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Bouin A, Wu G, Koyuncu OO, Ye Q, Kim KY, Wu MY, Tong L, Chen L, Phan S, Mackey MR, Ramachandra R, Ellisman MH, Holmes TC, Semler BL, Xu X. New rabies viral resources for multi-scale neural circuit mapping. Mol Psychiatry 2024; 29:1951-1967. [PMID: 38355784 PMCID: PMC11322437 DOI: 10.1038/s41380-024-02451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Comparisons and linkage between multiple imaging scales are essential for neural circuit connectomics. Here, we report 20 new recombinant rabies virus (RV) vectors that we have developed for multi-scale and multi-modal neural circuit mapping tools. Our new RV tools for mesoscale imaging express a range of improved fluorescent proteins. Further refinements target specific neuronal subcellular locations of interest. We demonstrate the discovery power of these new tools including the detection of detailed microstructural changes of rabies-labeled neurons in aging and Alzheimer's disease mouse models, live imaging of neuronal activities using calcium indicators, and automated measurement of infected neurons. RVs that encode GFP and ferritin as electron microscopy (EM) and fluorescence microscopy reporters are used for dual EM and mesoscale imaging. These new viral variants significantly expand the scale and power of rabies virus-mediated neural labeling and circuit mapping across multiple imaging scales in health and disease.
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Affiliation(s)
- Alexis Bouin
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Ginny Wu
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Orkide O Koyuncu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Qiao Ye
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Department Biomedical Engineering, University of California, Irvine, CA, 92697, USA
| | - Keun-Young Kim
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michele Y Wu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Liqi Tong
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Lujia Chen
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Department Biomedical Engineering, University of California, Irvine, CA, 92697, USA
| | - Sebastien Phan
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mason R Mackey
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ranjan Ramachandra
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mark H Ellisman
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Todd C Holmes
- Physiology & Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA.
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA.
| | - Xiangmin Xu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA.
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA.
- Department Biomedical Engineering, University of California, Irvine, CA, 92697, USA.
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA.
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2
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Caznok Silveira AC, Antunes ASLM, Athié MCP, da Silva BF, Ribeiro dos Santos JV, Canateli C, Fontoura MA, Pinto A, Pimentel-Silva LR, Avansini SH, de Carvalho M. Between neurons and networks: investigating mesoscale brain connectivity in neurological and psychiatric disorders. Front Neurosci 2024; 18:1340345. [PMID: 38445254 PMCID: PMC10912403 DOI: 10.3389/fnins.2024.1340345] [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: 11/17/2023] [Accepted: 01/29/2024] [Indexed: 03/07/2024] Open
Abstract
The study of brain connectivity has been a cornerstone in understanding the complexities of neurological and psychiatric disorders. It has provided invaluable insights into the functional architecture of the brain and how it is perturbed in disorders. However, a persistent challenge has been achieving the proper spatial resolution, and developing computational algorithms to address biological questions at the multi-cellular level, a scale often referred to as the mesoscale. Historically, neuroimaging studies of brain connectivity have predominantly focused on the macroscale, providing insights into inter-regional brain connections but often falling short of resolving the intricacies of neural circuitry at the cellular or mesoscale level. This limitation has hindered our ability to fully comprehend the underlying mechanisms of neurological and psychiatric disorders and to develop targeted interventions. In light of this issue, our review manuscript seeks to bridge this critical gap by delving into the domain of mesoscale neuroimaging. We aim to provide a comprehensive overview of conditions affected by aberrant neural connections, image acquisition techniques, feature extraction, and data analysis methods that are specifically tailored to the mesoscale. We further delineate the potential of brain connectivity research to elucidate complex biological questions, with a particular focus on schizophrenia and epilepsy. This review encompasses topics such as dendritic spine quantification, single neuron morphology, and brain region connectivity. We aim to showcase the applicability and significance of mesoscale neuroimaging techniques in the field of neuroscience, highlighting their potential for gaining insights into the complexities of neurological and psychiatric disorders.
