationarity in real time. We next design a robust controller to automatically determine the DBS frequency based on the estimated Parkinsonian neural state while reducing the system's sensitivity to high-frequency noise. We adopt and tune a biophysical cortex-BG-thalamus network model as an in-silico simulation testbed to generate nonlinear and non-stationary Parkinsonian neural dynamics for evaluating DBS methods.Main results. We find that under different nonlinear and non-stationary neural dynamics, our robust adaptive DBS method achieved accurate regulation of the BG Parkinsonian beta band oscillation power with small control error, bias, and deviation. Moreover, the accurate regulation generalizes across different therapeutic targets and consistently outperforms current on-off and LTI DBS methods.Significance. These results have implications for future designs of closed-loop DBS systems to treat PD.
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Affiliation(s)
- Hao Fang
- MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou 310058, People's Republic of China
- Nanhu Brain-computer Interface Institute, Hangzhou 311100, People's Republic of China
| | - Stephen A Berman
- College of Medicine, University of Central Florida, Orlando, FL 32816, United States of America
| | - Yueming Wang
- Nanhu Brain-computer Interface Institute, Hangzhou 311100, People's Republic of China
- Qiushi Academy for Advanced Studies, Hangzhou 310058, People's Republic of China
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310058, People's Republic of China
- State Key Laboratory of Brain-machine Intelligence, Hangzhou 310058, People's Republic of China
| | - Yuxiao Yang
- MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University, Hangzhou 310058, People's Republic of China
- Nanhu Brain-computer Interface Institute, Hangzhou 311100, People's Republic of China
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310058, People's Republic of China
- State Key Laboratory of Brain-machine Intelligence, Hangzhou 310058, People's Republic of China
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Hangzhou 310058, People's Republic of China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, People's Republic of China
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2
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Gambosi B, Jamal Sheiban F, Biasizzo M, Antonietti A, D'angelo E, Mazzoni A, Pedrocchi A. A Model with Dopamine Depletion in Basal Ganglia and Cerebellum Predicts Changes in Thalamocortical Beta Oscillations. Int J Neural Syst 2024:2450045. [PMID: 38886870 DOI: 10.1142/s012906572450045x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Parkinsonism is presented as a motor syndrome characterized by rigidity, tremors, and bradykinesia, with Parkinson's disease (PD) being the predominant cause. The discovery that those motor symptoms result from the death of dopaminergic cells in the substantia nigra led to focus most of parkinsonism research on the basal ganglia (BG). However, recent findings point to an active involvement of the cerebellum in this motor syndrome. Here, we have developed a multiscale computational model of the rodent brain's BG-cerebellar network. Simulations showed that a direct effect of dopamine depletion on the cerebellum must be taken into account to reproduce the alterations of neural activity in parkinsonism, particularly the increased beta oscillations widely reported in PD patients. Moreover, dopamine depletion indirectly impacted spike-time-dependent plasticity at the parallel fiber-Purkinje cell synapses, degrading associative motor learning as observed in parkinsonism. Overall, these results suggest a relevant involvement of cerebellum in parkinsonism associative motor symptoms.
