1
|
Chung MK, Che JB, Nair VA, Ramos CG, Mathis JR, Prabhakaran V, Meyerand E, Hermann BP, Binder JR, Struck AF. Topological Embedding of Human Brain Networks with Applications to Dynamics of Temporal Lobe Epilepsy. ARXIV 2024:arXiv:2405.07835v1. [PMID: 38800648 PMCID: PMC11118617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
We introduce a novel, data-driven topological data analysis (TDA) approach for embedding brain networks into a lower-dimensional space in quantifying the dynamics of temporal lobe epilepsy (TLE) obtained from resting-state functional magnetic resonance imaging (rs-fMRI). This embedding facilitates the orthogonal projection of 0D and 1D topological features, allowing for the visualization and modeling of the dynamics of functional human brain networks in a resting state. We then quantify the topological disparities between networks to determine the coordinates for embedding. This framework enables us to conduct a coherent statistical inference within the embedded space. Our results indicate that brain network topology in TLE patients exhibits increased rigidity in 0D topology but more rapid flections compared to that of normal controls in 1D topology.
Collapse
Affiliation(s)
- Moo K Chung
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | | | - Veena A Nair
- Department of Radiology, University of Wisconsin-Madison, USA
| | | | | | | | - Elizabeth Meyerand
- Departments of Medical Physics & Biomedical Engineering, University of Wisconsin-Madison, USA
| | - Bruce P Hermann
- Department of Neurology, University of Wisconsin-Madison, USA
| | | | - Aaron F Struck
- Department of Neurology, University of Wisconsin-Madison, USA
| |
Collapse
|
2
|
Chung MK, Huang SG, Carroll IC, Calhoun VD, Goldsmith HH. Topological state-space estimation of functional human brain networks. PLoS Comput Biol 2024; 20:e1011869. [PMID: 38739671 PMCID: PMC11115255 DOI: 10.1371/journal.pcbi.1011869] [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: 07/30/2023] [Revised: 05/23/2024] [Accepted: 01/29/2024] [Indexed: 05/16/2024] Open
Abstract
We introduce an innovative, data-driven topological data analysis (TDA) technique for estimating the state spaces of dynamically changing functional human brain networks at rest. Our method utilizes the Wasserstein distance to measure topological differences, enabling the clustering of brain networks into distinct topological states. This technique outperforms the commonly used k-means clustering in identifying brain network state spaces by effectively incorporating the temporal dynamics of the data without the need for explicit model specification. We further investigate the genetic underpinnings of these topological features using a twin study design, examining the heritability of such state changes. Our findings suggest that the topology of brain networks, particularly in their dynamic state changes, may hold significant hidden genetic information.
Collapse
Affiliation(s)
- Moo K. Chung
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America
| | | | - Ian C. Carroll
- Department of Child and Adolescent Psychiatry, New York University Grossman School of Medicine, New York, United States of America
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, United States of America
| | - H. Hill Goldsmith
- Department of Psychology & Waisman Center, University of Wisconsin, Madison, Wisconsin, United States of America
| |
Collapse
|
3
|
Chung MK, Azizi T, Hanson JL, Alexander AL, Pollak SD, Davidson RJ. Altered topological structure of the brain white matter in maltreated children through topological data analysis. Netw Neurosci 2024; 8:355-376. [PMID: 38711544 PMCID: PMC11073548 DOI: 10.1162/netn_a_00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/30/2023] [Indexed: 05/08/2024] Open
Abstract
Childhood maltreatment may adversely affect brain development and consequently influence behavioral, emotional, and psychological patterns during adulthood. In this study, we propose an analytical pipeline for modeling the altered topological structure of brain white matter in maltreated and typically developing children. We perform topological data analysis (TDA) to assess the alteration in the global topology of the brain white matter structural covariance network among children. We use persistent homology, an algebraic technique in TDA, to analyze topological features in the brain covariance networks constructed from structural magnetic resonance imaging and diffusion tensor imaging. We develop a novel framework for statistical inference based on the Wasserstein distance to assess the significance of the observed topological differences. Using these methods in comparing maltreated children with a typically developing control group, we find that maltreatment may increase homogeneity in white matter structures and thus induce higher correlations in the structural covariance; this is reflected in the topological profile. Our findings strongly suggest that TDA can be a valuable framework to model altered topological structures of the brain. The MATLAB codes and processed data used in this study can be found at https://github.com/laplcebeltrami/maltreated.
