2
|
Lee SH, Broadwater MA, Ban W, Wang TWW, Kim HJ, Dumas JS, Vetreno RP, Herman MA, Morrow AL, Besheer J, Kash TL, Boettiger CA, Robinson DL, Crews FT, Shih YYI. An isotropic EPI database and analytical pipelines for rat brain resting-state fMRI. Neuroimage 2021; 243:118541. [PMID: 34478824 PMCID: PMC8561231 DOI: 10.1016/j.neuroimage.2021.118541] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/08/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022] Open
Abstract
Resting-state functional magnetic resonance imaging (fMRI) has drastically expanded the scope of brain research by advancing our knowledge about the topologies, dynamics, and interspecies translatability of functional brain networks. Several databases have been developed and shared in accordance with recent key initiatives in the rodent fMRI community to enhance the transparency, reproducibility, and interpretability of data acquired at various sites. Despite these pioneering efforts, one notable challenge preventing efficient standardization in the field is the customary choice of anisotropic echo planar imaging (EPI) schemes with limited spatial coverage. Imaging with anisotropic resolution and/or reduced brain coverage has significant shortcomings including reduced registration accuracy and increased deviation in brain feature detection. Here we proposed a high-spatial-resolution (0.4 mm), isotropic, whole-brain EPI protocol for the rat brain using a horizontal slicing scheme that can maintain a functionally relevant repetition time (TR), avoid high gradient duty cycles, and offer unequivocal whole-brain coverage. Using this protocol, we acquired resting-state EPI fMRI data from 87 healthy rats under the widely used dexmedetomidine sedation supplemented with low-dose isoflurane on a 9.4 T MRI system. We developed an EPI template that closely approximates the Paxinos and Watson's rat brain coordinate system and demonstrated its ability to improve the accuracy of group-level approaches and streamline fMRI data pre-processing. Using this database, we employed a multi-scale dictionary-learning approach to identify reliable spatiotemporal features representing rat brain intrinsic activity. Subsequently, we performed k-means clustering on those features to obtain spatially discrete, functional regions of interest (ROIs). Using Euclidean-based hierarchical clustering and modularity-based partitioning, we identified the topological organizations of the rat brain. Additionally, the identified group-level FC network appeared robust across strains and sexes. The "triple-network" commonly adapted in human fMRI were resembled in the rat brain. Through this work, we disseminate raw and pre-processed isotropic EPI data, a rat brain EPI template, as well as identified functional ROIs and networks in standardized rat brain coordinates. We also make our analytical pipelines and scripts publicly available, with the hope of facilitating rat brain resting-state fMRI study standardization.
Collapse
Affiliation(s)
- Sung-Ho Lee
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA,Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Corresponding authors at: Center for Animal MRI, 125 Mason Farm Road, CB# 7513, University of North Carolina, Chapel Hill, NC 27599, USA. (S.-H. Lee), (Y.-Y.I. Shih)
| | - Margaret A. Broadwater
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA,Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA
| | - Woomi Ban
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA
| | - Tzu-Wen Winnie Wang
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA
| | - Hyeon-Joong Kim
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA
| | - Jaiden Seongmi Dumas
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA,Department of Quantitative Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Ryan P. Vetreno
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Melissa A. Herman
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - A. Leslie Morrow
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Joyce Besheer
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Thomas L. Kash
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Charlotte A. Boettiger
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC, USA
| | - Donita L. Robinson
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Fulton T. Crews
- Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Yen-Yu Ian Shih