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Affiliation(s)
- Ana Clara Caznok Silveira
- National Laboratory of Biosciences, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- School of Electrical and Computer Engineering, University of Campinas, Campinas, Brazil
| | | | - Maria Carolina Pedro Athié
- National Laboratory of Biosciences, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Bárbara Filomena da Silva
- National Laboratory of Biosciences, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | | | - Camila Canateli
- National Laboratory of Biosciences, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Marina Alves Fontoura
- National Laboratory of Biosciences, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Allan Pinto
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | | | - Simoni Helena Avansini
- National Laboratory of Biosciences, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Murilo de Carvalho
- National Laboratory of Biosciences, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
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3
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Bonosi L, Torrente A, Brighina F, Tito Petralia CC, Merlino P, Avallone C, Gulino V, Costanzo R, Brunasso L, Iacopino DG, Maugeri R. Corticocortical Evoked Potentials in Eloquent Brain Tumor Surgery. A Systematic Review. World Neurosurg 2024; 181:38-51. [PMID: 37832637 DOI: 10.1016/j.wneu.2023.10.028] [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] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Eloquent brain tumor surgery involves the delicate task of resecting tumors located in regions of the brain responsible for critical functions, such as language, motor control, and sensory perception. Preserving these functions is of paramount importance to maintain the patient's quality of life. Corticocortical evoked potentials (CCEPs) have emerged as a valuable intraoperative monitoring technique that aids in identifying and preserving eloquent cortical areas during surgery. This systematic review aimed to assess the utility of CCEPs in eloquent brain tumor surgery and determine their effectiveness in improving patient outcomes. A comprehensive literature search was conducted using electronic databases, including PubMed/Medline and Scopus. The search strategy identified 11 relevant articles for detailed analysis. The findings of the included studies consistently demonstrated the potential of CCEPs in guiding surgical decision making, minimizing the risk of postoperative neurological deficits, and mapping functional connectivity during surgery. However, further research and standardization are needed to fully establish the clinical benefits and refine the implementation of CCEPs in routine neurosurgical practice.
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Affiliation(s)
- Lapo Bonosi
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy.
| | - Angelo Torrente
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, Palermo, Italy
| | - Filippo Brighina
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, Palermo, Italy
| | - Cateno Concetto Tito Petralia
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Pietro Merlino
- Department of Neuroscience, Psychology, Pharmacology and Child Health, Neurosurgery Clinic, Careggi University Hospital and University of Florence, Florence, Italy
| | - Chiara Avallone
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Vincenzo Gulino
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Roberta Costanzo
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Lara Brunasso
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Domenico Gerardo Iacopino
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
| | - Rosario Maugeri
- Department of Biomedicine Neurosciences and Advanced Diagnostics, Neurosurgical Clinic, AOUP "Paolo Giaccone", Post Graduate Residency Program in NeurologiSurgery, School of Medicine, University of Palermo, Palermo, Italy
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4
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Xiao Y, Zhao L, Zang X, Xue S. Compressed primary-to-transmodal gradient is accompanied with subcortical alterations and linked to neurotransmitters and cellular signatures in major depressive disorder. Hum Brain Mapp 2023; 44:5919-5935. [PMID: 37688552 PMCID: PMC10619397 DOI: 10.1002/hbm.26485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/18/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023] Open
Abstract
Major depressive disorder (MDD) has been shown to involve widespread changes in low-level sensorimotor and higher-level cognitive functions. Recent research found that a primary-to-transmodal gradient could capture a cortical hierarchical organization ranging from perception and action to cognition in healthy subjects, but a prominent gradient dysfunction in MDD patients. However, whether and how this cortical gradient is linked to subcortical impairments and whether it is reflected in the microscale neurotransmitter systems and cell type-specific transcriptional signatures remain largely unknown. Data were acquired from 323 MDD patients and 328 sex- and age-matched healthy controls derived from the REST-meta-MDD project, and the human brain neurotransmitter systems density maps and gene expression data were drawn from two publicly available datasets. We investigated alterations of the primary-to-transmodal gradient in MDD patients and their correlations with clinical symptoms of depression and anxiety, as well as their paralleled subcortical impairments. The correlations between MDD-related gradient alterations and densities of the neurotransmitter systems and gene expression information were assessed, respectively. The results demonstrated that MDD patients had a compressed primary-to-transmodal gradient accompanied by paralleled alterations in subcortical regions including the caudate, amygdala, and thalamus. The case-control gradient differences were spatially correlated with the densities of the neurotransmitter systems including the serotonin and dopamine receptors, and meanwhile with gene expression enriched in astrocytes, excitatory and inhibitory neuronal cells. These findings mapped the paralleled subcortical impairments in cortical hierarchical organization and also helped us understand the possible molecular and cellular substrates of the co-occurrence of high-level cognitive impairments with low-level sensorimotor abnormalities in MDD.