Collapse
Affiliation(s)
- Moo K. Chung
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, WI, USA
| | - Tahmineh Azizi
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, WI, USA
| | - Jamie L. Hanson
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew L. Alexander
- Department of Medical Physics, University of Wisconsin–Madison, Madison, WI, USA
| | - Seth D. Pollak
- Department of Psychology, University of Wisconsin–Madison, Madison, WI, USA
| | | |
Collapse
|
4
|
Chung MK, Ramos CG, De Paiva FB, Mathis J, Prabhakaran V, Nair VA, Meyerand ME, Hermann BP, Binder JR, Struck AF. Unified topological inference for brain networks in temporal lobe epilepsy using the Wasserstein distance. Neuroimage 2023; 284:120436. [PMID: 37931870 PMCID: PMC11074922 DOI: 10.1016/j.neuroimage.2023.120436] [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: 05/15/2023] [Revised: 09/14/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023] Open
Abstract
Persistent homology offers a powerful tool for extracting hidden topological signals from brain networks. It captures the evolution of topological structures across multiple scales, known as filtrations, thereby revealing topological features that persist over these scales. These features are summarized in persistence diagrams, and their dissimilarity is quantified using the Wasserstein distance. However, the Wasserstein distance does not follow a known distribution, posing challenges for the application of existing parametric statistical models. To tackle this issue, we introduce a unified topological inference framework centered on the Wasserstein distance. Our approach has no explicit model and distributional assumptions. The inference is performed in a completely data driven fashion. We apply this method to resting-state functional magnetic resonance images (rs-fMRI) of temporal lobe epilepsy patients collected from two different sites: the University of Wisconsin-Madison and the Medical College of Wisconsin. Importantly, our topological method is robust to variations due to sex and image acquisition, obviating the need to account for these variables as nuisance covariates. We successfully localize the brain regions that contribute the most to topological differences. A MATLAB package used for all analyses in this study is available at https://github.com/laplcebeltrami/PH-STAT.
Collapse
Affiliation(s)
- Moo K Chung
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, USA.
| | | | | | | | | | - Veena A Nair
- Department of Radiology, University of Wisconsin-Madison, USA.
| | - Mary E Meyerand
- Departments of Medical Physics & Biomedical Engineering, University of Wisconsin-Madison, USA.
| | - Bruce P Hermann
- Department of Neurology, University of Wisconsin-Madison, USA.
| | | | - Aaron F Struck
- Department of Neurology, University of Wisconsin-Madison, USA.
| |
Collapse
|
5
|
Chung MK, Azizi T, Hanson JL, Alexander AL, Davidson RJ, Pollak SD. Altered Topological Structure of the Brain White Matter in Maltreated Children through Topological Data Analysis. ARXIV 2023:arXiv:2304.05908v3. [PMID: 37090232 PMCID: PMC10120754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Childhood maltreatment may adversely affect brain development and consequently influence behavioral, emotional, and psychological patterns during adulthood. In this study, we propose an analytical pipeline for modeling the altered topological structure of brain white matter in maltreated and typically developing children. We perform topological data analysis (TDA) to assess the alteration in the global topology of the brain white-matter structural covariance network among children. We use persistent homology, an algebraic technique in TDA, to analyze topological features in the brain covariance networks constructed from structural magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI). We develop a novel framework for statistical inference based on the Wasserstein distance to assess the significance of the observed topological differences. Using these methods in comparing maltreated children to a typically developing control group, we find that maltreatment may increase homogeneity in white matter structures and thus induce higher correlations in the structural covariance; this is reflected in the topological profile. Our findings strongly suggest that TDA can be a valuable framework to model altered topological structures of the brain. The MATLAB codes and processed data used in this study can be found at https://github.com/laplcebeltrami/maltreated.