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Affiliation(s)
- Benedetta Gambosi
- NearLab, Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milano, Italy
| | - Francesco Jamal Sheiban
- NearLab, Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milano, Italy
| | - Marco Biasizzo
- Department of Excellence in Robotics & AI Scuola Superiore Sant'Anna, Pisa, Italy
- The BioRobotics Institute, Scuola Superiore Sant'Anna, Pisa, Italy
- Department of Information Engineering (DIE), University of Pisa, Pisa, Italy
| | - Alberto Antonietti
- NearLab, Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milano, Italy
| | - Egidio D'angelo
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
- Digital Neuroscience Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Alberto Mazzoni
- Department of Excellence in Robotics & AI Scuola Superiore Sant'Anna, Pisa, Italy
- The BioRobotics Institute, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Alessandra Pedrocchi
- NearLab, Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milano, Italy
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Hong R, Zheng T, Marra V, Yang D, Liu JK. Multi-scale modelling of the epileptic brain: advantages of computational therapy exploration. J Neural Eng 2024; 21:021002. [PMID: 38621378 DOI: 10.1088/1741-2552/ad3eb4] [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: 08/29/2023] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
Objective: Epilepsy is a complex disease spanning across multiple scales, from ion channels in neurons to neuronal circuits across the entire brain. Over the past decades, computational models have been used to describe the pathophysiological activity of the epileptic brain from different aspects. Traditionally, each computational model can aid in optimizing therapeutic interventions, therefore, providing a particular view to design strategies for treating epilepsy. As a result, most studies are concerned with generating specific models of the epileptic brain that can help us understand the certain machinery of the pathological state. Those specific models vary in complexity and biological accuracy, with system-level models often lacking biological details.Approach: Here, we review various types of computational model of epilepsy and discuss their potential for different therapeutic approaches and scenarios, including drug discovery, surgical strategies, brain stimulation, and seizure prediction. We propose that we need to consider an integrated approach with a unified modelling framework across multiple scales to understand the epileptic brain. Our proposal is based on the recent increase in computational power, which has opened up the possibility of unifying those specific epileptic models into simulations with an unprecedented level of detail.Main results: A multi-scale epilepsy model can bridge the gap between biologically detailed models, used to address molecular and cellular questions, and brain-wide models based on abstract models which can account for complex neurological and behavioural observations.Significance: With these efforts, we move toward the next generation of epileptic brain models capable of connecting cellular features, such as ion channel properties, with standard clinical measures such as seizure severity.
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Affiliation(s)
- Rongqi Hong
- School of Computer Science, Centre for Human Brain Health, University of Birmingham, Birmingham, United Kingdom
| | - Tingting Zheng
- School of Computer Science, Centre for Human Brain Health, University of Birmingham, Birmingham, United Kingdom
| | | | - Dongping Yang
- Research Centre for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, People's Republic of China
| | - Jian K Liu
- School of Computer Science, Centre for Human Brain Health, University of Birmingham, Birmingham, United Kingdom
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4
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Kusch L, Diaz-Pier S, Klijn W, Sontheimer K, Bernard C, Morrison A, Jirsa V. Multiscale co-simulation design pattern for neuroscience applications. Front Neuroinform 2024; 18:1156683. [PMID: 38410682 PMCID: PMC10895016 DOI: 10.3389/fninf.2024.1156683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
Integration of information across heterogeneous sources creates added scientific value. Interoperability of data, tools and models is, however, difficult to accomplish across spatial and temporal scales. Here we introduce the toolbox Parallel Co-Simulation, which enables the interoperation of simulators operating at different scales. We provide a software science co-design pattern and illustrate its functioning along a neuroscience example, in which individual regions of interest are simulated on the cellular level allowing us to study detailed mechanisms, while the remaining network is efficiently simulated on the population level. A workflow is illustrated for the use case of The Virtual Brain and NEST, in which the CA1 region of the cellular-level hippocampus of the mouse is embedded into a full brain network involving micro and macro electrode recordings. This new tool allows integrating knowledge across scales in the same simulation framework and validating them against multiscale experiments, thereby largely widening the explanatory power of computational models.