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Affiliation(s)
- Yang Xiao
- Center for Cognition and Brain DisordersThe Affiliated Hospital of Hangzhou Normal UniversityHangzhouZhejiang ProvincePR China
- Institute of Psychological ScienceHangzhou Normal UniversityHangzhouZhejiang ProvincePR China
- Zhejiang Key Laboratory for Research in Assessment of Cognitive ImpairmentsHangzhouZhejiang ProvincePR China
| | - Lei Zhao
- Center for Cognition and Brain DisordersThe Affiliated Hospital of Hangzhou Normal UniversityHangzhouZhejiang ProvincePR China
- Institute of Psychological ScienceHangzhou Normal UniversityHangzhouZhejiang ProvincePR China
- Zhejiang Key Laboratory for Research in Assessment of Cognitive ImpairmentsHangzhouZhejiang ProvincePR China
| | - Xuelian Zang
- Center for Cognition and Brain DisordersThe Affiliated Hospital of Hangzhou Normal UniversityHangzhouZhejiang ProvincePR China
- Institute of Psychological ScienceHangzhou Normal UniversityHangzhouZhejiang ProvincePR China
- Zhejiang Key Laboratory for Research in Assessment of Cognitive ImpairmentsHangzhouZhejiang ProvincePR China
| | - Shao‐Wei Xue
- Center for Cognition and Brain DisordersThe Affiliated Hospital of Hangzhou Normal UniversityHangzhouZhejiang ProvincePR China
- Institute of Psychological ScienceHangzhou Normal UniversityHangzhouZhejiang ProvincePR China
- Zhejiang Key Laboratory for Research in Assessment of Cognitive ImpairmentsHangzhouZhejiang ProvincePR China
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5
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Katsumi Y, Zhang J, Chen D, Kamona N, Bunce JG, Hutchinson JB, Yarossi M, Tunik E, Dickerson BC, Quigley KS, Barrett LF. Correspondence of functional connectivity gradients across human isocortex, cerebellum, and hippocampus. Commun Biol 2023; 6:401. [PMID: 37046050 PMCID: PMC10097701 DOI: 10.1038/s42003-023-04796-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
Gradient mapping is an important technique to summarize high dimensional biological features as low dimensional manifold representations in exploring brain structure-function relationships at various levels of the cerebral cortex. While recent studies have characterized the major gradients of functional connectivity in several brain structures using this technique, very few have systematically examined the correspondence of such gradients across structures under a common systems-level framework. Using resting-state functional magnetic resonance imaging, here we show that the organizing principles of the isocortex, and those of the cerebellum and hippocampus in relation to the isocortex, can be described using two common functional gradients. We suggest that the similarity in functional connectivity gradients across these structures can be meaningfully interpreted within a common computational framework based on the principles of predictive processing. The present results, and the specific hypotheses that they suggest, represent an important step toward an integrative account of brain function.
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Affiliation(s)
- Yuta Katsumi
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
| | - Jiahe Zhang
- Department of Psychology, Northeastern University, Boston, MA, 02115, USA
| | - Danlei Chen
- Department of Psychology, Northeastern University, Boston, MA, 02115, USA
| | - Nada Kamona
- Department of Psychology, Northeastern University, Boston, MA, 02115, USA
| | - Jamie G Bunce
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | | | - Mathew Yarossi
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, 02115, USA
- Department of Physical Therapy, Movement, and Rehabilitation Science, Northeastern University, Boston, MA, 02115, USA
| | - Eugene Tunik
- Department of Physical Therapy, Movement, and Rehabilitation Science, Northeastern University, Boston, MA, 02115, USA
| | - Bradford C Dickerson
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Karen S Quigley
- Department of Psychology, Northeastern University, Boston, MA, 02115, USA
| | - Lisa Feldman Barrett
- Department of Psychology, Northeastern University, Boston, MA, 02115, USA
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
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6
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Huo T, Xia Y, Zhuang K, Chen Q, Sun J, Yang W, Qiu J. Linking functional connectome gradient to individual creativity. Cereb Cortex 2022; 32:5273-5284. [PMID: 35136988 DOI: 10.1093/cercor/bhac013] [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: 11/11/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Human brain network is organized as a hierarchical organization, exhibiting various connectome gradients. The principal gradient is anchored by the modality-specific primary areas and the transmodal regions. Previous studies have suggested that the unimodal-transmodal gradient in the functional connectome may offer an overarching framework for high-order cognitions of human brain. However, there is still a lacking of direct evidence to associate these two. OBJECTIVES Therefore, we aim to explore the association between creativity, a typical human high-order cognitive function, and unimodal-transmodal gradient, using two independent datasets of young adults. METHODS For each individual, we identified the unimodal-transmodal gradient in functional connectome and calculated its global measures. Then we correlated the individual creativity score with measures of unimodal-transmodal gradient at global-brain, subsystem, and regional level. RESULTS The results suggested that better creative performance was associated with greater distance between primary areas and transmodal regions in gradient axes, and less distance between ventral attention network and default mode network. Individual creativity was also found positively correlated with regional gradients in ventral attention network, and negatively correlated with gradients of regions in visual cortex. CONCLUSION Together, these findings directly link the unimodal-transmodal gradient to individual creativity, providing empirical evidence for the cognitive implications of functional connectome gradient.