Collapse
Affiliation(s)
- Moo K. Chung
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, USA
| | - Tahmineh Azizi
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, USA
| | | | | | | | - Seth D. Pollak
- Department of Psychology, University of Wisconsin-Madison, USA
| |
Collapse
|
6
|
Aganj I, Mora J, Frau-Pascual A, Fischl B. Exploratory Correlation of The Human Structural Connectome with Non-MRI Variables in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547308. [PMID: 37461543 PMCID: PMC10350016 DOI: 10.1101/2023.06.30.547308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
INTRODUCTION Discovery of the associations between brain structural connectivity and clinical and demographic variables can help to better understand the vulnerability and resilience of the brain architecture to neurodegenerative diseases and to discover biomarkers. METHODS We used four diffusion-MRI databases, three related to Alzheimer's disease, to exploratorily correlate structural connections between 85 brain regions with non-MRI variables, while stringently correcting the significance values for multiple testing and ruling out spurious correlations via careful visual inspection. We repeated the analysis with brain connectivity augmented with multi-synaptic neural pathways. RESULTS We found 85 and 101 significant relationships with direct and augmented connectivity, respectively, which were generally stronger for the latter. Age was consistently linked to decreased connectivity, and healthier clinical scores were generally linked to increased connectivity. DISCUSSION Our findings help to elucidate which structural brain networks are affected in Alzheimer's disease and aging and highlight the importance of including indirect connections.
Collapse
Affiliation(s)
- Iman Aganj
- Athinoula A. Martinos Center for Biomedical Imaging, Radiology Department, Massachusetts General Hospital, 149 13 St., Suite 2301, Boston, MA 02129, USA
- Radiology Department, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA
| | - Jocelyn Mora
- Athinoula A. Martinos Center for Biomedical Imaging, Radiology Department, Massachusetts General Hospital, 149 13 St., Suite 2301, Boston, MA 02129, USA
| | - Aina Frau-Pascual
- Athinoula A. Martinos Center for Biomedical Imaging, Radiology Department, Massachusetts General Hospital, 149 13 St., Suite 2301, Boston, MA 02129, USA
- Radiology Department, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA
| | - Bruce Fischl
- Athinoula A. Martinos Center for Biomedical Imaging, Radiology Department, Massachusetts General Hospital, 149 13 St., Suite 2301, Boston, MA 02129, USA
- Radiology Department, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA
| | | |
Collapse
|
7
|
Aganj I, Mora J, Frau‐Pascual A, Fischl B. Exploratory correlation of the human structural connectome with non-MRI variables in Alzheimer's disease. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2023; 15:e12511. [PMID: 38111597 PMCID: PMC10725839 DOI: 10.1002/dad2.12511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023]
Abstract
Introduction Discovery of the associations between brain structural connectivity and clinical and demographic variables can help to better understand the vulnerability and resilience of the brain architecture to neurodegenerative diseases and to discover biomarkers. Methods We used four diffusion-MRI databases, three related to Alzheimer's disease (AD), to exploratorily correlate structural connections between 85 brain regions with non-MRI variables, while stringently correcting the significance values for multiple testing and ruling out spurious correlations via careful visual inspection. We repeated the analysis with brain connectivity augmented with multi-synaptic neural pathways. Results We found 85 and 101 significant relationships with direct and augmented connectivity, respectively, which were generally stronger for the latter. Age was consistently linked to decreased connectivity, and healthier clinical scores were generally linked to increased connectivity. Discussion Our findings help to elucidate which structural brain networks are affected in AD and aging and highlight the importance of including indirect connections.
Collapse
Affiliation(s)
- Iman Aganj
- Athinoula A. Martinos Center for Biomedical ImagingRadiology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Radiology DepartmentHarvard Medical SchoolBostonMassachusettsUSA
| | - Jocelyn Mora
- Athinoula A. Martinos Center for Biomedical ImagingRadiology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
| | - Aina Frau‐Pascual
- Athinoula A. Martinos Center for Biomedical ImagingRadiology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Radiology DepartmentHarvard Medical SchoolBostonMassachusettsUSA
| | - Bruce Fischl
- Athinoula A. Martinos Center for Biomedical ImagingRadiology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Radiology DepartmentHarvard Medical SchoolBostonMassachusettsUSA
| | | |
Collapse
|
8
|
Chung MK, Ramos CG, De Paiva FB, Mathis J, Prabharakaren V, Nair VA, Meyerand E, Hermann BP, Binder JR, Struck AF. Unified Topological Inference for Brain Networks in Temporal Lobe Epilepsy Using the Wasserstein Distance. ARXIV 2023:arXiv:2302.06673v3. [PMID: 36824424 PMCID: PMC9949148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Persistent homology offers a powerful tool for extracting hidden topological signals from brain networks. It captures the evolution of topological structures across multiple scales, known as filtrations, thereby revealing topological features that persist over these scales. These features are summarized in persistence diagrams, and their dissimilarity is quantified using the Wasserstein distance. However, the Wasserstein distance does not follow a known distribution, posing challenges for the application of existing parametric statistical models. To tackle this issue, we introduce a unified topological inference framework centered on the Wasserstein distance. Our approach has no explicit model and distributional assumptions. The inference is performed in a completely data driven fashion. We apply this method to resting-state functional magnetic resonance images (rs-fMRI) of temporal lobe epilepsy patients collected from two different sites: the University of Wisconsin-Madison and the Medical College of Wisconsin. Importantly, our topological method is robust to variations due to sex and image acquisition, obviating the need to account for these variables as nuisance covariates. We successfully localize the brain regions that contribute the most to topological differences. A MATLAB package used for all analyses in this study is available at https://github.com/laplcebeltrami/PH-STAT.