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Affiliation(s)
- Lionel Kusch
- Institut de Neurosciences des Systèmes (INS), UMR1106, Aix-Marseille Université, Marseilles, France
| | - Sandra Diaz-Pier
- Simulation and Data Lab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wouter Klijn
- Simulation and Data Lab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Kim Sontheimer
- Simulation and Data Lab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christophe Bernard
- Institut de Neurosciences des Systèmes (INS), UMR1106, Aix-Marseille Université, Marseilles, France
| | - Abigail Morrison
- Simulation and Data Lab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
- Forschungszentrum Jülich GmbH, IAS-6/INM-6, JARA, Jülich, Germany
- Computer Science 3 - Software Engineering, RWTH Aachen University, Aachen, Germany
| | - Viktor Jirsa
- Institut de Neurosciences des Systèmes (INS), UMR1106, Aix-Marseille Université, Marseilles, France
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Idei H, Yamashita Y. Elucidating multifinal and equifinal pathways to developmental disorders by constructing real-world neurorobotic models. Neural Netw 2024; 169:57-74. [PMID: 37857173 DOI: 10.1016/j.neunet.2023.10.005] [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: 03/27/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
Vigorous research has been conducted to accumulate biological and theoretical knowledge about neurodevelopmental disorders, including molecular, neural, computational, and behavioral characteristics; however, these findings remain fragmentary and do not elucidate integrated mechanisms. An obstacle is the heterogeneity of developmental pathways causing clinical phenotypes. Additionally, in symptom formations, the primary causes and consequences of developmental learning processes are often indistinguishable. Herein, we review developmental neurorobotic experiments tackling problems related to the dynamic and complex properties of neurodevelopmental disorders. Specifically, we focus on neurorobotic models under predictive processing lens for the study of developmental disorders. By constructing neurorobotic models with predictive processing mechanisms of learning, perception, and action, we can simulate formations of integrated causal relationships among neurodynamical, computational, and behavioral characteristics in the robot agents while considering developmental learning processes. This framework has the potential to bind neurobiological hypotheses (excitation-inhibition imbalance and functional disconnection), computational accounts (unusual encoding of uncertainty), and clinical symptoms. Developmental neurorobotic approaches may serve as a complementary research framework for integrating fragmented knowledge and overcoming the heterogeneity of neurodevelopmental disorders.
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Affiliation(s)
- Hayato Idei
- Department of Information Medicine, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Yuichi Yamashita
- Department of Information Medicine, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan.
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Amato LG, Vergani AA, Lassi M, Fabbiani C, Mazzeo S, Burali R, Nacmias B, Sorbi S, Mannella R, Grippo A, Bessi V, Mazzoni A. Personalized modeling of Alzheimer's disease progression estimates neurodegeneration severity from EEG recordings. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2024; 16:e12526. [PMID: 38371358 PMCID: PMC10870085 DOI: 10.1002/dad2.12526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 02/20/2024]
Abstract
INTRODUCTION Early identification of Alzheimer's disease (AD) is necessary for a timely onset of therapeutic care. However, cortical structural alterations associated with AD are difficult to discern. METHODS We developed a cortical model of AD-related neurodegeneration accounting for slowing of local dynamics and global connectivity degradation. In a monocentric study we collected electroencephalography (EEG) recordings at rest from participants in healthy (HC, n = 17), subjective cognitive decline (SCD, n = 58), and mild cognitive impairment (MCI, n = 44) conditions. For each patient, we estimated neurodegeneration model parameters based on individual EEG recordings. RESULTS Our model outperformed standard EEG analysis not only in discriminating between HC and MCI conditions (F1 score 0.95 vs 0.75) but also in identifying SCD patients with biological hallmarks of AD in the cerebrospinal fluid (recall 0.87 vs 0.50). DISCUSSION Personalized models could (1) support classification of MCI, (2) assess the presence of AD pathology, and (3) estimate the risk of cognitive decline progression, based only on economical and non-invasive EEG recordings. Highlights Personalized cortical model estimating structural alterations from EEG recordings.Discrimination of Mild Cognitive Impairment (MCI) and Healthy (HC) subjects (95%)Prediction of biological markers of Alzheimer's in Subjective Decline (SCD) Subjects (87%)Transition correctly predicted for 3/3 subjects that converted from SCD to MCI after 1y.