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Affiliation(s)
- Tengbin Huo
- Key Laboratory of Cognition and Personality, Ministry of Education, Chongqing 400715, China.,School of Psychology, Southwest University (SWU), Chongqing 400715, China
| | - Yunman Xia
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China.,Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing 100875, China.,IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
| | - Kaixiang Zhuang
- Key Laboratory of Cognition and Personality, Ministry of Education, Chongqing 400715, China.,School of Psychology, Southwest University (SWU), Chongqing 400715, China
| | - Qunlin Chen
- Key Laboratory of Cognition and Personality, Ministry of Education, Chongqing 400715, China.,School of Psychology, Southwest University (SWU), Chongqing 400715, China
| | - Jiangzhou Sun
- Key Laboratory of Cognition and Personality, Ministry of Education, Chongqing 400715, China.,School of Psychology, Southwest University (SWU), Chongqing 400715, China
| | - Wenjing Yang
- Key Laboratory of Cognition and Personality, Ministry of Education, Chongqing 400715, China.,School of Psychology, Southwest University (SWU), Chongqing 400715, China
| | - Jiang Qiu
- Key Laboratory of Cognition and Personality, Ministry of Education, Chongqing 400715, China.,School of Psychology, Southwest University (SWU), Chongqing 400715, China.,Southwest University Branch, Collaborative Innovation Center of Assessment Toward Basic Education Quality, Beijing Normal University, Beijing 100875, China
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7
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Haueis P, Kästner L. Mechanistic inquiry and scientific pursuit: The case of visual processing. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2022; 93:123-135. [PMID: 35427838 DOI: 10.1016/j.shpsa.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 03/09/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Why is it rational for scientists to pursue multiple models of a phenomenon at the same time? The literatures on mechanistic inquiry and scientific pursuit each develop answers to a version of this question which is rarely discussed by the other. The mechanistic literature suggests that scientists pursue different complementary models because each model provides detailed insights into different aspects of the phenomenon under investigation. The pursuit literature suggests that scientists pursue competing models because alternative models promise to solve outstanding empirical and conceptual problems. Looking into research on visual processing as a case study, we suggest an integrated account of why it is rational for scientists to pursue both complementary and competing models of the same mechanism in scientific practice.
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Affiliation(s)
- Philipp Haueis
- Department of Philosophy, Bielefeld University, Germany.
| | - Lena Kästner
- Department of Philosophy, Saarland University, Germany; Department of Philosophy, University of Bayreuth, Germany
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8
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Chen J, Ren Y, Huang WL, Zhang L, Li J. Multilevel Mesoscale Complexities in Mesoregimes: Challenges in Chemical and Biochemical Engineering. Annu Rev Chem Biomol Eng 2022; 13:431-455. [PMID: 35378042 DOI: 10.1146/annurev-chembioeng-092220-115031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review discusses the complex behaviors in diverse chemical and biochemical systems to elucidate their commonalities and thus help develop a mesoscience methodology to address the complexities in even broader topics. This could possibly build a new scientific paradigm for different disciplines and could meanwhile provide effective tools to tackle the big challenges in various fields, thus paving a path toward combining the paradigm shift in science with the breakthrough in technique developments. Starting with our relatively fruitful understanding of chemical systems, the discussion focuses on the relatively pristine but very intriguing biochemical systems. It is recognized that diverse complexities are multilevel in nature, with each level being multiscale and the complexity emerging always at mesoscales in mesoregimes. Relevant advances in theoretical understandings and mathematical tools are summarized as well based on case studies, and the convergence between physics and mathematics is highlighted. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jianhua Chen
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
| | - Ying Ren
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
| | - Wen Lai Huang
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
| | - Lin Zhang
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
| | - Jinghai Li
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
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Bernhardt BC, Smallwood J, Keilholz S, Margulies DS. Gradients in Brain Organization. Neuroimage 2022; 251:118987. [PMID: 35151850 DOI: 10.1016/j.neuroimage.2022.118987] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
| | | | - Shella Keilholz
- Biomedical Engineering, Emory University / Georgia Institute of Technology, Atlanta, Georgia
| | - Daniel S Margulies
- Integrative Neuroscience and Cognition Center, Centre National de la Recherche Scientifique (CNRS) and Université de Paris, Paris, France
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10