Collapse
Affiliation(s)
- Moo K Chung
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, USA
| | | | | | | | | | - Veena A Nair
- Department of Radiology, University of Wisconsin-Madison, USA
| | - Elizabeth Meyerand
- Departments of Medical Physics & Biomedical Engineering, University of Wisconsin-Madison, USA
| | - Bruce P Hermann
- Department of Neurology, University of Wisconsin-Madison, USA
| | | | - Aaron F Struck
- Department of Neurology, University of Wisconsin-Madison, USA
| |
Collapse
|
9
|
Bukkieva T, Pospelova M, Efimtsev A, Fionik O, Alekseeva T, Samochernykh K, Gorbunova E, Krasnikova V, Makhanova A, Nikolaeva A, Tonyan S, Lepekhina A, Levchuk A, Trufanov G, Akshulakov S, Shevtsov M. Microstructural Properties of Brain White Matter Tracts in Breast Cancer Survivors: A Diffusion Tensor Imaging Study. PATHOPHYSIOLOGY 2022; 29:595-609. [PMID: 36278563 PMCID: PMC9624319 DOI: 10.3390/pathophysiology29040046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/29/2022] Open
Abstract
Complex breast cancer (BC) treatment can cause various neurological and psychiatric complications, such as postmastectomy pain syndrome, vestibulocerebellar ataxia, and depression, which can lead to microstructural damage of the white matter tracts of the brain. The purpose of the study is to assess microstructural changes in the white matter tracts of the brain in BC survivors using diffusion tensor imaging (DTI). Single DTI scans were performed on patients (n = 84) after complex BC treatment (i.e., surgery, chemotherapy and/or radiation therapy) and on the control group (n = 40). According to the results, a decrease in the quantitative anisotropy (FDR ≤ 0.05) was revealed in the bilateral corticospinal tracts, cerebellar tracts, corpus callosum, fornix, left superior corticostriatal and left corticopontine parietal in patients after BC treatment in comparison to the control group. A decrease in the quantitative anisotropy (FDR ≤ 0.05) was also revealed in the corpus callosum and right cerebellar tracts in patients after BC treatment with the presence of postmastectomy pain syndrome and vestibulocerebellar ataxia. The use of DTI in patients after BC treatment reveals microstructural properties of the white matter tracts in the brain. The results will allow for the improvement of treatment and rehabilitation approaches in patients receiving treatment for breast cancer.