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Affiliation(s)
- Lorenzo Gaetano Amato
- The BioRobotics InstituteSant'Anna School of Advanced StudiesPisaItaly
- Department of Excellence in Robotics and AISant'Anna School of Advanced StudiesPisaItaly
| | - Alberto Arturo Vergani
- The BioRobotics InstituteSant'Anna School of Advanced StudiesPisaItaly
- Department of Excellence in Robotics and AISant'Anna School of Advanced StudiesPisaItaly
| | - Michael Lassi
- The BioRobotics InstituteSant'Anna School of Advanced StudiesPisaItaly
- Department of Excellence in Robotics and AISant'Anna School of Advanced StudiesPisaItaly
| | - Carlo Fabbiani
- IRCSS Fondazione Don Carlo GnocchiFlorenceItaly
- Department of NeurosciencePsychology, Drug Research and Child HealthCareggi University HospitalFlorenceItaly
| | - Salvatore Mazzeo
- IRCSS Fondazione Don Carlo GnocchiFlorenceItaly
- Department of NeurosciencePsychology, Drug Research and Child HealthCareggi University HospitalFlorenceItaly
| | | | - Benedetta Nacmias
- IRCSS Fondazione Don Carlo GnocchiFlorenceItaly
- Department of NeurosciencePsychology, Drug Research and Child HealthCareggi University HospitalFlorenceItaly
| | - Sandro Sorbi
- IRCSS Fondazione Don Carlo GnocchiFlorenceItaly
- Department of NeurosciencePsychology, Drug Research and Child HealthCareggi University HospitalFlorenceItaly
| | | | | | - Valentina Bessi
- Department of NeurosciencePsychology, Drug Research and Child HealthCareggi University HospitalFlorenceItaly
| | - Alberto Mazzoni
- The BioRobotics InstituteSant'Anna School of Advanced StudiesPisaItaly
- Department of Excellence in Robotics and AISant'Anna School of Advanced StudiesPisaItaly
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7
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Cabrera-Álvarez J, Sánchez-Claros J, Carrasco-Gómez M, del Cerro-León A, Gómez-Ariza CJ, Maestú F, Mirasso CR, Susi G. Understanding the effects of cortical gyrification in tACS: insights from experiments and computational models. Front Neurosci 2023; 17:1223950. [PMID: 37655010 PMCID: PMC10467425 DOI: 10.3389/fnins.2023.1223950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/25/2023] [Indexed: 09/02/2023] Open
Abstract
The alpha rhythm is often associated with relaxed wakefulness or idling and is altered by various factors. Abnormalities in the alpha rhythm have been linked to several neurological and psychiatric disorders, including Alzheimer's disease. Transcranial alternating current stimulation (tACS) has been proposed as a potential tool to restore a disrupted alpha rhythm in the brain by stimulating at the individual alpha frequency (IAF), although some research has produced contradictory results. In this study, we applied an IAF-tACS protocol over parieto-occipital areas to a sample of healthy subjects and measured its effects over the power spectra. Additionally, we used computational models to get a deeper understanding of the results observed in the experiment. Both experimental and numerical results showed an increase in alpha power of 8.02% with respect to the sham condition in a widespread set of regions in the cortex, excluding some expected parietal regions. This result could be partially explained by taking into account the orientation of the electric field with respect to the columnar structures of the cortex, showing that the gyrification in parietal regions could generate effects in opposite directions (hyper-/depolarization) at the same time in specific brain regions. Additionally, we used a network model of spiking neuronal populations to explore the effects that these opposite polarities could have on neural activity, and we found that the best predictor of alpha power was the average of the normal components of the electric field. To sum up, our study sheds light on the mechanisms underlying tACS brain activity modulation, using both empirical and computational approaches. Non-invasive brain stimulation techniques hold promise for treating brain disorders, but further research is needed to fully understand and control their effects on brain dynamics and cognition. Our findings contribute to this growing body of research and provide a foundation for future studies aimed at optimizing the use of non-invasive brain stimulation in clinical settings.