- Center for Animal MRI, University of North Carolina, Chapel Hill, NC, USA,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, USA,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA,Bowles Center for Alcohol Studies University of North Carolina, Chapel Hill, NC, USA,Corresponding authors at: Center for Animal MRI, 125 Mason Farm Road, CB# 7513, University of North Carolina, Chapel Hill, NC 27599, USA. (S.-H. Lee), (Y.-Y.I. Shih)
| |
Collapse
|
3
|
Jeong UJ, Lee J, Chou N, Kim K, Shin H, Chae U, Yu HY, Cho IJ. A minimally invasive flexible electrode array for simultaneous recording of ECoG signals from multiple brain regions. LAB ON A CHIP 2021; 21:2383-2397. [PMID: 33955442 DOI: 10.1039/d1lc00117e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The minimal invasiveness of electrocorticography (ECoG) enabled its widespread use in clinical areas as well as in neuroscience research. However, most existing ECoG arrays require that the entire surface area of the brain that is to be recorded be exposed through a large craniotomy. We propose a device that overcomes this limitation, i.e., a minimally invasive, polyimide-based flexible array of electrodes that can enable the recording of ECoG signals in multiple regions of the brain with minimal exposure of the surface of the brain. Magnetic force-assisted positioning of a flexible electrode array enables recording from distant brain regions with a small cranial window. Also, a biodegradable organic compound used for attaching a magnet on the electrodes allows simple retrieval of the magnet. We demonstrate with an in vivo chronic recording that an implanted ECoG electrode array can record ECoG signals from the visual cortex and the motor cortex during a rat's free behavior. Our results indicate that the proposed device induced minimal damage to the animal. We expect the proposed device to be utilized for experiments for large-scale brain circuit analyses as well as clinical applications for intra-operative monitoring of epileptic activity.
Collapse
Affiliation(s)
- Ui-Jin Jeong
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea. and School of Electrical Engineering, Korea University, Seoul, Republic of Korea
| | - Jungpyo Lee
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea.
| | - Namsun Chou
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea.
| | - Kanghwan Kim
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea.
| | - Hyogeun Shin
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea. and Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea
| | - Uikyu Chae
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea. and School of Electrical Engineering, Korea University, Seoul, Republic of Korea
| | - Hyun-Yong Yu
- School of Electrical Engineering, Korea University, Seoul, Republic of Korea
| | - Il-Joo Cho
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea. and Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Republic of Korea and School of Electrical and Electronics Engineering, Yonsei University, Seoul, Republic of Korea and Yonsei-KIST Convergence Research Institute, Yonsei University, Seoul, Republic of Korea
| |
Collapse
|
6
|
Windt JM, Nielsen T, Thompson E. Does Consciousness Disappear in Dreamless Sleep? Trends Cogn Sci 2016; 20:871-882. [PMID: 27765517 DOI: 10.1016/j.tics.2016.09.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 11/27/2022]
Abstract
Consciousness is often said to disappear in deep, dreamless sleep. We argue that this assumption is oversimplified. Unless dreamless sleep is defined as unconscious from the outset there are good empirical and theoretical reasons for saying that a range of different types of sleep experience, some of which are distinct from dreaming, can occur in all stages of sleep. We introduce a novel taxonomy for describing different kinds of dreamless sleep experiences and suggest research methods for their investigation. Future studies should focus on three areas: memory consolidation, sleep disorders, and sleep state (mis)perception. Our proposal suggests new directions for sleep and dream science, as well as for the neuroscience of consciousness, and can also inform the diagnosis and treatment of sleep disorders.
Collapse
Affiliation(s)
- Jennifer M Windt
- Department of Philosophy, Monash University, Level 6, Menzies Building, Clayton Campus, 20 Chancellor's Walk, Monash University, VIC 3800, Australia
| | - Tore Nielsen
- Department of Psychiatry, Université de Montréal, and the Dream and Nightmare Laboratory, Centre for Advanced Research in Sleep Medicine, Hôpital du Sacré-Coeur de Montréal, 5400 Boulevard Gouin Ouest, Montréal, QC H4 J 1C5, Canada
| | - Evan Thompson
- Department of Philosophy, University of British Columbia, 1866 Main Mall, Vancouver, BC V6 T 1Z4, Canada.
| |
Collapse
|