Collapse
Affiliation(s)
- Tatyana Bukkieva
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Maria Pospelova
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Aleksandr Efimtsev
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Olga Fionik
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Tatyana Alekseeva
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Konstantin Samochernykh
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Elena Gorbunova
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Varvara Krasnikova
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Albina Makhanova
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Aleksandra Nikolaeva
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Samvel Tonyan
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Anna Lepekhina
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Anatoliy Levchuk
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Gennadiy Trufanov
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
| | - Serik Akshulakov
- National Center for Neurosurgery, Turan Ave., 34/1, Nur-Sultan 010000, Kazakhstan
| | - Maxim Shevtsov
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 St. Petersburg, Russia
- Department of Radiation Oncology, Technishe Universität München (TUM), Klinikum rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
- Laboratory of Biomedical Nanotechnologies, Institute of Cytology of the Russian Academy of Sciences (RAS), Tikhoretsky Ave., 4, 194064 St. Petersburg, Russia
| |
Collapse
|
10
|
Marimpis AD, Dimitriadis SI, Goebel R. Dyconnmap: Dynamic connectome mapping-A neuroimaging python module. Hum Brain Mapp 2021; 42:4909-4939. [PMID: 34250674 PMCID: PMC8449119 DOI: 10.1002/hbm.25589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/10/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Despite recent progress in the analysis of neuroimaging data sets, our comprehension of the main mechanisms and principles which govern human brain cognition and function remains incomplete. Network neuroscience makes substantial efforts to manipulate these challenges and provide real answers. For the last decade, researchers have been modelling brain structure and function via a graph or network that comprises brain regions that are either anatomically connected via tracts or functionally via a more extensive repertoire of functional associations. Network neuroscience is a relatively new multidisciplinary scientific avenue of the study of complex systems by pursuing novel ways to analyze, map, store and model the essential elements and their interactions in complex neurobiological systems, particularly the human brain, the most complex system in nature. Due to a rapid expansion of neuroimaging data sets' size and complexity, it is essential to propose and adopt new empirical tools to track dynamic patterns between neurons and brain areas and create comprehensive maps. In recent years, there is a rapid growth of scientific interest in moving functional neuroimaging analysis beyond simplified group or time‐averaged approaches and sophisticated algorithms that can capture the time‐varying properties of functional connectivity. We describe algorithms and network metrics that can capture the dynamic evolution of functional connectivity under this perspective. We adopt the word ‘chronnectome’ (integration of the Greek word ‘Chronos’, which means time, and connectome) to describe this specific branch of network neuroscience that explores how mutually informed brain activity correlates across time and brain space in a functional way. We also describe how good temporal mining of temporally evolved dynamic functional networks could give rise to the detection of specific brain states over which our brain evolved. This characteristic supports our complex human mind. The temporal evolution of these brain states and well‐known network metrics could give rise to new analytic trends. Functional brain networks could also increase the multi‐faced nature of the dynamic networks revealing complementary information. Finally, we describe a python module (https://github.com/makism/dyconnmap) which accompanies this article and contains a collection of dynamic complex network analytics and measures and demonstrates its great promise for the study of a healthy subject's repeated fMRI scans.
Collapse
Affiliation(s)
- Avraam D Marimpis
- Cognitive Neuroscience Department, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands.,Neuroinformatics Group, Cardiff University Brain Research Imaging Center (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.,Brain Innovation B.V, Maastricht, The Netherlands
| | - Stavros I Dimitriadis
- Neuroinformatics Group, Cardiff University Brain Research Imaging Center (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.,Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, United Kingdom.,Cardiff University Brain Research Imaging Center (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.,School of Psychology, Cardiff University, Cardiff, United Kingdom.,Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom.,MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Rainer Goebel
- Cognitive Neuroscience Department, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands.,Brain Innovation B.V, Maastricht, The Netherlands
| |
Collapse
|
11
|
Van Dyck A, Bollaerts I, Beckers A, Vanhunsel S, Glorian N, van Houcke J, van Ham TJ, De Groef L, Andries L, Moons L. Müller glia-myeloid cell crosstalk accelerates optic nerve regeneration in the adult zebrafish. Glia 2021; 69:1444-1463. [PMID: 33502042 DOI: 10.1002/glia.23972] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 12/18/2022]
Abstract
Neurodegenerative disorders, characterized by progressive neuronal loss, eventually lead to functional impairment in the adult mammalian central nervous system (CNS). Importantly, these deteriorations are irreversible, due to the very limited regenerative potential of these CNS neurons. Stimulating and redirecting neuroinflammation was recently put forward as an important approach to induce axonal regeneration, but it remains elusive how inflammatory processes and CNS repair are intertwined. To gain more insight into these interactions, we investigated how immunomodulation affects the regenerative outcome after optic nerve crush (ONC) in the spontaneously regenerating zebrafish. First, inducing intraocular inflammation using zymosan resulted in an acute inflammatory response, characterized by an increased infiltration and proliferation of innate blood-borne immune cells, reactivation of Müller glia, and altered retinal cytokine expression. Strikingly, inflammatory stimulation also accelerated axonal regrowth after optic nerve injury. Second, we demonstrated that acute depletion of both microglia and macrophages in the retina, using pharmacological treatments with both the CSF1R inhibitor PLX3397 and clodronate liposomes, compromised optic nerve regeneration. Moreover, we observed that csf1ra/b double mutant fish, lacking microglia in both retina and brain, displayed accelerated RGC axonal regrowth after ONC, which was accompanied with unusual Müller glia proliferative gliosis. Altogether, our results highlight the importance of altered glial cell interactions in the axonal regeneration process after ONC in adult zebrafish. Unraveling the relative contribution of the different cell types, as well as the signaling pathways involved, may pinpoint new targets to stimulate repair in the vertebrate CNS.