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Affiliation(s)
- Jesús Cabrera-Álvarez
- Centre for Cognitive and Computational Neuroscience, Complutense University of Madrid, Madrid, Spain
- Department of Experimental Psychology, Complutense University of Madrid, Madrid, Spain
| | - Jaime Sánchez-Claros
- Instituto de Física Interdisciplinar y Sistemas Complejos (IFISC, UIB-CSIC), Campus UIB, Palma de Mallorca, Spain
| | - Martín Carrasco-Gómez
- Centre for Cognitive and Computational Neuroscience, Complutense University of Madrid, Madrid, Spain
- Biomedical Image Technologies, ETSI Telecomunicación, Universidad Politécnica de Madrid, Madrid, Spain
| | - Alberto del Cerro-León
- Centre for Cognitive and Computational Neuroscience, Complutense University of Madrid, Madrid, Spain
- Department of Experimental Psychology, Complutense University of Madrid, Madrid, Spain
| | | | - Fernando Maestú
- Centre for Cognitive and Computational Neuroscience, Complutense University of Madrid, Madrid, Spain
- Department of Experimental Psychology, Complutense University of Madrid, Madrid, Spain
| | - Claudio R. Mirasso
- Instituto de Física Interdisciplinar y Sistemas Complejos (IFISC, UIB-CSIC), Campus UIB, Palma de Mallorca, Spain
| | - Gianluca Susi
- Centre for Cognitive and Computational Neuroscience, Complutense University of Madrid, Madrid, Spain
- Department of Structure of Matter, Thermal Physics and Electronics, School of Physics, Complutense University of Madrid, Madrid, Spain
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Castaldo F, Páscoa Dos Santos F, Timms RC, Cabral J, Vohryzek J, Deco G, Woolrich M, Friston K, Verschure P, Litvak V. Multi-modal and multi-model interrogation of large-scale functional brain networks. Neuroimage 2023; 277:120236. [PMID: 37355200 PMCID: PMC10958139 DOI: 10.1016/j.neuroimage.2023.120236] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
Existing whole-brain models are generally tailored to the modelling of a particular data modality (e.g., fMRI or MEG/EEG). We propose that despite the differing aspects of neural activity each modality captures, they originate from shared network dynamics. Building on the universal principles of self-organising delay-coupled nonlinear systems, we aim to link distinct features of brain activity - captured across modalities - to the dynamics unfolding on a macroscopic structural connectome. To jointly predict connectivity, spatiotemporal and transient features of distinct signal modalities, we consider two large-scale models - the Stuart Landau and Wilson and Cowan models - which generate short-lived 40 Hz oscillations with varying levels of realism. To this end, we measure features of functional connectivity and metastable oscillatory modes (MOMs) in fMRI and MEG signals - and compare them against simulated data. We show that both models can represent MEG functional connectivity (FC), functional connectivity dynamics (FCD) and generate MOMs to a comparable degree. This is achieved by adjusting the global coupling and mean conduction time delay and, in the WC model, through the inclusion of balance between excitation and inhibition. For both models, the omission of delays dramatically decreased the performance. For fMRI, the SL model performed worse for FCD and MOMs, highlighting the importance of balanced dynamics for the emergence of spatiotemporal and transient patterns of ultra-slow dynamics. Notably, optimal working points varied across modalities and no model was able to achieve a correlation with empirical FC higher than 0.4 across modalities for the same set of parameters. Nonetheless, both displayed the emergence of FC patterns that extended beyond the constraints of the anatomical structure. Finally, we show that both models can generate MOMs with empirical-like properties such as size (number of brain regions engaging in a mode) and duration (continuous time interval during which a mode appears). Our results demonstrate the emergence of static and dynamic properties of neural activity at different timescales from networks of delay-coupled oscillators at 40 Hz. Given the higher dependence of simulated FC on the underlying structural connectivity, we suggest that mesoscale heterogeneities in neural circuitry may be critical for the emergence of parallel cross-modal functional networks and should be accounted for in future modelling endeavours.