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Safron A, Klimaj V, Hipólito I. On the Importance of Being Flexible: Dynamic Brain Networks and Their Potential Functional Significances. Front Syst Neurosci 2022; 15:688424. [PMID: 35126062 PMCID: PMC8814434 DOI: 10.3389/fnsys.2021.688424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
In this theoretical review, we begin by discussing brains and minds from a dynamical systems perspective, and then go on to describe methods for characterizing the flexibility of dynamic networks. We discuss how varying degrees and kinds of flexibility may be adaptive (or maladaptive) in different contexts, specifically focusing on measures related to either more disjoint or cohesive dynamics. While disjointed flexibility may be useful for assessing neural entropy, cohesive flexibility may potentially serve as a proxy for self-organized criticality as a fundamental property enabling adaptive behavior in complex systems. Particular attention is given to recent studies in which flexibility methods have been used to investigate neurological and cognitive maturation, as well as the breakdown of conscious processing under varying levels of anesthesia. We further discuss how these findings and methods might be contextualized within the Free Energy Principle with respect to the fundamentals of brain organization and biological functioning more generally, and describe potential methodological advances from this paradigm. Finally, with relevance to computational psychiatry, we propose a research program for obtaining a better understanding of ways that dynamic networks may relate to different forms of psychological flexibility, which may be the single most important factor for ensuring human flourishing.
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Affiliation(s)
- Adam Safron
- Center for Psychedelic and Consciousness Research, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Kinsey Institute, Indiana University, Bloomington, IN, United States
- Cognitive Science Program, Indiana University, Bloomington, IN, United States
| | - Victoria Klimaj
- Cognitive Science Program, Indiana University, Bloomington, IN, United States
- Complex Networks and Systems, Informatics Department, Indiana University, Bloomington, IN, United States
| | - Inês Hipólito
- Department of Philosophy, Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
- Wellcome Centre for Human Neuroimaging, University College London, London, United Kingdom
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11
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Wei W, Yin Y, Zhang Y, Li X, Li M, Guo W, Wang Q, Deng W, Ma X, Zhao L, Palaniyappan L, Li T. Structural Covariance of Depth-Dependent Intracortical Myelination in the Human Brain and Its Application to Drug-Naïve Schizophrenia: A T1w/T2w MRI Study. Cereb Cortex 2021; 32:2373-2384. [PMID: 34581399 DOI: 10.1093/cercor/bhab337] [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: 06/02/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 02/05/2023] Open
Abstract
Aberrations in intracortical myelination are increasingly being considered as a cardinal feature in the pathophysiology of schizophrenia. We investigated the network-level distribution of intracortical myelination across various cortex depths. We enrolled 126 healthy subjects and 106 first-episode drug-naïve schizophrenia patients. We used T1w/T2w ratio as a proxy of intracortical myelination, parcellated cortex into several equivolumetric surfaces based on cortical depths and mapped T1w/T2w ratios to each surface. Non-negative matrix factorization was used to generate depth-dependent structural covariance networks (dSCNs) of intracortical myelination from 2 healthy controls datasets-one from our study and another from 100-unrelated dataset of the Human Connectome Project. For patient versus control comparisons, partial least squares approach was used; we also related myelination to clinical features of schizophrenia. We found that dSCNs were highly reproducible in 2 independent samples. Network-level myelination was reduced in prefrontal and cingulate cortex and increased in perisylvian cortex in schizophrenia. The abnormal network-level myelination had a canonical correlation with symptom burden in schizophrenia. Moreover, myelination of prefrontal cortex correlated with duration of untreated psychosis. In conclusion, we offer a feasible and sensitive framework to study depth-dependent myelination and its relationship with clinical features.
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Affiliation(s)
- Wei Wei
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Yubing Yin
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Yamin Zhang
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Xiaojing Li
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Mingli Li
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Wanjun Guo
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Qiang Wang
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Wei Deng
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Xiaohong Ma
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Liansheng Zhao
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China
| | - Lena Palaniyappan
- Department of Psychiatry, University of Western Ontario, London, Ontario N6A 3K7, Canada.,Robarts Research Institute, University of Western Ontario, London, Ontario N6A 3K7, Canada.,Lawson Health Research Institute, London, Ontario N6C 2R5, Canada
| | - Tao Li
- Psychiatric Laboratory and Mental Health Center, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan 610000, China.,Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310013, China
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