Collapse
Affiliation(s)
- Annelies Van Dyck
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Ilse Bollaerts
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - An Beckers
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Sophie Vanhunsel
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Nynke Glorian
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jessie van Houcke
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Lies De Groef
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Lien Andries
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium
| | - Lieve Moons
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven, Belgium.,Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| |
Collapse
|
12
|
Zhang L, Wang Q, Baier G. Dynamical Features of a Focal Epileptogenic Network Model for Stimulation-Based Control. IEEE Trans Neural Syst Rehabil Eng 2020; 28:1856-1865. [DOI: 10.1109/tnsre.2020.3002350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
13
|
Long X, Little G, Treit S, Beaulieu C, Gong G, Lebel C. Altered brain white matter connectome in children and adolescents with prenatal alcohol exposure. Brain Struct Funct 2020; 225:1123-1133. [PMID: 32239277 DOI: 10.1007/s00429-020-02064-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Diffuson tensor imaging (DTI) has demonstrated widespread alterations of brain white matter structure in children with prenatal alcohol exposure (PAE), yet it remains unclear how these alterations affect the structural brain network as a whole. The present study aimed to examine changes in the DTI-based structural connectome in children and adolescents with PAE compared to unexposed controls. Participants were 121 children and adolescents with PAE (51 females) and 119 typically-developing controls (49 females) aged 5-18 years with DTI data collected at one of four research centers across Canada. Graph-theory based analysis was performed on the connectivity matrix constructed from whole-brain white matter fibers via deterministic tractography. The PAE group had significantly decreased whole-brain global efficiency, degree centrality, and participation coefficients, as well as increased shortest path length and betweenness centrality compared to unexposed controls. Individuals with PAE had decreased connectivity between the attention, somatomotor, and default mode networks compared to controls. This study demonstrates decreased structural white matter connectivity in children and adolescents with PAE at a whole-brain level, suggesting widespread alterations in how networks are connected with each other. This decreased connectivity may underlie cognitive and behavioural difficulties in children with PAE.
Collapse
Affiliation(s)
- Xiangyu Long
- Department of Radiology, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, B4-513, University of Calgary, 2888 Shaganappi Trail, Calgary, NWAB, T3B 6A8, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Graham Little
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Sarah Treit
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Christian Beaulieu
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Gaolang Gong
- State Key Laboratory of Cognitive Neuroscience and Learning & IDG, McGovern Institute for Brain Research, Beijing, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing, China
| | - Catherine Lebel
- Department of Radiology, University of Calgary, Calgary, AB, Canada.
- Alberta Children's Hospital Research Institute, B4-513, University of Calgary, 2888 Shaganappi Trail, Calgary, NWAB, T3B 6A8, Canada.
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
14
|
Wang N, Mirando AJ, Cofer G, Qi Y, Hilton MJ, Johnson GA. Characterization complex collagen fiber architecture in knee joint using high-resolution diffusion imaging. Magn Reson Med 2020; 84:908-919. [PMID: 31962373 DOI: 10.1002/mrm.28181] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/26/2022]
Abstract
PURPOSE To evaluate the complex fiber orientations and 3D collagen fiber network of knee joint connective tissues, including ligaments, muscle, articular cartilage, and meniscus using high spatial and angular resolution diffusion imaging. METHODS Two rat knee joints were scanned using a modified 3D diffusion-weighted spin echo pulse sequence with the isotropic spatial resolution of 45 μm at 9.4T. The b values varied from 250 to 1250 s/mm2 with 31 diffusion encoding directions for 1 rat knee. The b value was fixed to 1000 s/mm2 with 147 diffusion encoding directions for the second knee. Both the diffusion tensor imaging (DTI) model and generalized Q-sampling imaging (GQI) method were used to investigate the fiber orientation distributions and tractography with the validation of polarized light microscopy. RESULTS To better resolve the crossing fibers, the b value should be great than or equal to 1000 s/mm2 . The tractography results were comparable between the DTI model and GQI method in ligament and muscle. However, the tractography exhibited apparent difference between DTI and GQI in connective tissues with more complex collagen fibers network, such as cartilage and meniscus. In articular cartilage, there were numerous crossing fibers found in superficial zone and transitional zone. Tractography generated with GQI also resulted in more intact tracts in articular cartilage than DTI. CONCLUSION High-resolution diffusion imaging with GQI method can trace the complex collagen fiber orientations and architectures of the knee joint at microscopic resolution.