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Affiliation(s)
- Francesca Castaldo
- Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, United Kingdom.
| | - Francisco Páscoa Dos Santos
- Eodyne Systems SL, Barcelona, Spain; Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ryan C Timms
- Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Joana Cabral
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - Portuguese Government Associate Laboratory, Braga/Guimarães, Portugal; Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, United United Kingdom
| | - Jakub Vohryzek
- Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, United United Kingdom; Centre for Brain and Cognition, Computational Neuroscience Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gustavo Deco
- Centre for Brain and Cognition, Computational Neuroscience Group, Universitat Pompeu Fabra, Barcelona, Spain; Institució Catalana de la Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; School of Psychological Sciences, Monash University, Melbourne, Australia
| | - Mark Woolrich
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, United Kingdom
| | - Karl Friston
- Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Paul Verschure
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Vladimir Litvak
- Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, United Kingdom
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Naddaf M. Europe spent €600 million to recreate the human brain in a computer. How did it go? Nature 2023; 620:718-720. [PMID: 37608010 DOI: 10.1038/d41586-023-02600-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
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10
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Cabrera-Álvarez J, Doorn N, Maestú F, Susi G. Modeling the role of the thalamus in resting-state functional connectivity: Nature or structure. PLoS Comput Biol 2023; 19:e1011007. [PMID: 37535694 PMCID: PMC10426958 DOI: 10.1371/journal.pcbi.1011007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/15/2023] [Accepted: 07/10/2023] [Indexed: 08/05/2023] Open
Abstract
The thalamus is a central brain structure that serves as a relay station for sensory inputs from the periphery to the cortex and regulates cortical arousal. Traditionally, it has been regarded as a passive relay that transmits information between brain regions. However, recent studies have suggested that the thalamus may also play a role in shaping functional connectivity (FC) in a task-based context. Based on this idea, we hypothesized that due to its centrality in the network and its involvement in cortical activation, the thalamus may also contribute to resting-state FC, a key neurological biomarker widely used to characterize brain function in health and disease. To investigate this hypothesis, we constructed ten in-silico brain network models based on neuroimaging data (MEG, MRI, and dwMRI), and simulated them including and excluding the thalamus, and raising the noise into thalamus to represent the afferences related to the reticular activating system (RAS) and the relay of peripheral sensory inputs. We simulated brain activity and compared the resulting FC to their empirical MEG counterparts to evaluate model's performance. Results showed that a parceled version of the thalamus with higher noise, able to drive damped cortical oscillators, enhanced the match to empirical FC. However, with an already active self-oscillatory cortex, no impact on the dynamics was observed when introducing the thalamus. We also demonstrated that the enhanced performance was not related to the structural connectivity of the thalamus, but to its higher noisy inputs. Additionally, we highlighted the relevance of a balanced signal-to-noise ratio in thalamus to allow it to propagate its own dynamics. In conclusion, our study sheds light on the role of the thalamus in shaping brain dynamics and FC in resting-state and allowed us to discuss the general role of criticality in the brain at the mesoscale level.
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Affiliation(s)
- Jesús Cabrera-Álvarez
- Department of Experimental Psychology, Complutense University of Madrid, Madrid, Spain
- Centre for Cognitive and Computational Neuroscience, Madrid, Spain
| | - Nina Doorn
- Department of Clinical Neurophysiology, University of Twente, Enschede, The Netherlands
| | - Fernando Maestú
- Department of Experimental Psychology, Complutense University of Madrid, Madrid, Spain
- Centre for Cognitive and Computational Neuroscience, Madrid, Spain
| | - Gianluca Susi
- Centre for Cognitive and Computational Neuroscience, Madrid, Spain
- Department of Structure of Matter, Thermal Physics and Electronics, Complutense University of Madrid, Madrid, Spain
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Dipietro L, Gonzalez-Mego P, Ramos-Estebanez C, Zukowski LH, Mikkilineni R, Rushmore RJ, Wagner T. The evolution of Big Data in neuroscience and neurology. JOURNAL OF BIG DATA 2023; 10:116. [PMID: 37441339 PMCID: PMC10333390 DOI: 10.1186/s40537-023-00751-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/08/2023] [Indexed: 07/15/2023]
Abstract
Neurological diseases are on the rise worldwide, leading to increased healthcare costs and diminished quality of life in patients. In recent years, Big Data has started to transform the fields of Neuroscience and Neurology. Scientists and clinicians are collaborating in global alliances, combining diverse datasets on a massive scale, and solving complex computational problems that demand the utilization of increasingly powerful computational resources. This Big Data revolution is opening new avenues for developing innovative treatments for neurological diseases. Our paper surveys Big Data's impact on neurological patient care, as exemplified through work done in a comprehensive selection of areas, including Connectomics, Alzheimer's Disease, Stroke, Depression, Parkinson's Disease, Pain, and Addiction (e.g., Opioid Use Disorder). We present an overview of research and the methodologies utilizing Big Data in each area, as well as their current limitations and technical challenges. Despite the potential benefits, the full potential of Big Data in these fields currently remains unrealized. We close with recommendations for future research aimed at optimizing the use of Big Data in Neuroscience and Neurology for improved patient outcomes. Supplementary Information The online version contains supplementary material available at 10.1186/s40537-023-00751-2.
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Affiliation(s)
| | - Paola Gonzalez-Mego
- Spaulding Rehabilitation/Neuromodulation Lab, Harvard Medical School, Cambridge, MA USA
| | | | | | | | | | - Timothy Wagner
- Highland Instruments, Cambridge, MA USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA USA
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12
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Páscoa Dos Santos F, Vohryzek J, Verschure PFMJ. Multiscale effects of excitatory-inhibitory homeostasis in lesioned cortical networks: A computational study. PLoS Comput Biol 2023; 19:e1011279. [PMID: 37418506 DOI: 10.1371/journal.pcbi.1011279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/18/2023] [Indexed: 07/09/2023] Open
Abstract
Stroke-related disruptions in functional connectivity (FC) often spread beyond lesioned areas and, given the localized nature of lesions, it is unclear how the recovery of FC is orchestrated on a global scale. Since recovery is accompanied by long-term changes in excitability, we propose excitatory-inhibitory (E-I) homeostasis as a driving mechanism. We present a large-scale model of the neocortex, with synaptic scaling of local inhibition, showing how E-I homeostasis can drive the post-lesion restoration of FC and linking it to changes in excitability. We show that functional networks could reorganize to recover disrupted modularity and small-worldness, but not network dynamics, suggesting the need to consider forms of plasticity beyond synaptic scaling of inhibition. On average, we observed widespread increases in excitability, with the emergence of complex lesion-dependent patterns related to biomarkers of relevant side effects of stroke, such as epilepsy, depression and chronic pain. In summary, our results show that the effects of E-I homeostasis extend beyond local E-I balance, driving the restoration of global properties of FC, and relating to post-stroke symptomatology. Therefore, we suggest the framework of E-I homeostasis as a relevant theoretical foundation for the study of stroke recovery and for understanding the emergence of meaningful features of FC from local dynamics.
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Affiliation(s)
- Francisco Páscoa Dos Santos
- Eodyne Systems SL, Barcelona, Spain
- Department of Information and Communication Technologies, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jakub Vohryzek
- Centre for Brain and Cognition, Computational Neuroscience Group, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
- Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, United Kingdom
| | - Paul F M J Verschure
- Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, The Netherlands
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13
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Kurtin DL, Giunchiglia V, Vohryzek J, Cabral J, Skeldon AC, Violante IR. Moving from phenomenological to predictive modelling: Progress and pitfalls of modelling brain stimulation in-silico. Neuroimage 2023; 272:120042. [PMID: 36965862 DOI: 10.1016/j.neuroimage.2023.120042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 03/27/2023] Open
Abstract
Brain stimulation is an increasingly popular neuromodulatory tool used in both clinical and research settings; however, the effects of brain stimulation, particularly those of non-invasive stimulation, are variable. This variability can be partially explained by an incomplete mechanistic understanding, coupled with a combinatorial explosion of possible stimulation parameters. Computational models constitute a useful tool to explore the vast sea of stimulation parameters and characterise their effects on brain activity. Yet the utility of modelling stimulation in-silico relies on its biophysical relevance, which needs to account for the dynamics of large and diverse neural populations and how underlying networks shape those collective dynamics. The large number of parameters to consider when constructing a model is no less than those needed to consider when planning empirical studies. This piece is centred on the application of phenomenological and biophysical models in non-invasive brain stimulation. We first introduce common forms of brain stimulation and computational models, and provide typical construction choices made when building phenomenological and biophysical models. Through the lens of four case studies, we provide an account of the questions these models can address, commonalities, and limitations across studies. We conclude by proposing future directions to fully realise the potential of computational models of brain stimulation for the design of personalized, efficient, and effective stimulation strategies.