Collapse
Affiliation(s)
- Nian Wang
- Center for In Vivo Microscopy, Duke University School of Medicine, Durham, North Carolina.,Department of Radiology, Duke University School of Medicine, Durham, North Carolina
| | - Anthony J Mirando
- Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, North Carolina
| | - Gary Cofer
- Center for In Vivo Microscopy, Duke University School of Medicine, Durham, North Carolina
| | - Yi Qi
- Center for In Vivo Microscopy, Duke University School of Medicine, Durham, North Carolina
| | - Matthew J Hilton
- Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, North Carolina.,Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina
| | - G Allan Johnson
- Center for In Vivo Microscopy, Duke University School of Medicine, Durham, North Carolina.,Department of Radiology, Duke University School of Medicine, Durham, North Carolina
| |
Collapse
|
15
|
Chung MK, Luo Z, Adluru N, Alexander AL, Davidson RJ, Goldsmith HH. Heritability of nested hierarchical structural brain network. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2019; 2018:554-557. [PMID: 30440457 DOI: 10.1109/embc.2018.8512359] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
When a brain network is constructed by an existing parcellation method, the topological structure of the network changes depending on the scale of the parcellation. To avoid the scale dependency, we propose to construct a nested hierarchical structural brain network by subdividing the existing parcellation hierarchically. The method is applied in diffusion tensor imaging study of 111 twins in characterizing the topology of the brain network. The genetic contribution of the whole brain structural connectivity is determined and shown to be robustly present over different network scales.
Collapse
|
16
|
Frau-Pascual A, Fogarty M, Fischl B, Yendiki A, Aganj I. Quantification of structural brain connectivity via a conductance model. Neuroimage 2019; 189:485-496. [PMID: 30677502 PMCID: PMC6585945 DOI: 10.1016/j.neuroimage.2019.01.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/27/2018] [Accepted: 01/12/2019] [Indexed: 02/07/2023] Open
Abstract
Connectomics has proved promising in quantifying and understanding the effects of development, aging and an array of diseases on the brain. In this work, we propose a new structural connectivity measure from diffusion MRI that allows us to incorporate direct brain connections, as well as indirect ones that would not be otherwise accounted for by standard techniques and that may be key for the better understanding of function from structure. From our experiments on the Human Connectome Project dataset, we find that our measure of structural connectivity better correlates with functional connectivity than streamline tractography does, meaning that it provides new structural information related to function. Through additional experiments on the ADNI-2 dataset, we demonstrate the ability of this new measure to better discriminate different stages of Alzheimer's disease. Our findings suggest that this measure is useful in the study of the normal brain structure, and for quantifying the effects of disease on the brain structure.
Collapse
Affiliation(s)
- Aina Frau-Pascual
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.
| | - Morgan Fogarty
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Bruce Fischl
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anastasia Yendiki
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Iman Aganj
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
17
|
Yang HE, Kim SW, Yoo WK. Diffusion Metrics as a Potential Prognostic Biomarker in Cervical Myelopathy. BRAIN & NEUROREHABILITATION 2019. [DOI: 10.12786/bn.2019.12.e1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Hea-Eun Yang
- Department of Physical Medicine and Rehabilitation, VHS Medical Center, Seoul, Korea
| | - Seok Woo Kim
- Spine Center, Hallym University Sacred Heart Hospital, Anyang, Korea
- Department of Orthopedic Surgery, Hallym University Sacred Heart Hospital, Anyang, Korea
| | - Woo-Kyoung Yoo
- Department of Physical Medicine and Rehabilitation, Hallym University Sacred Heart Hospital, Anyang, Korea
| |
Collapse
|
18
|
Abstract
We explore the main characteristics of big brain network data that offer unique statistical challenges. The brain networks are biologically expected to be both sparse and hierarchical. Such unique characterizations put specific topological constraints onto statistical approaches and models we can use effectively. We explore the limitations of the current models used in the field and offer alternative approaches and explain new challenges.
Collapse
|