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Affiliation(s)
- Danielle L Kurtin
- Neuromodulation Laboratory, School of Psychology, University of Surrey, Guildford, GU2 7XH, United Kingdom; Department of Brain Sciences, Imperial College London, London, United Kingdom.
| | | | - Jakub Vohryzek
- Centre for Brain and Cognition, Computational Neuroscience Group, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain; Centre for Eudaimonia and Human Flourishing, Linacre College, University of Oxford, UK
| | - Joana Cabral
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
| | - Anne C Skeldon
- Department of Mathematics, Centre for Mathematical and Computational Biology, University of Surrey, Guildford, United Kingdom
| | - Ines R Violante
- Neuromodulation Laboratory, School of Psychology, University of Surrey, Guildford, GU2 7XH, United Kingdom
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Lee JH, Liu Q, Dadgar-Kiani E. Solving brain circuit function and dysfunction with computational modeling and optogenetic fMRI. Science 2022; 378:493-499. [PMID: 36327349 PMCID: PMC10543742 DOI: 10.1126/science.abq3868] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Can we construct a model of brain function that enables an understanding of whole-brain circuit mechanisms underlying neurological disease and use it to predict the outcome of therapeutic interventions? How are pathologies in neurological disease, some of which are observed to have spatial spreading mechanisms, associated with circuits and brain function? In this review, we discuss approaches that have been used to date and future directions that can be explored to answer these questions. By combining optogenetic functional magnetic resonance imaging (fMRI) with computational modeling, cell type-specific, large-scale brain circuit function and dysfunction are beginning to be quantitatively parameterized. We envision that these developments will pave the path for future therapeutics developments based on a systems engineering approach aimed at directly restoring brain function.
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Affiliation(s)
- Jin Hyung Lee
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
- Department of Electrical Engineering, Stanford University, CA 94305, USA
| | - Qin Liu
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Ehsan Dadgar-Kiani
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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15
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Multiscale co-simulation of deep brain stimulation with brain networks in neurodegenerative disorders. BRAIN MULTIPHYSICS 2022. [DOI: 10.1016/j.brain.2022.100058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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D'Angelo E, Jirsa V. The quest for multiscale brain modeling. Trends Neurosci 2022; 45:777-790. [PMID: 35906100 DOI: 10.1016/j.tins.2022.06.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/20/2022] [Accepted: 06/21/2022] [Indexed: 01/07/2023]
Abstract
Addressing the multiscale organization of the brain, which is fundamental to the dynamic repertoire of the organ, remains challenging. In principle, it should be possible to model neurons and synapses in detail and then connect them into large neuronal assemblies to explain the relationship between microscopic phenomena, large-scale brain functions, and behavior. It is more difficult to infer neuronal functions from ensemble measurements such as those currently obtained with brain activity recordings. In this article we consider theories and strategies for combining bottom-up models, generated from principles of neuronal biophysics, with top-down models based on ensemble representations of network activity and on functional principles. These integrative approaches are hoped to provide effective multiscale simulations in virtual brains and neurorobots, and pave the way to future applications in medicine and information technologies.
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Affiliation(s)
- Egidio D'Angelo
- Department of Brain and Behavioral Sciences, University of Pavia, and Brain Connectivity Center, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy.
| | - Viktor Jirsa
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1106, Centre National de la Recherche Scientifique (CNRS), and University of Aix-Marseille, Marseille, France
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